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  • 1.
    Alva, Omar
    et al.
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Leroy, Anais
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Heiske, Margit
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Pereda-Loth, Veronica
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Tisseyre, Lenka
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Boland, Anne
    Ctr Natl Genotypage, Inst Genom, Commissariat Energie Atom, F-91000 Evry, France..
    Deleuze, Jean-Francois
    Ctr Natl Genotypage, Inst Genom, Commissariat Energie Atom, F-91000 Evry, France..
    Rocha, Jorge
    Univ Porto, InBIO Lab Associado, Ctr Invest Biodiversidade & Recursos, CIBIO, Campus Vairao, P-4485661 Vairao, Portugal.;Univ Porto, Fac Ciencias, Dept Biol, P-4099002 Porto, Portugal.;CIBIO, BIOPOLIS Program Genom Biodivers & Land Planning, Campus Vairao, P-4485661 Vairao, Portugal..
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Fortes-Lima, Cesar A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Stoneking, Mark
    Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, D-04103 Leipzig, Germany.;Univ Lyon 1, Lab Biometrie & Biol Evolut, CNRS, UMR 5558, Villeurbanne, France..
    Radimilahy, Chantal
    Univ Antananarivo, Musee Art & Archeol, Antananarivo, Madagascar..
    Rakotoarisoa, Jean-Aime
    Univ Antananarivo, Musee Art & Archeol, Antananarivo, Madagascar..
    Letellier, Thierry
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Pierron, Denis
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    The loss of biodiversity in Madagascar is contemporaneous with major demographic events2022Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 32, nr 23, s. 4997-+Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large- bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.

  • 2.
    Anava, Sarit
    et al.
    Tel Aviv Univ, George Wise Fac Life Sci, Dept Neurobiol, IL-6997801 Tel Aviv, Israel..
    Neuhof, Moran
    Tel Aviv Univ, George Wise Fac Life Sci, Dept Neurobiol, IL-6997801 Tel Aviv, Israel..
    Gingold, Hila
    Tel Aviv Univ, George Wise Fac Life Sci, Dept Neurobiol, IL-6997801 Tel Aviv, Israel..
    Sagy, Or
    Tel Aviv Univ, George Wise Fac Life Sci, Dept Neurobiol, IL-6997801 Tel Aviv, Israel..
    Munters, Arielle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Svensson, Emma M.
    Uppsala Univ, Dept Organismal Biol, Human Evolut, S-75105 Uppsala, Sweden.;Uppsala Univ, SciLife Lab, S-75105 Uppsala, Sweden..
    Afshinnekoo, Ebrahim
    Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10065 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10065 USA.;WorldQuant Initiat Quantitate Predict, New York, NY 10065 USA..
    Danko, David
    Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10065 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10065 USA.;WorldQuant Initiat Quantitate Predict, New York, NY 10065 USA..
    Foox, Jonathan
    Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10065 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10065 USA.;WorldQuant Initiat Quantitate Predict, New York, NY 10065 USA..
    Shor, Pnina
    Israel Antiqu Author, Dead Sea Scroll Projects, IL-91710 Jerusalem, Israel..
    Riestra, Beatriz
    Israel Antiqu Author, Dead Sea Scroll Projects, IL-91710 Jerusalem, Israel..
    Huchon, Dorothee
    Tel Aviv Univ, Steinhardt Museum Nat Hist, IL-6997801 Tel Aviv, Israel.;Tel Aviv Univ, Israel Natl Ctr Biodivers Studies, IL-6997801 Tel Aviv, Israel.;Tel Aviv Univ, Dept Zool, George S Wise Fac Life Sci, IL-6997801 Tel Aviv, Israel..
    Mason, Christopher E.
    Weill Cornell Med, Dept Physiol & Biophys, New York, NY 10065 USA.;Weill Cornell Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10065 USA.;WorldQuant Initiat Quantitate Predict, New York, NY 10065 USA..
    Mizrahi, Noam
    Tel Aviv Univ, Lester & Sally Entin Fac Humanities, Dept Bibl Studies, IL-6997801 Tel Aviv, Israel..
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Rechavi, Oded
    Tel Aviv Univ, George Wise Fac Life Sci, Dept Neurobiol, IL-6997801 Tel Aviv, Israel..
    Illuminating Genetic Mysteries of the Dead Sea Scrolls2020Inngår i: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 181, nr 6, s. 1218-+Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together'' scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint'' pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.

  • 3.
    Atag, Gözde
    et al.
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Kaptan, Damla
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Yüncü, Eren
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Vural, Kivilcim Basak
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Mereu, Paolo
    Univ Sassari, Dept Biochem Sci, Sassari, Italy..
    Pirastru, Monica
    Univ Sassari, Dept Biochem Sci, Sassari, Italy..
    Barbato, Mario
    Univ Messina, Dept Vet Sci, Messina, Italy..
    Leoni, Giovanni Giuseppe
    Univ Sassari, Dept Biochem Sci, Sassari, Italy..
    Güler, Merve Nur
    Middle East Tech Univ, Grad Sch Informat, Dept Hlth Informat, Ankara, Turkiye..
    Er, Tugce
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Eker, Elifnaz
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Yazici, Tunca Deniz
    Ludwig Maximillian Univ Munich, Grad Sch Evolut Ecol & Systemat, Munich, Germany..
    Kilic, Muhammed Siddik
    Middle East Tech Univ, Grad Sch Informat, Dept Hlth Informat, Ankara, Turkiye..
    Altinisik, Nefize Ezgi
    Hacettepe Univ, Dept Anthropol, Ankara, Turkiye..
    Celik, Ecem Ayse
    Middle East Tech Univ, Dept Settlement Archeol, Ankara, Turkiye..
    Morell Miranda, Pedro
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Dehasque, Marianne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Floridia, Viviana
    Department of Veterinary Sciences, University of Messina, Messina, Italy.
    Götherström, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.;Stockholm Univ, Ctr Palaeogenet, Stockholm, Sweden..
    Bilgin, Cemal Can
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Togan, Inci
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Özer, Füsun
    Hacettepe Univ, Dept Anthropol, Ankara, Turkiye..
    Hadjisterkotis, Eleftherios
    Minist Agr Rural Dev & Environm, Agr Res Inst, Nicosia, Cyprus..
    Somel, Mehmet
    Middle East Tech Univ, Dept Biol Sci, Ankara, Turkiye..
    Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages2024Inngår i: Genome Biology and Evolution, E-ISSN 1759-6653, Vol. 16, nr 5, artikkel-id evae090Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (N-e). Meanwhile, N-e and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term N-e, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.

    Fulltekst (pdf)
    fulltext
  • 4.
    Ausmees, Kristiina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Sanchez-Quinto, Federico
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Instituto Nacional de Medicina Genómica (INMEGEN) , Mexico City 14610, Mexico.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Nettelblad, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    An empirical evaluation of genotype imputation of ancient DNA2022Inngår i: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 12, nr 6, artikkel-id jkac089Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.

    Fulltekst (pdf)
    fulltext
  • 5.
    Avila-Arcos, Maria C.
    et al.
    Univ Nacl Autonoma Mexico, Int Lab Human Genome Res, Queretaro, Mexico..
    Raghavan, Maanasa
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA..
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Palaeo Res Inst, Johannesburg, South Africa.;SciLifeLab, Uppsala, Sweden..
    Going local with ancient DNA: A review of human histories from regional perspectives2023Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 382, nr 6666, s. 53-58Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.

  • 6.
    Barcala, Maximiliano Estravis
    et al.
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    van der Valk, Tom
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Ctr Palaeogenet, Stockholm, Sweden.;Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.;Sci Life Lab, Stockholm, Sweden..
    Chen, Zhiqiang
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    Funda, Tomas
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    Chaudhary, Rajiv
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    Klingberg, Adam
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden.;Skogforsk, Uppsala, Sweden..
    Fundova, Irena
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden.;Norwegian Inst Bioecon Res NIBIO, Dept Forest Genet & Regenerat, As, Norway..
    Suontama, Mari
    Skogforsk, Uppsala, Sweden..
    Hallingback, Henrik
    Bernhardsson, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Dept Plant Biol, Uppsala, Sweden..
    Nystedt, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ingvarsson, Par K.
    Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Dept Plant Biol, Uppsala, Sweden..
    Sherwood, Ellen
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.;KTH Royal Inst Technol, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden..
    Street, Nathaniel
    Umeå Univ, Umeå Plant Sci Ctr UPSC, Dept Plant Physiol, Umeå, Sweden..
    Gyllensten, Ulf B.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Nilsson, Ove
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    Wu, Harry X.
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr UPSC, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species2024Inngår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 117, nr 3, s. 944-955Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype-environment and genotype-phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

    Fulltekst (pdf)
    fulltext
  • 7.
    Bergfeldt, Nora
    et al.
    Stockholm Univ, Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden.;Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    Kirdök, Emrah
    Mersin Univ, Inst Sci, Dept Biotechnol, Mersin, Turkiye..
    Oskolkov, Nikolay
    Lund Univ, Dept Biol, Sci Life Lab, Natl Bioinformat Infrastructure Sweden, Lund, Sweden..
    Mirabello, Claudio
    Linköping Univ, Dept Phys Chem & Biol, Sci Life Lab, Linköping, Sweden..
    Unneberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Fraser, Magdalena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Sanchez-Quinto, Federico
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Jorgensen, Roger
    Univ Tromso, Arctic Univ Norway, Tromso Univ Museum, Tromso, Norway..
    Skar, Birgitte
    NTNU Univ Museum, Dept Archaeol & Cultural Hist, Trondheim, Norway..
    Liden, Kerstin
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Götherström, Anders
    Stockholm Univ, Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Identification of microbial pathogens in Neolithic Scandinavian humans2024Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 14, nr 1, artikkel-id 5630Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.

    Fulltekst (pdf)
    FULLTEXT01
  • 8.
    Bernhardsson, Carolina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Umeå Univ, Dept Ecol & Environm Sci, Umeå, Sweden..
    Zan, Yanjun
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    Chen, Zhiqiang
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, Umeå, Sweden..
    Ingvarsson, Pär K.
    Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Uppsala BioCtr, Dept Plant Biol, Uppsala, Sweden..
    Wu, Harry X.
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, Umeå, Sweden.;Beijing Forestry Univ, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Beijing, Peoples R China.;CSIRO Natl Res Collect Australia, Black Mt Lab, Canberra, ACT, Australia..
    Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species2021Inngår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 21, nr 3, s. 880-896Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome-wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS-based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two-step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high-confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high-quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.

    Fulltekst (pdf)
    fulltext
  • 9.
    Blank, Malou
    et al.
    Univ Gothenburg, Dept Hist Studies, Gothenburg, Sweden..
    Sjögren, Karl-Göran
    Univ Gothenburg, Dept Hist Studies, Gothenburg, Sweden..
    Knipper, Corina
    Curt Engelhorn Ctr Archaeometry, Mannheim, Germany..
    Frei, Karin M.
    Natl Museum Denmark, Environm Archaeol & Mat Sci, Lyngby, Denmark..
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Ctr Anthropol Res, Johannesburg, South Africa.
    Fraser, Magdalena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Svensson, Emma M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Yngve, Hannes
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Ctr Anthropol Res, Johannesburg, South Africa.
    Götherström, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Ctr Palaeogenet, Stockholm, Sweden..
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, Stockholm, Sweden..
    Mobility patterns in inland southwestern Sweden during the Neolithic and Early Bronze Age2021Inngår i: Archaeological and Anthropological Sciences, ISSN 1866-9557, E-ISSN 1866-9565, Vol. 13, nr 4, artikkel-id 64Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper, we investigate population dynamics in the Scandinavian Neolithic and Early Bronze Age in southwestern Sweden. Human mobility patterns in Falbygden were studied by applying strontium isotope analysis combined with archaeological and bioarchaeological data, including mtDNA and sex assessment on a large dataset encompassing 141 individuals from 21 megalithic graves. In combination with other archaeological and anthropological records, we investigated the temporal and spatial scale of individual movement, mobility patterns of specific categories of people and possible social drivers behind them. Our results of strontium and biomolecular analyses suggest that mobility increased in the Late Neolithic and Early Bronze Age compared to the earlier parts of the Neolithic. The data indicate individuals moving both into and away from Falbygden. Mobility patterns and contact networks also shift over time.

    Fulltekst (pdf)
    FULLTEXT01
  • 10.
    Blank, Malou
    et al.
    Univ Gothenburg, Dept Hist Studies, Gothenburg, Sweden..
    Tornberg, Anna
    Lund Univ, Dept Archaeol & Ancient Hist, Lund, Sweden..
    Sjögren, Karl-Göran
    Univ Gothenburg, Dept Hist Studies, Gothenburg, Sweden..
    Knipper, Corina
    Curt Engelhorn Ctr Archaeometry, Mannheim, Germany..
    Frei, Karin M.
    Natl Museum Denmark, Environm Archaeol & Mat Sci, Lyngby, Denmark..
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Fraser, Magdalena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, Stockholm, Sweden..
    Interdisciplinary analyses of the remains from three gallery graves at Kinnekulle: tracing Late Neolithic and Early Bronze Age societies in inland Southwestern Sweden2023Inngår i: Archaeological and Anthropological Sciences, ISSN 1866-9557, E-ISSN 1866-9565, Vol. 15, artikkel-id 94Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper, we investigate the Scandinavian Late Neolithic and Early Bronze Age of Kinnekulle in southwestern Sweden. The above-mentioned periods in the study area are poorly understood and the archaeological record consists of a few stray finds and a concentration of 20 gallery graves. This study focuses on three of the gallery graves where commingled skeletons from successive burials were recovered. The human remains and the artefacts from the graves were used for discussing individual life stories as well as living societies with the aim of gaining new knowledge of the last part of the Neolithic and the beginning of the Early Bronze Age in southwestern Sweden. We focused on questions concerning health and trauma, mobility and exchange networks, and diet and subsistence of the people using the graves. Chronological, bioarchaeological, and biomolecular aspects of the burials were approached through the application of archaeological and osteological studies, as well as stable isotope, strontium isotope, radiocarbon, and mtDNA analyses. The study provides evidence for high mobility and diverse diets, as well as inhumations primarily dated to the transition between the Late Neolithic and Early Bronze Age. We suggest that the mountain plateau of Kinnekulle was mainly reserved for the dead, while the people lived in agriculture-based groups in the surrounding lower lying regions.

    Fulltekst (pdf)
    FULLTEXT01
  • 11.
    Bouakaze, Caroline
    et al.
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Inst Natl Police Sci, Lab Police Sci Lyon, 31 Ave Franklin Roosevelt, F-69134 Ecully, France..
    Delehelle, Franklin
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;UMR 5505 CNRS, REVA Unit, F-31400 Toulouse, France.;Univ Toulouse, Inst Rech Informat Toulouse, F-31400 Toulouse, France..
    Saenz-Oyhereguy, Nancy
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Moreira, Andreia
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Schiavinato, Stephanie
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Croze, Myriam
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Ewha Womans Univ, Div EcoSci, Seoul, South Korea..
    Delon, Solene
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Fortes-Lima, Cesar A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Gibert, Morgane
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Bujan, Louis
    Hop Paule de Viguier, Equipe Acceuil EA3694, 330 Ave Grande Bretagne,TSA 70034, F-31059 Toulouse 9, France..
    Huyghe, Eric
    Hop Paule de Viguier, Equipe Acceuil EA3694, 330 Ave Grande Bretagne,TSA 70034, F-31059 Toulouse 9, France..
    Bellis, Gil
    INED Inst Natl Etud Demog, 133 Blvd Davout, F-75980 Paris 20, France..
    Calderon, Rosario
    Univ Complutense Madrid, Fac Biol, Dept Biodivers Ecol & Evolut, Madrid 28040, Spain..
    Lucia Hernandez, Candela
    Univ Complutense Madrid, Fac Biol, Dept Biodivers Ecol & Evolut, Madrid 28040, Spain..
    Avendano-Tamayo, Efren
    Inst Univ, Tecnol Antioquia, Grp Ciencias Basicas Aplicadas Tecnol Antioquia, Medellin 050034, Colombia..
    Bedoya, Gabriel
    Univ Antioquia Medellin Colombia, Inst Biol, GENMOL Genet Mol, Medellin, Colombia..
    Salas, Antonio
    Univ Santiago de Compostela, Hosp Clin Univ Santiago SERGAS, Fac Med,Unidade Xenet,GenPoB Res Grp, Inst Invest Sanitarias IDIS,Inst Ciencias Forense, Galicia, Spain..
    Mazieres, Stephane
    Aix Marseille Univ, ADES, EFS, CNRS, Marseille, France..
    Charioni, Jacques
    Aix Marseille Univ, ADES, EFS, CNRS, Marseille, France.;Etab Francais Sang PACA Corse, Marseille, France..
    Migot-Nabias, Florence
    Univ Paris, MERIT, IRD, F-75006 Paris, France..
    Ruiz-Linares, Andres
    Aix Marseille Univ, ADES, EFS, CNRS, Marseille, France.;Fudan Univ, Sch Life Sci, Key Lab Contemporary Anthropol, Minist Educ, Shanghai, Peoples R China..
    Dugoujon, Jean-Michel
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Theves, Catherine
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Mollereau-Manaute, Catherine
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Nous, Camille
    CNRS, Lab Cogitamous, F-31000 Toulouse, France.;Univ Toulouse III, F-31000 Toulouse, France..
    Poulet, Nicolas
    Pole Ecohydraul AFB IMT, Allee Pr Camille Soula, F-31400 Toulouse, France..
    King, Turi
    Univ Leicester, Dept Genet, Leicester, Leics, England..
    D'Amato, Maria Eugenia
    Univ Western Cape, Fac Nat Sci, Dept Biotechnol, Forens DNA Lab, Cape Town, South Africa..
    Balaresque, Patricia
    UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France..
    Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters2020Inngår i: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 48, artikkel-id 102342Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.

  • 12.
    Breton, Gwenna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Human demographic history: Insights on the human past based on genomes from Southern through Central Africa2020Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming.

    I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution.

    I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-like. The estimated times for the admixture between a presumably local hunter-gatherer population and incoming agropastoralist groups are consistent with archaeological records.

    In this thesis, I investigated questions related to human history in Sub-Saharan Africa, from the emergence of modern humans ~300 kya to recent events related to the expansion of farming.

    Delarbeid
    1. Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens
    Åpne denne publikasjonen i ny fane eller vindu >>Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens
    Vise andre…
    2020 (engelsk)Inngår i: Molecular biology and evolution, ISSN 0737-4038, Vol. 37, nr 10, s. 2944-2954Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

    sted, utgiver, år, opplag, sider
    Oxford University Press (OUP), 2020
    Emneord
    Khoe-San, southern Africa, population structure
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-416638 (URN)10.1093/molbev/msaa140 (DOI)000593115800013 ()32697301 (PubMedID)
    Merknad

    The three first authors contributed equally to the work.

    Tilgjengelig fra: 2020-07-25 Laget: 2020-07-25 Sist oppdatert: 2021-04-26bibliografisk kontrollert
    2. Comparison of sequencing data processing pipelines and application to underrepresented human populations
    Åpne denne publikasjonen i ny fane eller vindu >>Comparison of sequencing data processing pipelines and application to underrepresented human populations
    Vise andre…
    (engelsk)Inngår i: BMC Bioinformatics, E-ISSN 1471-2105Artikkel i tidsskrift (Fagfellevurdert) Submitted
    Abstract [en]

    Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture human diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its “Best Practices” bioinformatic pipelines. However, studies often focus on few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification.

    We started by surveying 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies, that the GATK “Best Practices” are seldom followed strictly and that processing pipelines are often not reported in full details. We then compared three versions of the GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipeline on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called.

    We conclude that applying the GATK “Best Practices” pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for a coverage of >30X, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-416640 (URN)
    Tilgjengelig fra: 2020-07-25 Laget: 2020-07-25 Sist oppdatert: 2024-01-17
    3. Deciphering early human history using Approximate Bayesian Computation and 74 whole genomes from Central and Southern Africa
    Åpne denne publikasjonen i ny fane eller vindu >>Deciphering early human history using Approximate Bayesian Computation and 74 whole genomes from Central and Southern Africa
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Human evolutionary history in Africa before and after the out-of-Africa event remains largely unexplored, due to lack of genome sequence data, limited representation of populations and limitations of presently available inference methods. We generated high-coverage genomes from 49 Central African individuals, from five rainforest hunter-gatherer populations and four neighboring populations, and from 25 Khoe-San individuals, from five populations. We analyzed these genomes jointly with 104 comparative genomes from worldwide populations. We showed that rainforest hunter-gatherers and Khoe-San populations define two distinct major axes of genetic variation both at the worldwide and Sub-Saharan scales. This new data provides unprecedented resolution to unravel complex genetic differentiation among rainforest hunter-gatherer populations in particular. Using both deterministic and Approximate Bayesian Computation inferences, we found strong support for gene flow throughout the entire history of Central and Southern Africa, and an early divergence, some 250-370 kya ago, of Khoe-San ancestors from the lineage ancestral to all Central African populations. This event was followed, still in the presence of gene-flow, some 80-240 kya, by the divergence of lineages ancestral to rainforest hunter-gatherers and their neighbors. Finally, divergence between the different Khoe-San populations likely predated that of eastern and western rainforest hunter-gatherers which occurred 16-44 kya. Altogether, our results indicate that a tree-like history of Central Africa incorporating gene-flow among ancient lineages as well as among recent lineages can explain genomic variation observed among populations today.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-416642 (URN)
    Tilgjengelig fra: 2020-07-26 Laget: 2020-07-26 Sist oppdatert: 2020-07-31
    4. The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groups
    Åpne denne publikasjonen i ny fane eller vindu >>The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groups
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Sub-equatorial Africa is inhabited today predominantly by Bantu-speaking farmers of west African descent. However, before the arrival of agriculture and pastoralism ~2,000 years ago, the region was inhabited by hunter-gatherers. The incoming farmer populations replaced, displaced or admixed with local hunter-gatherer groups. In some regions such as southern and central Africa, current-day farming populations have absorbed a large local hunter-gatherer genetic component. In other regions, such as Malawi, and Mozambique current-day populations have absorbed little to none of the local component. In this study, we generated genome-wide SNP data from two populations from Zambia thought to represent former hunter-gatherers, known locally as “BaTwa”, but for which no direct evidence exists of a hunter-gatherer past, either in language or lifestyle. We compared the BaTwa data to three Bantu-speaker agropastoralist populations from Zambia, and to other African and non-African populations. We show that the two BaTwa populations harbor a hunter-gatherer-like genetic component, representing respectively ~20% and ~30% of their genetic ancestry, while the rest is similar to Bantu-speaker agropastoralists. Although the component is closest related to current-day Khoe-San populations from southern Africa, results still suggest a unique local hunter-gatherer component. These results accord with Middle and Late Holocene skeletal evidence from Zambia and Malawi for a regionally separate hunter-gatherer population, which is now only detectable among the BaTwa. A two-way admixture scenario between a Bantu-speaker agropastoralist-like source and a hunter-gatherer-like source is supported for the two populations, occurring ~40 and ~16 generations ago respectively. These estimates are consistent with archaeological records for the arrival of agropastoralists in northern and central Zambia respectively. The study demonstrate the value of studying underrepresented minority groups to better understand the complexity of regional population histories.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-416641 (URN)
    Tilgjengelig fra: 2020-07-26 Laget: 2020-07-26 Sist oppdatert: 2020-07-28
    Fulltekst (pdf)
    fulltext
    Download (jpg)
    presentationsbild
  • 13.
    Breton, Gwenna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Barham, Lawrence
    Department of Archaeology, Classics & Egyptology, University of Liverpool, Liverpool L69 7WZ, UK.
    Mudenda, George
    Livingstone Museum, Mosi-o-tunya Road, Livingstone, Zambia.
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa.
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groupsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Sub-equatorial Africa is inhabited today predominantly by Bantu-speaking farmers of west African descent. However, before the arrival of agriculture and pastoralism ~2,000 years ago, the region was inhabited by hunter-gatherers. The incoming farmer populations replaced, displaced or admixed with local hunter-gatherer groups. In some regions such as southern and central Africa, current-day farming populations have absorbed a large local hunter-gatherer genetic component. In other regions, such as Malawi, and Mozambique current-day populations have absorbed little to none of the local component. In this study, we generated genome-wide SNP data from two populations from Zambia thought to represent former hunter-gatherers, known locally as “BaTwa”, but for which no direct evidence exists of a hunter-gatherer past, either in language or lifestyle. We compared the BaTwa data to three Bantu-speaker agropastoralist populations from Zambia, and to other African and non-African populations. We show that the two BaTwa populations harbor a hunter-gatherer-like genetic component, representing respectively ~20% and ~30% of their genetic ancestry, while the rest is similar to Bantu-speaker agropastoralists. Although the component is closest related to current-day Khoe-San populations from southern Africa, results still suggest a unique local hunter-gatherer component. These results accord with Middle and Late Holocene skeletal evidence from Zambia and Malawi for a regionally separate hunter-gatherer population, which is now only detectable among the BaTwa. A two-way admixture scenario between a Bantu-speaker agropastoralist-like source and a hunter-gatherer-like source is supported for the two populations, occurring ~40 and ~16 generations ago respectively. These estimates are consistent with archaeological records for the arrival of agropastoralists in northern and central Zambia respectively. The study demonstrate the value of studying underrepresented minority groups to better understand the complexity of regional population histories.

  • 14.
    Breton, Gwenna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Johansson, Anna C. V.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Sjödin, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Comparison of sequencing data processing pipelines and application to underrepresented African human populations2021Inngår i: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 22, nr 1, artikkel-id 488Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its "Best Practices" bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification. Results We surveyed 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies and that the GATK "Best Practices" are seldom followed strictly. We then compared three versions of a GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipelines on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called. Conclusions We conclude that applying the GATK "Best Practices" pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for coverage of > 30X if identifying most variants is important, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.

    Fulltekst (pdf)
    FULLTEXT01
  • 15.
    Breton, Gwenna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Johansson, Anna C. V.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sjödin, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa.
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa.
    Comparison of sequencing data processing pipelines and application to underrepresented human populationsInngår i: BMC Bioinformatics, E-ISSN 1471-2105Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture human diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its “Best Practices” bioinformatic pipelines. However, studies often focus on few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification.

    We started by surveying 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies, that the GATK “Best Practices” are seldom followed strictly and that processing pipelines are often not reported in full details. We then compared three versions of the GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipeline on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called.

    We conclude that applying the GATK “Best Practices” pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for a coverage of >30X, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.

  • 16.
    Breton, Gwenna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Sjödin, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Zervakis, Panagiotis
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Laurent, Romain
    UMR7206 Ecoanthropology, CNRS-MNHN-Université de Paris, Paris, France.
    Froment, Alain
    UMR 208 Patrimoines locaux, IRD-MNHN, Paris, France.
    Sjöstrand, Agnès E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Hewlett, Barry S.
    Department of Anthropology, Washington State University, Vancouver, Washington, USA.
    Barreiro, Luis B.
    Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA.
    Perry, George H.
    Department of Anthropology, Pennsylvania State University, University Park, PA 16801, USA.
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa.
    Heyer, Evelyne
    UMR7206 Ecoanthropology, CNRS-MNHN-Université de Paris, Paris, France.
    Schlebusch, Carina M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Verdu, Paul
    UMR7206 Ecoanthropology, CNRS-MNHN-Université de Paris, Paris, France.
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Deciphering early human history using Approximate Bayesian Computation and 74 whole genomes from Central and Southern AfricaManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Human evolutionary history in Africa before and after the out-of-Africa event remains largely unexplored, due to lack of genome sequence data, limited representation of populations and limitations of presently available inference methods. We generated high-coverage genomes from 49 Central African individuals, from five rainforest hunter-gatherer populations and four neighboring populations, and from 25 Khoe-San individuals, from five populations. We analyzed these genomes jointly with 104 comparative genomes from worldwide populations. We showed that rainforest hunter-gatherers and Khoe-San populations define two distinct major axes of genetic variation both at the worldwide and Sub-Saharan scales. This new data provides unprecedented resolution to unravel complex genetic differentiation among rainforest hunter-gatherer populations in particular. Using both deterministic and Approximate Bayesian Computation inferences, we found strong support for gene flow throughout the entire history of Central and Southern Africa, and an early divergence, some 250-370 kya ago, of Khoe-San ancestors from the lineage ancestral to all Central African populations. This event was followed, still in the presence of gene-flow, some 80-240 kya, by the divergence of lineages ancestral to rainforest hunter-gatherers and their neighbors. Finally, divergence between the different Khoe-San populations likely predated that of eastern and western rainforest hunter-gatherers which occurred 16-44 kya. Altogether, our results indicate that a tree-like history of Central Africa incorporating gene-flow among ancient lineages as well as among recent lineages can explain genomic variation observed among populations today.

  • 17.
    Capador‐Barreto, Hernán D.
    et al.
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Bernhardsson, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala Biocentre Department of Plant Biology Swedish University of Agricultural Sciences Uppsala Sweden.
    Milesi, Pascal
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Vos, Ingrid
    Forestry Research Institute of Sweden (Skogforsk) Ekebo Sweden.
    Lundén, Karl
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Wu, Harry X.
    Umeå Plant Science Centre Department of Forest Genetics and Plant Physiology Swedish University of Agricultural Sciences Umeå Sweden.
    Karlsson, Bo
    Forestry Research Institute of Sweden (Skogforsk) Ekebo Sweden.
    Ingvarsson, Pär K.
    Uppsala Biocentre Department of Plant Biology Swedish University of Agricultural Sciences Uppsala Sweden.
    Stenlid, Jan
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Elfstrand, Malin
    Uppsala Biocentre Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden.
    Killing two enemies with one stone?: Genomics of resistance to two sympatric pathogens in Norway spruce2021Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 30, nr 18, s. 4433-4447Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.

    Fulltekst (pdf)
    fulltext
  • 18.
    Cerny, Viktor
    et al.
    Acad Sci Czech Republ, Archaeogenet Lab, Inst Archaeol, Letenska 1, Prague 11801, Czech Republic..
    Priehodová, Edita
    Acad Sci Czech Republ, Archaeogenet Lab, Inst Archaeol, Letenska 1, Prague 11801, Czech Republic..
    Fortes-Lima, Cesar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    A Population Genetic Perspective on Subsistence Systems in the Sahel/Savannah Belt of Africa and the Historical Role of Pastoralism2023Inngår i: Genes, E-ISSN 2073-4425, Vol. 14, nr 3, artikkel-id 758Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    This review focuses on the Sahel/Savannah belt, a large region of Africa where two alternative subsistence systems (pastoralism and agriculture), nowadays, interact. It is a long-standing question whether the pastoralists became isolated here from other populations after cattle began to spread into Africa (similar to 8 thousand years ago, kya) or, rather, began to merge with other populations, such as agropastoralists, after the domestication of sorghum and pearl millet (similar to 5 kya) and with the subsequent spread of agriculture. If we look at lactase persistence, a trait closely associated with pastoral lifestyle, we see that its variants in current pastoralists distinguish them from their farmer neighbours. Most other (mostly neutral) genetic polymorphisms do not, however, indicate such clear differentiation between these groups; they suggest a common origin and/or an extensive gene flow. Genetic affinity and ecological symbiosis between the two subsistence systems can help us better understand the population history of this African region. In this review, we show that genomic datasets of modern Sahel/Savannah belt populations properly collected in local populations can complement the still insufficient archaeological research of this region, especially when dealing with the prehistory of mobile populations with perishable material culture and therefore precarious archaeological visibility.

    Fulltekst (pdf)
    FULLTEXT01
  • 19.
    Cervantes, Sandra
    et al.
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland.;Univ Oulu, Bioctr Oulu, Oulu, Finland..
    Kesalähti, Robert
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland..
    Kumpula, Timo A.
    Univ Oulu, Bioctr Oulu, Oulu, Finland.;Univ Oulu, Res Unit Translat Med, Lab Canc Genet & Tumor Biol, Oulu, Finland..
    Mattila, Tiina M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Helanterä, Heikki
    Univ Oulu, Dept Ecol & Genet, Oulu, Finland..
    Pyhäjärvi, Tanja
    Univ Helsinki, Dept Forest Sci, Helsinki, Finland..
    Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory2023Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 40, nr 8, artikkel-id msad183Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The masking theory states that genes expressed in a haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in a diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intraspecific competition. Evidence from other plant groups is scarce, and results show no support for the masking theory. Here, we have used a gymnosperm Scots pine megagametophyte, a maternally derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue and that this signal of strong selection is not an artifact driven by high expression levels.

    Fulltekst (pdf)
    fulltext
  • 20.
    Chen, Hwei-yen
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Jolly, Cecile
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Bublys, Kasparas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Marcu, Daniel
    Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England..
    Immler, Simone
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England.
    Trade-off between somatic and germline repair in a vertebrate supports the expensive germ line hypothesis2020Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, nr 16, s. 8973-8979Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The disposable soma theory is a central tenet of the biology of aging where germline immortality comes at the cost of an aging soma [T. B. L. Kirkwood, Nature 270, 301–304 (1977); T. B. L. Kirkwood, Proc. R. Soc. Lond. B Biol. Sci. 205, 531–546 (1979); T. B. L. Kirkwood, S. N. Austad, Nature 408, 233–238 (2000)]. Limited resources and a possible trade-off between the repair and maintenance of the germ cells and growth and maintenance of the soma may explain the deterioration of the soma over time. Here we show that germline removal allows accelerated somatic healing under stress. We tested “the expensive germ line” hypothesis by generating germline-free zebrafish Danio rerio and testing the effect of the presence and absence of the germ line on somatic repair under benign and stressful conditions. We exposed male fish to sublethal low-dose ionizing radiation, a genotoxic stress affecting the soma and the germ line, and tested how fast the soma recovered following partial fin ablation. We found that somatic recovery from ablation occurred substantially faster in irradiated germline-free fish than in the control germline-carrying fish where somatic recovery was stunned. The germ line did show signs of postirradiation recovery in germline-carrying fish in several traits related to offspring number and fitness. These results support the theoretical conjecture that germline maintenance is costly and directly trades off with somatic maintenance.

    Fulltekst (pdf)
    FULLTEXT01
  • 21.
    Chen, Hwei-yen
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Lund Univ, Dept Biol, Lund, Sweden.;Uppsala Univ, Dept Ecol & Genet, S-75236 Uppsala, Sweden..
    Krieg, Therese
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Mautz, Brian
    Vanderbilt Univ, Dept Med, Div Epidemiol, Nashville, TN USA..
    Jolly, Cecile
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Scofield, Douglas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Maklakov, Alexei A.
    Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, England..
    Immler, Simone
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, England.;Uppsala Univ, Dept Ecol & Genet, S-75236 Uppsala, Sweden..
    Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei2023Inngår i: Evolution Letters, E-ISSN 2056-3744, Vol. 7, nr 6, s. 478-489Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effect of parental age on germline mutation rate across generations is not fully understood. While some studies report a positive linear relationship of mutation rate with increasing age, others suggest that mutation rate varies with age but not in a linear fashion. We investigated the effect of parental age on germline mutations by generating replicated mutation accumulation lines in Caenorhabditis remanei at three parental ages ("Young T1" [Day 1], "Peak T2" [Day 2], and "Old T5" [Day 5] parents). We conducted whole-genome resequencing and variant calling to compare differences in mutation rates after three generations of mutation accumulation. We found that Peak T2 lines had an overall reduced mutation rate compared to Young T1 and Old T5 lines, but this pattern of the effect varied depending on the variant impact. Specifically, we found no high-impact variants in Peak T2 lines, and modifiers and up- and downstream gene variants were less frequent in these lines. These results suggest that animals at the peak of reproduction have better DNA maintenance and repair compared to young and old animals. We propose that C. remanei start to reproduce before they optimize their DNA maintenance and repair, trading the benefits of earlier onset of reproduction against offspring mutation load. The increase in offspring mutation load with age likely represents germline senescence. Germline mutations play a key role in evolution through the generation of novel genotypes. Estimating the mutation rate in species, populations, and individuals is one way to understand the relative timeframe of evolutionary processes, for the timing of historical events and for estimating heritability of traits and diseases. Individual age at reproduction is known to affect the number of mutations being transferred into the next generation and generally mutation rate is thought to increase with increasing parental age. However, preventing mutations in germ cells is potentially costly and it may pay off to optimize germline genome repair and maintenance during peak reproductive periods, and relax it during nonpeak periods. This idea has been put forward to explain for example the reduction of gonad size in seasonally reproducing animals during nonreproductive periods and supported by the finding that the mutation rate seems to be higher in teenage men compared to men during their peak reproductive ages. We further tested this idea of a nonlinear relationship between age and mutation rate by performing a mutation accumulation experiment in a short-lived nematode. We kept experimental lines and allowed adults to reproduce at different ages in different lines, with some lines reproducing before, some during, and some after their reproductive peak. We found that mutation rates are higher in nematode lines reproducing before or after the reproductive peak compared to those reproducing during the peak. Our results therefore support the idea that germline genome maintenance and repair is potentially costly and that the mutation rate does not just increase with age but is optimized during the peak reproductive age of an organism.

    Fulltekst (pdf)
    fulltext
  • 22.
    Choin, Jeremy
    et al.
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France.;Univ Paris Diderot, Sorbonne Paris Cite, Paris, France..
    Mendoza-Revilla, Javier
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France..
    Arauna, Lara R.
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France..
    Cuadros-Espinoza, Sebastian
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France.;Sorbonne Univ, Coll Doctoral, Paris, France..
    Cassar, Olivier
    Inst Pasteur, CNRS, Oncogen Virus Epidemiol & Pathophysiol, UMR 3569, Paris, France..
    Larena, Maximilian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Ko, Albert Min-Shan
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing, Peoples R China..
    Harmant, Christine
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France..
    Laurent, Romain
    Univ Paris, CNRS, UMR7206, Museum Natl Hist Nat, Paris, France..
    Verdu, Paul
    Univ Paris, CNRS, UMR7206, Museum Natl Hist Nat, Paris, France..
    Laval, Guillaume
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France..
    Boland, Anne
    Univ Paris Saclay, Ctr Natl Rech Genom Humaine CNRGH, Inst Biol Francois Jacob, CEA, Evry, France..
    Olaso, Robert
    Univ Paris Saclay, Ctr Natl Rech Genom Humaine CNRGH, Inst Biol Francois Jacob, CEA, Evry, France..
    Deleuze, Jean-Francois
    Univ Paris Saclay, Ctr Natl Rech Genom Humaine CNRGH, Inst Biol Francois Jacob, CEA, Evry, France..
    Valentin, Frederique
    CNRS, UMR 7041, Maison Archeol & Ethnol, Nanterre, France..
    Ko, Ying-Chin
    China Med Univ & Hosp, Environm Omics Dis Res Ctr, Taichung, Taiwan..
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Gessain, Antoine
    Inst Pasteur, CNRS, Oncogen Virus Epidemiol & Pathophysiol, UMR 3569, Paris, France..
    Excoffier, Laurent
    Univ Bern, Inst Ecol & Evolut, Bern, Switzerland.;Swiss Inst Bioinformat, Lausanne, Switzerland..
    Stoneking, Mark
    Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany..
    Patin, Etienne
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France..
    Quintana-Murci, Lluis
    Inst Pasteur, Human Evolutionary Genet Unit, CNRS, UMR 2000, Paris, France.;Coll France, Paris, France..
    Genomic insights into population history and biological adaptation in Oceania2021Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 592, nr 7855, s. 583-589Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes(1). However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago(2-4). Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.

  • 23.
    Choudhury, Ananyo
    et al.
    Univ Witwatersrand, Fac Hlth Sci, Sydney Brenner Inst Mol Biosci, ZA-2193 Johannesburg, South Africa..
    Sengupta, Dhriti
    Univ Witwatersrand, Fac Hlth Sci, Sydney Brenner Inst Mol Biosci, ZA-2193 Johannesburg, South Africa..
    Ramsay, Michele
    Univ Witwatersrand, Fac Hlth Sci, Sydney Brenner Inst Mol Biosci, ZA-2193 Johannesburg, South Africa..
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, ZA-2006 Auckland Pk, South Africa..
    Bantu-speaker migration and admixture in southern Africa2021Inngår i: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 30, nr R1, s. R56-R63Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    The presence of Early and Middle Stone Age human remains and associated archeological artifacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa has largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East-African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies providing evidence for the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.

    Fulltekst (pdf)
    fulltext
  • 24.
    Chylenski, Maciej
    et al.
    Adam Mickiewicz Univ, Inst Human Biol & Evolut, Fac Biol, Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland..
    Makarowicz, Przemyslaw
    Adam Mickiewicz Univ, Fac Archaeol, Uniwersytetu Poznanskiego 7, PL-61614 Poznan, Poland..
    Juras, Anna
    Adam Mickiewicz Univ, Inst Human Biol & Evolut, Fac Biol, Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland..
    Krzewinska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.;Ctr Palaeogent, Svante Arrhenius Vag 20C, S-10691 Stockholm, Sweden..
    Pospieszny, Lukasz
    Univ Gdansk, Inst Archaeol, Ul Bielanska 5, PL-80851 Gdansk, Poland.;Univ Bristol, Dept Anthropol & Archaeol, 43 Woodland Rd, Bristol BS8 1UU, England..
    Ehler, Edvard
    Czech Acad Sci, Inst Mol Genet, Lab Genom & Bioinformat, Videnska 1083, Prague 4, Czech Republic..
    Breszka, Agnieszka
    Adam Mickiewicz Univ, Inst Human Biol & Evolut, Fac Biol, Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland..
    Gorski, Jacek
    Univ Pope Jan Pawel II, Dept Hist & Cultural Heritage, Kanonicza 9, PL-31002 Krakow, Poland.;Archaeol Museum Cracow, Senacka 3, PL-31002 Krakow, Poland..
    Taras, Halina
    Mar Curie Sklodowska Univ, Inst Archaeol, MC Sklodowska Sq 4, PL-20031 Lublin, Poland..
    Szczepanek, Anita
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska 17, PL-31016 Krakow, Poland..
    Polanska, Marta
    Lublin Museum, Dept Mat & Spiritual Culture, Zamkowa 9, PL-20117 Lublin, Poland..
    Wlodarczak, Piotr
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska 17, PL-31016 Krakow, Poland..
    Lasota-Kus, Anna
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska 17, PL-31016 Krakow, Poland..
    Wojcik, Irena
    Archaeol Museum Cracow, Senacka 3, PL-31002 Krakow, Poland..
    Romaniszyn, Jan
    Adam Mickiewicz Univ, Fac Archaeol, Uniwersytetu Poznanskiego 7, PL-61614 Poznan, Poland..
    Szmyt, Marzena
    Adam Mickiewicz Univ, Fac Archaeol, Uniwersytetu Poznanskiego 7, PL-61614 Poznan, Poland.;Archaeol Museum Poznan, Wodna 27, PL-61781 Poznan, Poland..
    Kosko, Aleksander
    Adam Mickiewicz Univ, Fac Archaeol, Uniwersytetu Poznanskiego 7, PL-61614 Poznan, Poland..
    Ignaczak, Marcin
    Adam Mickiewicz Univ, Fac Archaeol, Uniwersytetu Poznanskiego 7, PL-61614 Poznan, Poland..
    Sadowski, Sylwester
    Mar Curie Sklodowska Univ, Inst Archaeol, MC Sklodowska Sq 4, PL-20031 Lublin, Poland..
    Matoga, Andrzej
    Archaeol Museum Cracow, Senacka 3, PL-31002 Krakow, Poland..
    Grossman, Anna
    Muzeum Archeol Biskupinie, Biskupin 17, PL-88410 Gasawa, Poland..
    Ilchyshyn, Vasyl
    Zaliztsi Museum Local Lore, Schevchenka 51, UA-47243 Zalizhtsi, Ternopil, Ukraine..
    Yahodinska, Maryna O.
    Ternopil Reg Ctr Protect & Res Cultural Heritage S, Kyyivska 3?, UA-46016 Ternopol, Ukraine..
    Romanska, Adriana
    Wojewodzki Urzad Ochrony Zabytkow, Goleb 2, PL-61840 Poznan, Poland..
    Tunia, Krzysztof
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska 17, PL-31016 Krakow, Poland..
    Przybyla, Marcin
    Archaeol Co Dolmen Marcin Przybyla, Michal Podsiadlo Sc, Serkowskiego Sq 8-3, PL-30512 Krakow, Poland..
    Grygiel, Ryszard
    Museum Archaeol & Ethnog Lodz, Plac Wolnocci 14, PL-91415 Lodz, Poland..
    Szostek, Krzysztof
    Cardinal Stefan Wyszynski Univ Warsaw, Inst Biol Sci, Woycickiego 1-3, PL-01938 Warsaw, Poland..
    Dabert, Miroslawa
    Adam Mickiewicz Univ, Fac Biol, Mol Biol Tech Lab, Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland..
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.;Ctr Palaeogent, Svante Arrhenius Vag 20C, S-10691 Stockholm, Sweden..
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Ctr Anthropol Res, Auckland Pk, ZA-2006 Johannesburg, South Africa.;SciLifeLab, Stockholm, Sweden..
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Ctr Anthropol Res, Auckland Pk, ZA-2006 Johannesburg, South Africa..
    Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age2023Inngår i: Nature Communications, E-ISSN 2041-1723, Vol. 14, artikkel-id 4395Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups. By analysing 91 Bronze Age genomes from East-Central Europe, the authors discovered that Middle Bronze Age populations were formed by an admixture event involving hunter-gatherers and that the social structure of resulting population was primarily patrilocal.

    Fulltekst (pdf)
    FULLTEXT01
  • 25.
    Coutinho, Alexandra
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Where our feet have taken us: Examples of human contact, migration, and adaptation as revealed by ancient DNA2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In spite of our extensive knowledge of the human past, certain key questions remain to be answered about human prehistory. One involves the nature of cultural change in material culture through time from the perspective of how different ancient human groups interacted with one another. The other is how humans have adapted to the different environments as they migrated and populated the rest of the world from their origin in Africa. For my thesis I have investigated examples of human evolutionary history using genetic information from ancient human remains. Chapter 1 focused on the nature of possible interaction between the Pitted Ware Culture (PWC) and Battle Axe Culture (BAC) on the island of Gotland, in the Baltic Sea. Through the analysis of 4500 year old human remains from three PWC burial sites, I found that the existence of BAC influences in these burial sites was the result of cultural and not demic influence from the BAC. In chapter 2, I investigated the ancestry of a Late Stone Age individual from the southwestern Cape of South Africa. Population genetic analyses revealed that this individual was genetically affiliated with Khoe groups in southern Africa, a genetic make-up that is today absent from the Cape. Chapter 3 investigated the genetic landscape of prehistoric individuals from southern Africa. Specifically, I explored frequencies of adaptive variants between Late Stone Age and Iron Age individuals. I found an increase in disease resistance alleles in Iron Age individuals and attributed this to the effects of the Bantu expansion. Chapter 4 incorporated a wider range of trait-associated variants among a greater number of modern-day populations and ancient individuals in Africa. I found that many allele frequency patterns found in modern populations follow the routes of major migrations which took place in the African Holocene. The thesis attests to the complexity of human demographic history in general, and how migration contributes to adaptation by dispersing novel adaptive variants to populations.

    Delarbeid
    1. The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
    Åpne denne publikasjonen i ny fane eller vindu >>The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
    Vise andre…
    2020 (engelsk)Inngår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 172, nr 4, s. 638-649Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Objectives

    In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub‐Neolithic hunter‐gatherer Pitted Ware culture. By investigating the genetic make‐up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture‐influenced burials), we could determine the impact of migration and the impact of cultural influences.

    Methods

    We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene‐pools.

    Results

    The genomic data show that all individuals belonged to one genetic population—a population associated with the Pitted Ware culture—irrespective of the burial style.

    Conclusion

    We conclude that the Pitted Ware culture communities were not impacted by gene‐flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.

    Emneord
    admixture, ancient DNA, migration, Stone Age
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot människans evolution och genetik
    Identifikatorer
    urn:nbn:se:uu:diva-397180 (URN)10.1002/ajpa.24079 (DOI)000537595500001 ()32497286 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council, 2017-02503Knut and Alice Wallenberg FoundationRiksbankens Jubileumsfond, M13-0904:1Swedish Research Council, 2013-1905Swedish Research Council, 2017-05267
    Merknad

    Title in thesis list of papers: The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture

    De två sista författarna delar sistaförfattarskapet

    Tilgjengelig fra: 2019-11-17 Laget: 2019-11-17 Sist oppdatert: 2021-04-07bibliografisk kontrollert
    2. Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
    Åpne denne publikasjonen i ny fane eller vindu >>Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
    Vise andre…
    2021 (engelsk)Inngår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 174, nr 4, s. 701-713Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter–gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry “Coloured” groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.

    sted, utgiver, år, opplag, sider
    John Wiley & Sons, 2021
    Emneord
    admixture, genomics, human history
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot människans evolution och genetik
    Identifikatorer
    urn:nbn:se:uu:diva-397032 (URN)10.1002/ajpa.24236 (DOI)000614599500001 ()33539553 (PubMedID)
    Forskningsfinansiär
    Göran Gustafsson Foundation for Research in Natural Sciences and MedicineKnut and Alice Wallenberg FoundationThe Research Council of Norway, 262618Swedish Research Council, 621-2014-5211Swedish Research Council, 642-2013-8019
    Merknad

    Authors in thesis list of papers: Coutinho, A., Edlund, H., Malmström, H., Henshilwood, C., van Niekerk, K., Lombard, M., Schlebusch, C. & Jakobsson, M.

    Tilgjengelig fra: 2019-11-18 Laget: 2019-11-18 Sist oppdatert: 2024-01-15bibliografisk kontrollert
    3. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
    Åpne denne publikasjonen i ny fane eller vindu >>Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
    Vise andre…
    2017 (engelsk)Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, nr 6363, s. 652-655Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-334636 (URN)10.1126/science.aao6266 (DOI)000414240500038 ()28971970 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council, 642-2013-8019; 621-2014-5211Knut and Alice Wallenberg FoundationGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyWenner-Gren Foundations
    Merknad

    Carina M. Schlebusch and Helena Malmström contributed equally to this work

    Tilgjengelig fra: 2017-11-24 Laget: 2017-11-24 Sist oppdatert: 2021-10-25bibliografisk kontrollert
    4. The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
    Åpne denne publikasjonen i ny fane eller vindu >>The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.

    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot människans evolution och genetik
    Identifikatorer
    urn:nbn:se:uu:diva-397169 (URN)
    Tilgjengelig fra: 2019-11-16 Laget: 2019-11-16 Sist oppdatert: 2019-11-18
    Fulltekst (pdf)
    fulltext
    Download (jpg)
    presentationsbild
  • 26.
    Coutinho, Alexandra
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Munters, Arielle R.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Svensson, Emma M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Götherström, Anders
    Department of Archaeology and Classical Studies, Stockholm University.
    Storå, Jan
    Department of Archaeology and Classical Studies, Stockholm University.
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. University of Johannesburg.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. University of Johannesburg.
    The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders2020Inngår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 172, nr 4, s. 638-649Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objectives

    In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub‐Neolithic hunter‐gatherer Pitted Ware culture. By investigating the genetic make‐up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture‐influenced burials), we could determine the impact of migration and the impact of cultural influences.

    Methods

    We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene‐pools.

    Results

    The genomic data show that all individuals belonged to one genetic population—a population associated with the Pitted Ware culture—irrespective of the burial style.

    Conclusion

    We conclude that the Pitted Ware culture communities were not impacted by gene‐flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.

    Fulltekst (pdf)
    fulltext
  • 27.
    Coutinho, Alexandra
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. University of Johannesburg.
    Edlund, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Henshilwood, Christopher
    University of Bergen; University of Witwatersrand.
    van Niekerk, Karen
    Department of Archaeology, History, Cultural Studies and Religion, Universitetet i Bergen.
    Lombard, Marlize
    Department of Anthropology and Development Studies, University of Johannesburg.
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. University of Johannesburg.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. University of Johannesburg.
    Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups2021Inngår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 174, nr 4, s. 701-713Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter–gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry “Coloured” groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.

    Fulltekst (pdf)
    fulltext
  • 28.
    Coutinho, Alexandra
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan AfricaManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.

  • 29.
    Cubas, Miriam
    et al.
    University of York, York, UK; Sociedad de Ciencias Aranzadi, Donostia, San Sebastian, Spain.
    Peyroteo Stjerna, Rita
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. University of Lisbon, Lisbon, Portugal.
    Fontanals-Coll, Maria
    University of York, York, UK.
    Llorente-Rodríguez, Laura
    Universiteit Leiden, Leiden, Netherlands.
    Lucquin, Alexandre
    University of York, York, UK.
    Craig, Oliver Edward
    University of York, York, UK.
    Colonese, André Carlo
    University of York, York, UK.
    Long-term dietary change in Atlantic and Mediterranean Iberia with the introduction of agriculture: a stable isotope perspective2019Inngår i: Archaeological and Anthropological Sciences, ISSN 1866-9557, E-ISSN 1866-9565, Vol. 11, nr 8, s. 3825-3836Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Neolithic expansion in the Iberian Peninsula is marked by the introduction of livestock and domesticated crops which modified subsistence strategies in an unprecedented manner. Bulk collagen stable carbon and nitrogen isotope analysis has been essential to track these changes, which have largely been discussed in relation to particular geographic areas or single case studies. This paper reviews the available isotope literature to provide a regional, long-term synthesis of dietary changes associated with the expansion of the Neolithic and the establishment of farming economy in the Iberian Peninsula. Bulk collagen stable carbon and nitrogen isotope values of 763 human individuals and 283 faunal remains from the Mesolithic to the Late Neolithic period in Iberia (ca. 8000–3000 cal BC) were collated and analysed using a Bayesian mixing model. The results show that Mesolithic diets were isotopically diverse in both the Atlantic and Mediterranean regions of the Iberian Peninsula, and that a significant decrease in variability happened with the Neolithisation, culminating with the establishment of farming economies and reliance on terrestrial resources in the Late Neolithic.

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    fulltext
  • 30. De Loma, Jessica
    et al.
    Vicente, Mário
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Tirado, Noemi
    Ascui, Franz
    Vahter, Marie
    Gardon, Jacques
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Broberg, Karin
    Human adaptation to arsenic in Bolivians living in the Andes2022Inngår i: Chemosphere, ISSN 0045-6535, E-ISSN 1879-1298, Vol. 301, artikkel-id 134764Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Humans living in the Andes Mountains have been historically exposed to arsenic from natural sources, including drinking water. Enzymatic methylation of arsenic allows it to be excreted more efficiently by the human body. Adaptation to high-arsenic environments via enhanced methylation and excretion of arsenic was first reported in indigenous women in the Argentinean Andes, but whether adaptation to arsenic is a general phenomenon across native populations from the Andes Mountains remains unclear. Therefore, we evaluated whether adaptation to arsenic has occurred in the Bolivian Andes by studying indigenous groups who belong to the Aymara-Quechua and Uru ethnicities and have lived in the Bolivian Andes for generations. Our population genetics methods, including genome-wide selection scans based on linkage disequilibrium patterns and allele frequency differences, in combination with targeted and whole-genome sequencing and genotype-phenotype association analyses, detected signatures of positive selection near the gene encoding arsenite methyltransferase (AS3MT), the main arsenic methylating enzyme. This was among the strongest selection signals (top 0.5% signals via locus-specific branch length and extended haplotype homozygosity tests) at a genome-wide level in the Bolivian study groups. We found a large haplotype block of 676 kb in the AS3MT region and identified candidate functional variants for further analysis. Moreover, our analyses revealed associations between AS3MT variants and the fraction of monomethylated arsenic in urine and showed that the Bolivian study groups had the highest frequency of alleles associated with more efficient arsenic metabolism reported so far. Our data support the idea that arsenic exposure has been a driver for human adaptation to tolerate arsenic through more efficient arsenic detoxification in different Andean populations.

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    fulltext
  • 31.
    Debortoli, Guilherme
    et al.
    Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada.
    Abbatangelo, Cristina
    Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada.
    Ceballos, Francisco
    Department of Biological Sciences, Middle East Technical University, Çankaya, Turkey.
    Fortes-Lima, Cesar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Norton, Heather L.
    Department of Anthropology, University of Cincinnati, Cincinnati, OH, USA.
    Ozarkar, Shantanu
    Department of Anthropology, Savitribai Phule Pune University, Pune, India.
    Parra, Esteban J.
    Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada.
    Jonnalagadda, Manjari
    Symbiosis School for Liberal Arts, Symbiosis International (Deemed University), Pune, India.
    Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data2020Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 10, nr 1, artikkel-id 10075Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.

    Fulltekst (pdf)
    fulltext
  • 32.
    Debortoli, Guilherme
    et al.
    Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada.
    de Araujo, Gilderlanio Santana
    Program in Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil.
    Fortes-Lima, Cesar A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Parra, Esteban J
    Department of Anthropology, University of Toronto at Mississauga, Mississauga, ON, Canada.
    Suarez-Kurtz, Guilherme
    Instituto Nacional de Câncer and Rede Nacional de Farmacogenética, Rio de Janeiro, Brazil.
    Identification of ancestry proportions in admixed groups across the Americas using clinical pharmacogenomic SNP panels2021Inngår i: Scientific Reports, E-ISSN 2045-2322, Vol. 11, nr 1, artikkel-id 1007Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We evaluated the performance of three PGx panels to estimate biogeographical ancestry: the DMET panel, and the VIP and Preemptive PGx panels described in the literature. Our analysis indicate that the three panels capture quite well the individual variation in admixture proportions observed in recently admixed populations throughout the Americas, with the Preemptive PGx and DMET panels performing better than the VIP panel. We show that these panels provide reliable information about biogeographic ancestry and can be used to guide the implementation of PGx clinical decision-support (CDS) tools. We also report that using these panels it is possible to control for the effects of population stratification in association studies in recently admixed populations, as exemplified with a warfarin dosing GWA study in a sample from Brazil.

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  • 33. Diniz, Mariana
    et al.
    Arias Cabal, Pablo
    Araújo, Ana Cristina
    Peyroteo Stjerna, Rita
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Debating Neolithization from a Mesolithic point of view: The Sado Valley (Portugal) experience2021Inngår i: Foraging Assemblages: vol 2 / [ed] Dušan Borić, Dragana Antonović, Bojana Mihailović, The Italian Academy for Advanced Studies in America , 2021, s. 713-719Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    In this paper we discuss how the Late Mesolithic Sado Valley hunter-gatherers interacted with the first agropastoralist societies settled in southern Portugal in the course of the second half of the sixth millennium cal BC. The archaeological record available during this period in southern Portugal reflects the presence of two distinct cultural groups. Differences can be detected not only on an economic level but also in settlement patterns, material culture, and symbolic behaviour. By the end of the first quarter of the fifth millennium cal BC, the Sado shell middens seem to have been abandoned, raising the question of how and why these last hunter-gatherers left their traditional territory, since no environmental change is recorded in the area that could explain it. Using chronological information and some Neolithic elements found in the area of the shell middens, we will debate the Neolithization process from a Mesolithic point of view.

    Fulltekst (pdf)
    Debating Neolithization_chapter
  • 34.
    Domínguez-Andrés, Jorge
    et al.
    Radboud Univ Nijmegen, Dept Internal Med, Med Ctr, Nijmegen, Netherlands; Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, Nijmegen, Netherlands.;RadboudUniv, Radboud Inst Mol Life Sci RIMLS, Med Ctr, Nijmegen, Netherlands.
    Kuijpers, Yunus
    Ctr Individualised Infect Med CiiM, Dept Computat Biol Individualised Infect Med, Hannover, Germany; Ctr Expt & Clin Infect Res, TWINCORE, Hannover, Germany.
    Bakker, Olivier B.
    Univ Med Ctr Groningen, Dept Genet, Nijmegen, Netherlands.
    Jaeger, Martin
    Radboud Univ Nijmegen, Dept Internal Med, Med Ctr, Nijmegen, Netherlands; Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, Nijmegen, Netherlands.;RadboudUniv, Radboud Inst Mol Life Sci RIMLS, Med Ctr, Nijmegen, Netherlands.
    Xu, Cheng-Jian
    Radboud Univ Nijmegen, Dept Internal Med, Med Ctr, Nijmegen, Netherlands; Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, Nijmegen, Netherlands; Ctr Individualised Infect Med CiiM, Dept Computat Biol Individualised Infect Med, Hannover, Germany; Ctr Expt & Clin Infect Res, TWINCORE, Hannover, Germany.
    Van der Meer, Jos WM
    Radboud Univ Nijmegen, Dept Internal Med, Med Ctr, Nijmegen, Netherlands.;Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, Nijmegen, Netherlands.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Ctr Anthropol Res, Dept Anthropol & Dev Studies, Auckland Pk, South Africa.
    Bertranpetit, Jaume
    Univ Pompeu Fabra, Inst Biol Evolut UPF CSIC, Barcelona, Spain.
    Ab Joosten, Leo
    Radboud Univ Nijmegen, Dept Internal Med, Med Ctr, Nijmegen, Netherlands; Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, Nijmegen, Netherlands; Radboud Univ, Radboud Inst Mol Life Sci RIMLS, Med Ctr, Nijmegen, Netherlands.
    Li, Yang
    Radboud Univ Nijmegen, Dept Internal Med, Med Ctr, Nijmegen, Netherlands; Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, Nijmegen, Netherlands; Radboud Univ, Radboud Inst Mol Life Sci RIMLS, Med Ctr, Nijmegen, Netherlands; Ctr Individualised Infect Med CiiM, Dept Computat Biol Individualised Infect Med, Hannover, Germany; Ctr Expt & Clin Infect Res, TWINCORE, Hannover, Germany.
    Netea, Mihai G.
    Radboud Univ Nijmegen, Dept Internal Med, Med Ctr, Nijmegen, Netherlands; Radboud Univ Nijmegen, Radboud Ctr Infect Dis RCI, Med Ctr, Nijmegen, Netherlands; Radboud Univ, Radboud Inst Mol Life Sci RIMLS, Med Ctr, Nijmegen, Netherlands; Univ Bonn, Life & Med Sci Inst LIMES, Dept Genom & Immunoregulat, Bonn, Germany.
    Evolution of cytokine production capacity in ancient and modern European populations2021Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 10, artikkel-id e64971Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    As our ancestors migrated throughout different continents, natural selection increased the presence of alleles advantageous in the new environments. Heritable variations that alter the susceptibility to diseases vary with the historical period, the virulence of the infections, and their geographical spread. In this study we built polygenic scores for heritable traits that influence the genetic adaptation in the production of cytokines and immune-mediated disorders, including infectious, inflammatory, and autoimmune diseases, and applied them to the genomes of several ancient European populations. We observed that the advent of the Neolithic was a turning point for immune-mediated traits in Europeans, favoring those alleles linked with the development of tolerance against intracellular pathogens and promoting inflammatory responses against extracellular microbes. These evolutionary patterns are also associated with an increased presence of traits related to inflammatory and auto-immune diseases.

    Fulltekst (pdf)
    FULLTEXT01
  • 35.
    Eklöf, Helena
    et al.
    Umeå Univ, Umeå Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umeå, Sweden.
    Bernhardsson, Carolina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Ingvarsson, Pär K.
    Swedish Univ Agr Sci, Linnean Ctr Plant Biol, Dept Plant Biol, SE-75007 Uppsala, Sweden.
    Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies2020Inngår i: Forests, E-ISSN 1999-4907, Vol. 11, nr 11, artikkel-id 1185Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

    Fulltekst (pdf)
    FULLTEXT01
  • 36.
    Feuerborn, Tatiana R.
    et al.
    Univ Copenhagen, Globe Inst, Copenhagen, Denmark; Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden.
    Palkopoulou, Eleftheria
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    van der Valk, Tom
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden.
    von Seth, Johanna
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Munters, Arielle R.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Pecnerova, Patricia
    Univ Copenhagen, Dept Biol, Copenhagen, Denmark.
    Dehasque, Marianne
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Ureña, Irene
    INIA, Dept Anim Breeding, Madrid, Spain.
    Ersmark, Erik
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden.
    Kempe Lagerholm, Vendela
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden.
    Krzewinska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden.
    Rodriguez-Varela, Ricardo
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden.
    Götherström, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden.
    Dalén, Love
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Diez-del-Molino, David
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden.
    Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets2020Inngår i: BMC Genomics, E-ISSN 1471-2164, Vol. 21, nr 1, artikkel-id 844Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background

    After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.

    Results

    Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.

    Conclusions

    We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.

    Fulltekst (pdf)
    FULLTEXT01
  • 37.
    Fortes-Lima, Cesar A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Burgarella, Concetta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Montpellier, AGAP Inst, Inst Agro, CIRAD,INRAE, Montpellier, France..
    Hammarén, Rickard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Eriksson, Anders
    Univ Tartu, Inst Genom, cGEM, Tartu, Estonia..
    Vicente, Mario
    Univ Stockholm, Ctr Palaeogenet, Stockholm, Sweden.;Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden..
    Jolly, Cecile
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Semo, Armando
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, Vairao, Portugal.;CIBIO, BIOPOLIS Program Genom Biodivers & Land Planning, Campus Vairao, Vairao, Portugal.;Univ Porto, Fac Ciencias, Dept Biol, Porto, Portugal..
    Gunnink, Hilde
    Univ Ghent, UGent Ctr Bantu Studies BantUGent, Dept Languages & Cultures, Ghent, Belgium.;Leiden Univ, Ctr Linguist, Leiden, Netherlands..
    Pacchiarotti, Sara
    Univ Ghent, UGent Ctr Bantu Studies BantUGent, Dept Languages & Cultures, Ghent, Belgium..
    Mundeke, Leon
    Univ Kinshasa, Kinshasa, DEM REP CONGO..
    Matonda, Igor
    Univ Kinshasa, Kinshasa, DEM REP CONGO..
    Muluwa, Joseph Koni
    Inst Super Pedag Kikwit, Kikwit, DEM REP CONGO..
    Coutros, Peter
    Univ Ghent, UGent Ctr Bantu Studies BantUGent, Dept Languages & Cultures, Ghent, Belgium..
    Nyambe, Terry S.
    Livingstone Museum, Livingstone, Zambia..
    Cikomola, Justin Cirhuza
    Catholic Univ Bukavu, Fac Med, Bukavu, DEM REP CONGO..
    Coetzee, Vinet
    Univ Pretoria, Dept Biochem Genet & Microbiol, Pretoria, South Africa..
    de Castro, Minique
    Agr Res Council, Biotechnol Platform, Pretoria, South Africa..
    Ebbesen, Peter
    Aalborg Univ, Dept Hlth Sci & Technol, Aalborg, Denmark..
    Delanghe, Joris
    Univ Ghent, Dept Diagnost Sci, Ghent, Belgium..
    Stoneking, Mark
    Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany.;Univ Lyon 1, Lab Biometrie & Biol Evolut, UMR 5558, CNRS, Villeurbanne, France..
    Barham, Lawrence
    Univ Liverpool, Dept Archaeol Class & Egyptol, Liverpool, England..
    Lombard, Marlize
    Univ Johannesburg, Palaeo Res Inst, Johannesburg, South Africa..
    Meyer, Anja
    Univ Witwatersrand, Fac Hlth Sci, Sch Anat Sci, Human Variat & Identificat Res Unit, Johannesburg, South Africa..
    Steyn, Maryna
    Univ Witwatersrand, Fac Hlth Sci, Sch Anat Sci, Human Variat & Identificat Res Unit, Johannesburg, South Africa..
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Univ Johannesburg, Palaeo Res Inst, Johannesburg, South Africa..
    Rocha, Jorge
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, Vairao, Portugal.;CIBIO, BIOPOLIS Program Genom Biodivers & Land Planning, Campus Vairao, Vairao, Portugal.;Univ Porto, Fac Ciencias, Dept Biol, Porto, Portugal..
    Soodyall, Himla
    Univ Witwatersrand, Fac Hlth Sci, Sch Pathol, Div Human Genet, Johannesburg, South Africa.;Acad Sci South Africa, Pretoria, South Africa..
    Pakendorf, Brigitte
    CNRS, Dynam Langage, UMR5596, Lyon, France.;Univ Lyon, Lyon, France..
    Bostoen, Koen
    Univ Ghent, UGent Ctr Bantu Studies BantUGent, Dept Languages & Cultures, Ghent, Belgium..
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, Johannesburg, South Africa..
    The genetic legacy of the expansion of Bantu-speaking peoples in Africa2024Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 625, nr 7995, s. 540-547Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.

    Fulltekst (pdf)
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  • 38.
    Fortes-Lima, Cesar A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Hammarén, Rickard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Burgarella, Concetta
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Eriksson, Anders
    cGEM, Institute of Genomics, University of Tartu, Tartu, Estonia.
    Vicente, Mário
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Jolly, Cecile
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Semo, Armando
    CIBIO–Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.
    Gunnink, Hilde
    UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgiu.
    Pacchiarotti, Sara
    UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgiu.
    Mundeke, Leon
    University of Kinshasa, Kinshasa, DRC.
    Mundeke, Igor
    University of Kinshasa, Kinshasa, DRC.
    Koni Muluwa, Joseph
    Institut Supérieur Pédagogique de Kikwit, Kikwit, DRC.
    Nyambe, Terry S.
    Livingstone Museum, Livingstone, Zambia.
    Cikomola, Cirhuza
    Internal Medicine, Université Catholique de Bukavu, Bukavu, DRC.
    Coetzee, Vinet
    Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
    Ebbesen, Peter
    Department of Health Science and Technology, University of Aalborg, Aalborg, Denmark.
    Joris, Delanghe
    Department of Diagnostic Sciences, Ghent University, Ghent, Belgium..
    Stoneking, Mark
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
    Rocha, Jorge
    UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgium.
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.; Academy of Science of South Africa, Pretoria, South Africa..
    Coutros, Peter
    University of Kinshasa, Kinshasa, DRC.
    Pakendorf, Brigitte
    Research unit «Dynamique Du Langage», UMR5596, CNRS & Université de Lyon, Lyon, France.
    Bostoen, Koen
    UGent Centre for Bantu Studies (BantUGent), Department of Languages and Cultures, Ghent University, Ghent, Belgium.
    Schlebusch, Carina M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Population structure and admixture during the expansion of Bantu-speaking peoples across sub-Saharan AfricaManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The migration of Bantu-speaking groups out of West Africa, thought to have started around 4 000 years ago, is known as the Bantu expansion. This movement of people changed the genetic landscape of sub-equatorial Africa. To investigate the demographic history and population structure in Bantu-speaking populations (BSP), we genotyped 1,740 individuals, including 1,487 Bantu speakers from 143 populations across 13 sub-Saharan African countries. We find patterns of fine-scale population structure that correlate with linguistics and geography. Bantu speakers received significant amounts of admixture through interaction with local groups from the regions that they expanded into. Spatial modeling indicated possible migration corridors during the Bantu-expansion. Inferences based on modern-day genomes, however, need to be supported by ancient DNA studies. We demonstrated the utility of our dataset as an exhaustive modern-day African comparative dataset for ancient DNA studies by comparing our data to published aDNA studies. By gathering the largest set of genome-wide data to date, enriched with new data from previously unsampled regions and people, we shed new light on the intricacies of the Bantu expansion.

  • 39.
    Fortes-Lima, Cesar A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Laurent, Romain
    UMR7206 Eco‐anthropologie, CNRS, Muséum National d’Histoire Naturelle, Université de Paris, Paris, France.
    Thouzeau, Valentin
    UMR7534 Centre de Recherche en Mathématiques de la Décision, CNRS, Université Paris‐Dauphine, PSL University, Paris, France; Laboratoire de Sciences Cognitives et Psycholinguistique, Département d'Etudes Cognitives, ENS, PSL University, EHESS, CNRS, Paris, France.
    Toupance, Bruno
    UMR7206 Eco‐anthropologie, CNRS, Muséum National d’Histoire Naturelle, Université de Paris, Paris, France.
    Verdu, Paul
    UMR7206 Eco‐anthropologie, CNRS, Muséum National d’Histoire Naturelle, Université de Paris, Paris, France.
    Complex genetic admixture histories reconstructed with Approximate Bayesian Computation2021Inngår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 21, nr 4, s. 1098-1117Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Admixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum-likelihood approaches based on allele frequencies and linkage-disequilibrium have been extensively used to infer admixture processes from genome-wide data sets, mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically challenging to reconstruct. We developed an Approximate Bayesian Computation (ABC) framework to reconstruct highly complex admixture histories from independent genetic markers. We built the software package MetHis to simulate independent SNPs or microsatellites in a two-way admixed population for scenarios with multiple admixture pulses, monotonically decreasing or increasing recurring admixture, or combinations of these scenarios. MetHis allows users to draw model-parameter values from prior distributions set by the user, and, for each simulation, MetHis can calculate numerous summary statistics describing genetic diversity patterns and moments of the distribution of individual admixture fractions. We coupled MetHis with existing machine-learning ABC algorithms and investigated the admixture history of admixed populations. Results showed that random forest ABC scenario-choice could accurately distinguish among most complex admixture scenarios, and errors were mainly found in regions of the parameter space where scenarios were highly nested, and, thus, biologically similar. We focused on African American and Barbadian populations as two study-cases. We found that neural network ABC posterior parameter estimation was accurate and reasonably conservative under complex admixture scenarios. For both admixed populations, we found that monotonically decreasing contributions over time, from Europe and Africa, explained the observed data more accurately than multiple admixture pulses. This approach will allow for reconstructing detailed admixture histories when maximum-likelihood methods are intractable.

    Fulltekst (pdf)
    fulltext
  • 40.
    Fortes-Lima, Cesar A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Evolutionary Biology Centre, Uppsala University.
    Mtetwa, Ezekia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi. Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Afrikansk och jämförande arkeologi.
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Unraveling African diversity from a cross‐disciplinary perspective2019Inngår i: Evolutionary anthropology (Print), ISSN 1060-1538, E-ISSN 1520-6505, Vol. 28, nr 6, s. 288-292Artikkel i tidsskrift (Fagfellevurdert)
    Fulltekst (pdf)
    fulltext
  • 41.
    Fortes-Lima, Cesar A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa.
    Closing the Gaps in Genomic Research2021Inngår i: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 37, nr 2, s. 104-106Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Despite Africa's central role in the origin of our species, our knowledge of the genomic diversity in Africa is remarkably sparse. A recent publication by Choudhury et al. underscores the scientific imperative for a broader characterisation of African genomic diversity to better understand demographic history and improve global human health.

    Fulltekst (pdf)
    fulltext
  • 42.
    Fortes-Lima, Cesar A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Triska, Petr
    Czech Acad Sci, Archaeogenet Lab, Inst Archaeol, Prague, Czech Republic..
    Cizkova, Martina
    Czech Acad Sci, Archaeogenet Lab, Inst Archaeol, Prague, Czech Republic..
    Podgorna, Eliska
    Czech Acad Sci, Archaeogenet Lab, Inst Archaeol, Prague, Czech Republic..
    Diallo, Mame Yoro
    Czech Acad Sci, Archaeogenet Lab, Inst Archaeol, Prague, Czech Republic.;Charles Univ Prague, Fac Sci, Dept Anthropol & Human Genet, Prague, Czech Republic..
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeores Inst, Johannesburg, South Africa..
    Cerny, Viktor
    Czech Acad Sci, Archaeogenet Lab, Inst Archaeol, Prague, Czech Republic.;Charles Univ Prague, Fac Sci, Dept Anthropol & Human Genet, Prague, Czech Republic..
    Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt2022Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 39, nr 10, artikkel-id msac209Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Sahel/Savannah belt harbors diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated dense genome-wide genotype data of 327 individuals-comprising 14 ethnolinguistic groups, including 10 previously unsampled populations. Our results highlight fine-scale population structure and complex patterns of admixture, particularly in Fulani groups and Arabic-speaking populations. Among all studied Sahelian populations, only the Rashaayda Arabic-speaking population from eastern Sudan shows a lack of gene flow from African groups, which is consistent with the short history of this population in the African continent. They are recent migrants from Saudi Arabia with evidence of strong genetic isolation during the last few generations and a strong demographic bottleneck. This population also presents a strong selection signal in a genomic region around the CNR1 gene associated with substance dependence and chronic stress. In Western Sahelian populations, signatures of selection were detected in several other genetic regions, including pathways associated with lactase persistence, immune response, and malaria resistance. Taken together, these findings refine our current knowledge of genetic diversity, population structure, migration, admixture and adaptation of human populations in the Sahel/Savannah belt and contribute to our understanding of human history and health.

    Fulltekst (pdf)
    fulltext
  • 43.
    Fortes-Lima, Cesar
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Verdu, Paul
    Unité Mixte de Recherche7206 Eco-Anthropology, CNRS-MNHN-Université de Paris, Musée de l’Homme , Paris, 75016, France.
    Anthropological genetics perspectives on the transatlantic slave trade2021Inngår i: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 30, nr R1, s. R79-R87Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    During the Trans-Atlantic Slave Trade (TAST), around twelve million Africans were enslaved and forcibly moved from Africa to the Americas and Europe, durably influencing the genetic and cultural landscape of a large part of humanity since the 15th century. Following historians, archaeologists, and anthropologists, population geneticists have, since the 1950's mainly, extensively investigated the genetic diversity of populations on both sides of the Atlantic. These studies shed new lights into the largely unknown genetic origins of numerous enslaved-African descendant communities in the Americas, by inferring their genetic relationships with extant African, European, and Native American populations. Furthermore, exploring genome-wide data with novel statistical and bioinformatics methods, population geneticists have been increasingly able to infer the last 500 years of admixture histories of these populations. These inferences have highlighted the diversity of histories experienced by enslaved-African descendants, and the complex influences of socioeconomic, political, and historical contexts on human genetic diversity patterns during and after the slave trade. Finally, the recent advances of paleogenomics unveiled crucial aspects of the life and health of the first generation of enslaved-Africans in the Americas. Altogether, human population genetics approaches in the genomic and paleogenomic era need to be coupled with history, archaeology, anthropology, and demography in interdisciplinary research, to reconstruct the multifaceted and largely unknown history of the TAST and its influence on human biological and cultural diversities today. Here, we review anthropological genomics studies published over the past 15 years and focusing on the history of enslaved-African descendant populations in the Americas.

  • 44.
    Fraser, Magdalena
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution. Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi.
    Sanchez-Quinto, Federico
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Evans, Jane
    Natural Environment Research Council, Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK.
    Storå, Jan
    Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    Wallin, Paul
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi.
    Knutsson, Kjel
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    New insights on cultural dualism and population structure in the MiddleNeolithic Funnel Beaker culture on the island of Gotland2018Inngår i: Journal of Archaeological Science: Reports, ISSN 2352-409X, E-ISSN 2352-4103, Vol. 17, s. 325-334Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In recent years it has been shown that the Neolithization of Europe was partly driven by migration of farming groups admixing with local hunter-gatherer groups as they dispersed across the continent. However, little research has been done on the cultural duality of contemporaneous foragers and farming populations in the same region. Here we investigate the demographic history of the Funnel Beaker culture [Trichterbecherkultur or TRB, c. 4000–2800 cal BCE], and the sub-Neolithic Pitted Ware culture complex [PWC, c. 3300–2300 cal BCE] during the Nordic Middle Neolithic period on the island of Gotland, Sweden. We use a multidisciplinary approach to investigate individuals buried in the Ansarve dolmen, the only confirmed TRB burial on the island. We present new radiocarbon dating, isotopic analyses for diet and mobility, and mitochondrial DNA haplogroup data to infer maternal inheritance. We also present a new Sr-baseline of 0.71208 ± 0.0016 for the local isotope variation. We compare and discuss our findings together with that of contemporaneous populations in Sweden and the North European mainland.

    The radiocarbon dating and Strontium isotopic ratios show that the dolmen was used between c. 3300–2700 cal BCE by a population which displayed local Sr-signals. Mitochondrial data show that the individuals buried in the Ansarve dolmen had maternal genetic affinity to that of other Early and Middle Neolithic farming cultures in Europe, distinct from that of the contemporaneous PWC on the island. Furthermore, they exhibited a strict terrestrial and/or slightly varied diet in contrast to the strict marine diet of the PWC. The findings indicate that two different contemporary groups coexisted on the same island for several hundred years with separate cultural identity, lifestyles, as well as dietary patterns.

  • 45.
    Fraser, Magdalena
    et al.
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Sjödin, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Sanchez-Quinto, Federico
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Evans, Jane
    Natural Environment Research Council, Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK.
    Svedjemo, Gustaf
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi.
    Knutsson, Kjel
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Wallin, Paul
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi.
    Storå, Jan
    Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    The Stone Cist Conundrum: A multidisciplinary approach to investigate Late Neolithic/ Early Bronze Age population demography on the Island of Gotland2018Inngår i: Journal of Archaeological Science: Reports, ISSN 2352-409X, E-ISSN 2352-4103, Vol. 20, s. 324-337Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Late Neolithic period in Scandinavia [LN, c. 2350-1700 cal BCE] marks a time of considerable changes in settlement patterns, economy, and material culture. This shift also lays the foundation for the demographic developments in the Early Bronze Age [EBA, c. 1700-1100 cal BCE]. However, little is presently known regarding the developments from these time-periods on the island of Gotland in the Baltic Sea. During the Middle Neolithic period [MN, c. 3300-2350 cal BCE], Gotland was inhabited by groups associated with the Funnel Beaker culture [TRB, c. 4000-2700 cal BCE], and the sub-Neolithic Pitted Ware culture [PWC, c. 3300-2300 cal BCE]. Some indications of connections with the Bathe Axe/Corded Ware cultures [BAC/CWC, c. 2800-2300 cal BCE] have also been found, but no typical BAC/CWC burials have been located on the island to date. Here, we investigate the chronological and internal relationship of twenty-three individuals buried in four LN/EBA stone cist burials; Haffinds, Hagur, Suderkvie, and Utalskog on Gotland. We present eleven mitochondrial genomes [from 23 X to 1271 X coverage], and twenty-three new radiocarbon dates, as well as stable isotope data for diet. We examine the local Sr-baseline range for Gotland, and present new Sr-data to discuss mobility patterns of the individuals. The genetic results are compared and discussed in light of earlier cultural periods from Gotland [TRB and PWC], and CWC from the European continent, as well as contemporaneous LN secondary burials in the MN Ansarve dolmen. We find that all burials were used into the EBA, but only two of the cists showed activity already during the LN. We also see some mobility to Gotland during the LN/EBA period based on Strontium and mitochondrial data. We see a shift in the dietary pattern compared to the preceding period on the island [TRB and PWC], and the two LN individuals from the Ansarve dolmen exhibited different dietary and mobility patterns compared to the individuals from the LN/EBA stone cist burials. We find that most of the cist burials were used by individuals local to the area of the burials, with the exception of the large LN/EBA Haffinds cist burial which showed higher levels of mobility. Our modeling of ancestral mitochondrial contribution from chronologically older individuals recovered in the cultural contexts of TRB, PWC and CWC show that the best model is a 55/45 mix of CWC and TRB individuals. A 3-way model with a slight influx from PWC [5%] also had a good fit. This is difficult to reconcile with the current archaeological evidence on the island. We suggest that the maternal CWC/TRB contribution we see in the local LN/EBA individuals derives from migrants after the Scandinavian MN period, which possible also admixed with smaller local groups connected with the PWC. Further genomic analyses of these groups on Gotland will help to clarify the demographic history during the MN to EBA time periods.

  • 46.
    Ginja, Catarina
    et al.
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, ArchGen Grp,InBIO,BIOPOLIS, Vairao, Portugal..
    Guimaraes, Silvia
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, ArchGen Grp,InBIO,BIOPOLIS, Vairao, Portugal..
    da Fonseca, Rute R.
    Univ Copenhagen, GLOBE Inst, Ctr Global Mt Biodivers, Copenhagen, Denmark..
    Rasteiro, Rita
    Univ Bristol, MRC Integrat Epidemiol Unit, Bristol, England..
    Rodriguez-Varela, Ricardo
    Stockholm Univ, Ctr Palaeogenet, CPG, Stockholm, Sweden..
    Simões, Luciana G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Sarmento, Cindy
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, ArchGen Grp,InBIO,BIOPOLIS, Vairao, Portugal..
    Belarte, Maria Carme
    Inst Catalade Recerca & Estudis Avancats, ICREA, Barcelona, Spain.;Inst Catala Arqueol Classica, ICAC, Tarragona, Spain..
    Kallala, Nabil
    Inst Natl Patrimoine, INP, Tunis, Tunisia.;Univ Tunis, Fac Sci Humaines & Sociales, Tunis, Tunisia..
    Torres, Joan Ramon
    Consell Insular Eivissa, Eivissa, Spain..
    Sanmarti, Joan
    Univ Barcelona, Dept Prehist Hist Antiga & Arqueol, Barcelona, Spain..
    Arruda, Ana Margarida
    Univ Lisbon, Fac Letras, Ctr Arqueol, UNIARQ, Lisbon, Portugal..
    Detry, Cleia
    Univ Lisbon, Fac Letras, Ctr Arqueol, UNIARQ, Lisbon, Portugal..
    Davis, Simon
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, ArchGen Grp,InBIO,BIOPOLIS, Vairao, Portugal.;Direccao Geral Patrimonio Cultural, Lab Arqueociencias, LARC DGPC, Lisbon, Portugal..
    Matos, Jose
    Inst Nacl Invest Agr & Vet, Unidade Estrateg Invest & Serv Biotecnol & Recurso, IP, Oeiras, Portugal.;Univ Lisbon, Ctr Ecol Evolucao & Alteracces Ambientais, CE3C, Lisbon, Portugal..
    Gotherstrom, Anders
    Pires, Ana Elisabete
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, ArchGen Grp,InBIO,BIOPOLIS, Vairao, Portugal.;Univ Lusofona, Fac Med Vet, Lisbon, Portugal..
    Valenzuela-Lamas, Silvia
    Univ Lisbon, Fac Letras, Ctr Arqueol, UNIARQ, Lisbon, Portugal.;CSIC, Inst Mila & Fontanals Humanitats, IMF, Archaeol Social Dynam, Barcelona, Spain..
    Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle2023Inngår i: iScience, E-ISSN 2589-0042 , Vol. 26, nr 7, artikkel-id 107196Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on auto-somal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (similar to 2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Magh-reb, i.e. Althiburos (El Kef, Tunisia). D -loop sequences were obtained for an addi-tional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althi-buros specimens, respectively. Our results can be explained by post -domestica-tion hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and pre-sent-day African taurine cattle.

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  • 47.
    Goellner, Tobias
    et al.
    Univ Vienna, Fac Life Sci, Dept Evolutionary Anthropol, Vienna, Austria.;Univ Vienna, HEAS Network Human Evolut & Archeol Sci, Vienna, Austria..
    Larena, Maximilian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Kutanan, Wibhu
    Khon Kaen Univ, Fac Sci, Dept Biol, Khon Kaen, Thailand..
    Lukas, Helmut
    Austrian Acad Sci, Inst Social Anthropol, Vienna, Austria..
    Fieder, Martin
    Univ Vienna, Fac Life Sci, Dept Evolutionary Anthropol, Vienna, Austria.;Univ Vienna, HEAS Network Human Evolut & Archeol Sci, Vienna, Austria..
    Schaschl, Helmut
    Univ Vienna, Fac Life Sci, Dept Evolutionary Anthropol, Vienna, Austria..
    Unveiling the Genetic History of the Maniq, a Primary Hunter-Gatherer Society2022Inngår i: Genome Biology and Evolution, E-ISSN 1759-6653, Vol. 14, nr 4, artikkel-id evac021Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Maniq of southern Thailand is one of the last remaining practicing hunter-gatherer communities in the world. However, our knowledge on their genetic origins and demographic history is still largely limited. We present here the genotype data covering similar to 2.3 million single nucleotide polymorphisms of 11 unrelated Maniq individuals. Our analyses reveal the Maniq to be closely related to the Semang populations of Malaysia (Malay Negritos), who altogether carry an Andamanese-related ancestry linked to the ancient Hoabinhian hunter-gatherers of Mainland Southeast Asia (MSEA). Moreover, the Maniq possess similar to 35% East Asian-related ancestry, likely brought about by recent admixture with surrounding agriculturist communities in the region. In addition, the Maniq exhibit one of the highest levels of genetic differentiation found among living human populations, indicative of their small population size and historical practice of endogamy. Similar to other hunter-gatherer populations of MSEA, we also find the Maniq to possess low levels of Neanderthal ancestry and undetectable levels of Denisovan ancestry. Altogether, we reveal the Maniq to be a Semang group that experienced intense genetic drift and exhibits signs of ancient Hoabinhian ancestry.

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  • 48.
    Goldberg, Amy
    et al.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Rosenberg, Noah A.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Neolithic familial migration contrasts Bronze Age male migration inferred from ancient X chromosomes2017Inngår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, nr S64, s. 196-196Artikkel i tidsskrift (Annet vitenskapelig)
  • 49.
    Gopalakrishnan, Shyam
    et al.
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Ebenesersdottir, S. Sunna
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland.;Univ Iceland, Sch Social Sci, Dept Anthropol, IS-102 Reykjavik, Iceland..
    Lundström, Inge K. C.
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Turner-Walker, Gordon
    Natl Yunlin Univ Sci & Technol, 123 Univ Rd,Sect 3, Touliu 64002, Yunlin, Taiwan.;Natl Museum Nat Sci, Dept Archaeol & Anthropol, 1 Guanqian Rd, Taichung 404023, Taiwan..
    Moore, Kristjan H. S.
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland..
    Luisi, Pierre
    Univ Nacl Cordoba, Fac Filosofia & Humanidades, Cordoba, Argentina.;Inst Pasteur, Microbial Paleogen Unit, 25-28 Rue Dr Roux, F-75015 Paris, France..
    Margaryan, Ashot
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Martin, Michael D.
    Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, N-7491 Trondheim, Norway..
    Ellegaard, Martin Rene
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, N-7491 Trondheim, Norway..
    Magnusson, Olafur P.
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland..
    Sigurosson, Asgeir
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland..
    Snorradottir, Steinunn
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland..
    Magnusdottir, Droplaug N.
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland..
    Laffoon, Jason E.
    Leiden Univ, Fac Archaeol, Dept Archaeol Sci, Leiden, Netherlands..
    van Dorp, Lucy
    UCL, UCL Genet Inst, Dept Genet Evolut & Environm, Darwin Bldg,Gower St, London WC1E 6BT, England..
    Liu, Xiaodong
    Univ Copenhagen, Dept Biol, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark..
    Moltke, Ida
    Univ Copenhagen, Dept Biol, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark..
    Avila-Arcos, Maria C.
    Univ Nacl Autonoma Mexico, Int Lab Human Genome Res, Lab Int Invest Genoma Humano LIIGH, 3001 Blvd Juriquilla, Queretaro 76230, Mexico..
    Schraiber, Joshua G.
    Illumina Inc, Illumina Artificial Intelligence Lab, San Diego, CA USA..
    Rasmussen, Simon
    Univ Copenhagen, Novo Nordisk Fdn Ctr Prot Res, Blegdamsvej 3, DK-2200 Copenhagen, Denmark..
    Juan, David
    Inst Evolutionary Biol UPF CSIC, PRBB, Dr Aiguader 88, Barcelona 08003, Spain..
    Gelabert, Pere
    Inst Evolutionary Biol UPF CSIC, PRBB, Dr Aiguader 88, Barcelona 08003, Spain.;Univ Vienna, Dept Evolutionary Anthropol, Vienna, Austria..
    de-Dios, Toni
    Inst Evolutionary Biol UPF CSIC, PRBB, Dr Aiguader 88, Barcelona 08003, Spain..
    Fotakis, Anna K.
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Iraeta-Orbegozo, Miren
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Vågene, Åshild J.
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Max Planck Inst Sci Human Hist, Kahlaische Str 10, D-07745 Jena, Germany.;Univ Tubingen, Inst Archaeol Sci, Tubingen, Germany..
    Denham, Sean Dexter
    Univ Stavanger, Museum Archaeol, Stavanger, Norway..
    Christophersen, Axel
    Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, N-7491 Trondheim, Norway..
    Stenøien, Hans K.
    Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, N-7491 Trondheim, Norway..
    Vieira, Filipe G.
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Liu, Shanlin
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China..
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Kivisild, Toomas
    Katholieke Univ Leuven, Herestr 49, B-3000 Leuven, Belgium.;Univ Tartu, Inst Genom, Riia 23b, EE-51010 Tartu, Estonia..
    Moseng, Ole Georg
    Univ South Eastern Norway, Dept Business Hist & Social Sci, Notodden, Norway..
    Skar, Birgitte
    Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, N-7491 Trondheim, Norway..
    Cheung, Christina
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Univ Paris Diderot, EA Ecoanthropol UMR 7206, Museum Natl Hist Nat, CNRS, Paris, France..
    Sandoval-Velasco, Marcela
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Wales, Nathan
    Univ York, Dept Archaeol, Kings Manor & Principals House,Exhibit Sq, York YO1 7EP, N Yorkshire, England..
    Schroeder, Hannes
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark..
    Campos, Paula F.
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Univ Porto, Ctr Interdisciplinar Invest Marinha & Ambiental, Terminal Cruzeiros Porto Leixoes, Ave Gen Norton Matos, Matosinhos, Portugal..
    Guomundsdottir, Valdis B.
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland.;Univ Iceland, Sch Social Sci, Dept Anthropol, IS-102 Reykjavik, Iceland..
    Sicheritz-Ponten, Thomas
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Asian Inst Med Sci & Technol AIMST, Fac Appl Sci, Ctr Excellence Om Driven Computat Biodiscovery CO, Bedong 08100, Kedah, Malaysia..
    Peterson, Bent
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Asian Inst Med Sci & Technol AIMST, Fac Appl Sci, Ctr Excellence Om Driven Computat Biodiscovery CO, Bedong 08100, Kedah, Malaysia..
    Halgunset, Jostein
    St Olavs Hosp HF, Biobank1, Trondheim, Norway..
    Gilbert, Edmund
    RCSI, Sch Pharm & Biomol Sci, Dublin, Ireland.;RCSI, FutureNeuro SFI Res Ctr, Dublin, Ireland..
    Cavalleri, Gianpiero L.
    RCSI, Sch Pharm & Biomol Sci, Dublin, Ireland.;RCSI, FutureNeuro SFI Res Ctr, Dublin, Ireland..
    Hovig, Eivind
    Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, Oslo, Norway.;Univ Oslo, Ctr Bioinformat, Dept Informat, Oslo, Norway..
    Kockum, Ingrid
    Karolinska Inst, Ctr Mol Med, Dept Clin Neurosci, Neuroimmunol Unit, Stockholm, Sweden..
    Olsson, Tomas
    Karolinska Inst, Ctr Mol Med, Dept Clin Neurosci, Neuroimmunol Unit, Stockholm, Sweden..
    Alfredsson, Lars
    Karolinska Inst, Inst Environm Med, Stockholm, Sweden..
    Hansen, Thomas F.
    Copenhagen Mental Hlth Serv, Inst Biol Psychiat, Copenhagen, Denmark.;Copenhagen Univ Hosp, Danish Headache Ctr, Dept Neurol, DK-2600 Glostrup, Denmark..
    Werge, Thomas
    Copenhagen Mental Hlth Serv, Inst Biol Psychiat, Copenhagen, Denmark.;Univ Copenhagen, Dept Clin Med, Copenhagen, Denmark.;Lundbeck Fdn Initiat Integrat Psychiat Res, IPSYCH, Copenhagen, Denmark.;Lundbeck Fdn Ctr Geogenet, Globe Inst, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark..
    Willerslev, Eske
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Univ Cambridge, Dept Zool, Cambridge CB2 3EJ, England..
    Balloux, Francois
    UCL, UCL Genet Inst, Dept Genet Evolut & Environm, Darwin Bldg,Gower St, London WC1E 6BT, England..
    Marques-Bonet, Tomas
    Inst Evolutionary Biol UPF CSIC, PRBB, Dr Aiguader 88, Barcelona 08003, Spain.;Catalan Inst Res & Adv Studies ICREA, Passeig Lluis Companys 23, Barcelona 08010, Spain.;Barcelona Inst Sci & Technol BIST, Ctr Genom Regulat CRG, CNAG CRG, Baldiri & Reixac 4, Barcelona 08028, Spain.;Univ Autonoma Barcelona, Inst Catala Paleontol Miquel Crusafont, Edifici ICTA ICP,C Columnes S-N, E-08193 Barcelona, Spain..
    Lalueza-Fox, Carles
    Inst Evolutionary Biol UPF CSIC, PRBB, Dr Aiguader 88, Barcelona 08003, Spain.;Museu Ciencies Nat Barcelona, Barcelona 08019, Spain..
    Nielsen, Rasmus
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Univ Calif Berkeley, Dept Integrat Biol, 3060 Valley Life Sci Bldg 3140, Berkeley, CA 94720 USA..
    Stefansson, Kari
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland.;Univ Iceland, Fac Med, Reykjavik, Iceland..
    Holgason, Agnar
    AMGEN Inc, deCODE Genet, Sturlugata 8, IS-102 Reykjavik, Iceland.;Univ Iceland, Sch Social Sci, Dept Anthropol, IS-102 Reykjavik, Iceland..
    Gilbert, M. Thomas P.
    Univ Copenhagen, GLOBE Inst, Fac Hlth & Med Sci, Oster Farimagsgade 5A, DK-1353 Copenhagen, Denmark.;Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, N-7491 Trondheim, Norway..
    The population genomic legacy of the second plague pandemic2022Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 32, nr 21, s. 4743-4751.e6Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.

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  • 50.
    Gummesson, Sara
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Molin, Fredrik
    Natl Hist Museums, Linkoping, Sweden.
    Sjöström, Arne
    Lund Univ, Dept Archeol & Ancient Hist, Lund, Sweden.
    The Spatial Organization of Bone Crafting During the Middle and Late Mesolithic at Ringsjöholm and Strandvägen in Sweden2019Inngår i: Journal of field archaeology, ISSN 0093-4690, E-ISSN 2042-4582, Vol. 44, nr 3, s. 165-179Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper focuses on the spatial distribution of bone tool production waste from two Mesolithic sites in Sweden, Ringsjoholm and Strandvagen, with well-preserved faunal remains including bone and antler artifacts. Local production on both sites has generated a variety of identifiable waste products deriving from complete chains of production, including unmodified bones, debitage and finished products. Identified categories include: blanks, removed epiphyses, bone flakes, and preforms. Identification of species shows that antler and bone from red deer were the preferred raw materials. Spatial statistical analyses confirm that different stages of bone tool production were organized within separate areas of the sites and that larger items were discarded in the water along the shorelines. Interestingly, blanks and preforms seem to have been stored under water for future use and demarcated clusters of bone flakes in association with dwellings represent "bone knapping floors" where production was more intense than in other areas.

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