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Simões, L. G., Peyroteo Stjerna, R., Marchand, G., Bernhardsson, C., Vialet, A., Chetty, D., . . . Jakobsson, M. (2024). Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France. Proceedings of the National Academy of Sciences of the United States of America, 121(10), Article ID e2310545121.
Open this publication in new window or tab >>Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France
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2024 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 121, no 10, article id e2310545121Article in journal (Other academic) Published
Abstract [en]

Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.

Place, publisher, year, edition, pages
Proceedings of the National Academy of Sciences (PNAS), 2024
National Category
Evolutionary Biology Genetics Archaeology
Identifiers
urn:nbn:se:uu:diva-493351 (URN)10.1073/pnas.2310545121 (DOI)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2018-05537Swedish Research Council, 2022-04642Swedish Research Council, 2017-05267
Note

Authors in the list of papers of Lucianan G. Simões thesis: Luciana G. Simões, Rita Peyroteo-Stjerna, Carolina Bernhardsson, Torsten Günther, Grégor Marchand, Hanna Edlund, Darshan Chetty, Denis Bouquin, Nicolas Garmond, Amélie Vialet, Mattias Jakobsson

Available from: 2023-01-12 Created: 2023-01-12 Last updated: 2024-06-27Bibliographically approved
Bergfeldt, N., Kirdök, E., Oskolkov, N., Mirabello, C., Unneberg, P., Malmström, H., . . . Götherström, A. (2024). Identification of microbial pathogens in Neolithic Scandinavian humans. Scientific Reports, 14(1), Article ID 5630.
Open this publication in new window or tab >>Identification of microbial pathogens in Neolithic Scandinavian humans
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2024 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 14, no 1, article id 5630Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Springer Nature, 2024
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-526578 (URN)10.1038/s41598-024-56096-0 (DOI)001185083700029 ()38453993 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC), SNIC 2021/5-335Swedish National Infrastructure for Computing (SNIC), SNIC 2021/6-260Swedish National Infrastructure for Computing (SNIC), SNIC 2022/5-100Swedish National Infrastructure for Computing (SNIC), SNIC 2022/6-46Swedish National Infrastructure for Computing (SNIC), SNIC 2022/22-507Swedish National Infrastructure for Computing (SNIC), SNIC 2022/23-275Swedish Research Council, 2018-05973Swedish Research Council, 2019-00849Swedish Research Council, 2017-02503Knut and Alice Wallenberg FoundationRiksbankens Jubileumsfond, P21-0266Riksbankens Jubileumsfond, P19.0740:1
Available from: 2024-04-12 Created: 2024-04-12 Last updated: 2024-04-12Bibliographically approved
Kirdök, E., Kashuba, N., Damlien, H., Manninen, M. A., Nordqvist, B., Kjellström, A., . . . Götherström, A. (2024). Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals. Scientific Reports, 13(1), Article ID 22125.
Open this publication in new window or tab >>Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
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2024 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, no 1, article id 22125Article in journal (Refereed) Published
Abstract [en]

Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.

Place, publisher, year, edition, pages
Springer Nature, 2024
National Category
Bioinformatics and Systems Biology Bioinformatics (Computational Biology) Genetics
Identifiers
urn:nbn:se:uu:diva-522281 (URN)10.1038/s41598-023-48762-6 (DOI)001144707500001 ()38238372 (PubMedID)
Funder
Riksbankens JubileumsfondSwedish Research Council, 2019-00849The Research Council of Norway, 231305UPPMAX, snic-2018/150-9
Available from: 2024-02-02 Created: 2024-02-02 Last updated: 2024-03-03Bibliographically approved
Zeberg, H., Jakobsson, M. & Paabo, S. (2024). The genetic changes that shaped Neandertals, Denisovans, and modern humans. Cell, 187(5), 1047-1058
Open this publication in new window or tab >>The genetic changes that shaped Neandertals, Denisovans, and modern humans
2024 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 187, no 5, p. 1047-1058Article, review/survey (Refereed) Published
Abstract [en]

Modern human ancestors diverged from the ancestors of Neandertals and Denisovans about 600,000 years ago. Until about 40,000 years ago, these three groups existed in parallel, occasionally met, and exchanged genes. A critical question is why modern humans, and not the other two groups, survived, became numerous, and developed complex cultures. Here, we discuss genetic differences among the groups and some of their functional consequences. As more present-day genome sequences become available from diverse groups, we predict that very few, if any, differences will distinguish all modern humans from all Neandertals and Denisovans. We propose that the genetic basis of what constitutes a modern human is best thought of as a combination of genetic features, where perhaps none of them is present in each and every present-day individual.

Place, publisher, year, edition, pages
Elsevier, 2024
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-528000 (URN)10.1016/j.cell.2023.12.029 (DOI)001209798200001 ()38367615 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2021-03050Swedish Research Council, 2018-05537Swedish Research Council, 2022-04642
Available from: 2024-05-13 Created: 2024-05-13 Last updated: 2024-05-13Bibliographically approved
Mattila, T. M., Svensson, E. M., Juras, A., Günther, T., Kashuba, N., Ala-Hulkko, T., . . . Jakobsson, M. (2023). Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe. Communications Biology, 6(1), Article ID 793.
Open this publication in new window or tab >>Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe
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2023 (English)In: Communications Biology, E-ISSN 2399-3642, Vol. 6, no 1, article id 793Article in journal (Refereed) Published
Abstract [en]

The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River. Genome-wide sequencing of 56 ancient hunter-gatherer and early farmer individuals from Stone Age Central and Eastern Europe reveals striking population continuity in the east in contrast to central Europe that displays extensive admixture.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-510703 (URN)10.1038/s42003-023-05131-3 (DOI)001045489100002 ()37558731 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), snic2018-8-304Swedish National Infrastructure for Computing (SNIC), snic2019-8-270Swedish National Infrastructure for Computing (SNIC), snic2020-2-10Swedish National Infrastructure for Computing (SNIC), snic2021-22-823Knut and Alice Wallenberg FoundationSwedish Research Council, 2017-02503Riksbankens Jubileumsfond, P21-0266
Available from: 2023-09-06 Created: 2023-09-06 Last updated: 2023-09-06Bibliographically approved
Simões, L. G., Günther, T., Martínez-Sánchez, R. M., Vera-Rodríguez, J. C., Iriarte, E., Rodríguez-Varela, R., . . . Jakobsson, M. (2023). Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature, 618(7965), 550-556
Open this publication in new window or tab >>Northwest African Neolithic initiated by migrants from Iberia and Levant
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2023 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 618, no 7965, p. 550-556Article in journal (Refereed) Published
Abstract [en]

In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1,2,3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-507442 (URN)10.1038/s41586-023-06166-6 (DOI)001005804900020 ()37286608 (PubMedID)
Funder
Swedish Research Council, 2018-05973Knut and Alice Wallenberg FoundationEU, European Research Council, AdG 230561UPPMAXSwedish National Infrastructure for Computing (SNIC)Swedish Research Council, 2018-05537Swedish Research Council, 2022-04642Swedish Research Council, 2017-05267
Note

Title in the list of papers of Luciana G. Simões' thesis: Neolithization of Northwestern Africa was ignited by migrants from Iberia and Levant

Available from: 2023-07-07 Created: 2023-07-07 Last updated: 2024-06-11Bibliographically approved
Chylenski, M., Makarowicz, P., Juras, A., Krzewinska, M., Pospieszny, L., Ehler, E., . . . Malmström, H. (2023). Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age. Nature Communications, 14, Article ID 4395.
Open this publication in new window or tab >>Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age
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2023 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 14, article id 4395Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Archaeology Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-511896 (URN)10.1038/s41467-023-40072-9 (DOI)001048667500017 ()37528090 (PubMedID)
Funder
Riksbankens Jubileumsfond, M13-0904:1Riksbankens Jubileumsfond, P21-0266Knut and Alice Wallenberg FoundationSwedish Research Council, 2017-02503Swedish Research Council, 2018-05973Swedish National Infrastructure for Computing (SNIC), SNIC 2022/2-11Swedish National Infrastructure for Computing (SNIC), SNIC 2022-/22-299Swedish National Infrastructure for Computing (SNIC), SNIC 2022/23-163
Available from: 2023-09-21 Created: 2023-09-21 Last updated: 2023-09-21Bibliographically approved
Rifkin, R. F. F., Vikram, S., Alcorta, J., Ramond, J.-B., Cowan, D. A. A., Jakobsson, M., . . . Lombard, M. (2023). Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago. Communications Biology, 6, Article ID 240.
Open this publication in new window or tab >>Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago
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2023 (English)In: Communications Biology, E-ISSN 2399-3642, Vol. 6, article id 240Article in journal (Refereed) Published
Abstract [en]

The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.

Place, publisher, year, edition, pages
Springer Nature, 2023
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-499932 (URN)10.1038/s42003-023-04582-y (DOI)000943534900002 ()36869137 (PubMedID)
Funder
EU, Horizon 2020, 759933Knut and Alice Wallenberg Foundation
Available from: 2023-04-06 Created: 2023-04-06 Last updated: 2023-04-06Bibliographically approved
Rodríguez-Varela, R., Moore, K. H. .., Ebenesersdóttir, S. S., Kilinc, G. M., Kjellström, A., Papmehl-Dufay, L., . . . Götherström, A. (2023). The genetic history of Scandinavia from the Roman Iron Age to the present. Cell, 186(1), 32-46.e19
Open this publication in new window or tab >>The genetic history of Scandinavia from the Roman Iron Age to the present
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2023 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 186, no 1, p. 32-46.e19Article in journal (Refereed) Published
Abstract [en]

We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.

Place, publisher, year, edition, pages
Elsevier, 2023
National Category
Archaeology
Research subject
Archaeology
Identifiers
urn:nbn:se:uu:diva-492657 (URN)10.1016/j.cell.2022.11.024 (DOI)000921955500001 ()36608656 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 2019-00849Riksbankens Jubileumsfond
Available from: 2023-01-09 Created: 2023-01-09 Last updated: 2023-02-24Bibliographically approved
Ausmees, K., Sanchez-Quinto, F., Jakobsson, M. & Nettelblad, C. (2022). An empirical evaluation of genotype imputation of ancient DNA. G3: Genes, Genomes, Genetics, 12(6), Article ID jkac089.
Open this publication in new window or tab >>An empirical evaluation of genotype imputation of ancient DNA
2022 (English)In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 12, no 6, article id jkac089Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Oxford University Press, 2022
National Category
Computational Mathematics Genetics
Research subject
Scientific Computing
Identifiers
urn:nbn:se:uu:diva-396336 (URN)10.1093/g3journal/jkac089 (DOI)000791204600001 ()35482488 (PubMedID)
Projects
eSSENCE
Funder
Swedish Research Council Formas, 2020-00712
Available from: 2019-11-04 Created: 2019-11-04 Last updated: 2024-01-17Bibliographically approved
Projects
The exodus from Africa: linking human history and genomic patterns of variation [2009-05129_VR]; Uppsala UniversityHuman evolutionary history revealed by variation in African genomes [2013-08019_VR]; Uppsala UniversityAnsökan från Amy Goldberg inom programmet Graduate Research Opportunity Worldwide [2014-04830_VR]; Uppsala UniversityExploring deep human roots in south-central African ancient and modern genomes [2018-05537_VR]; Uppsala University; Publications
Simões, L. G., Günther, T., Martínez-Sánchez, R. M., Vera-Rodríguez, J. C., Iriarte, E., Rodríguez-Varela, R., . . . Jakobsson, M. (2023). Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature, 618(7965), 550-556Peyroteo-Stjerna, R., Simões, L. G., Fernandes, R., Lopes, G., Günther, T. & Jakobsson, M. (2022). Multidisciplinary investigation reveals an individual of West African origin buried in a Portuguese Mesolithic shell midden four centuries ago. Journal of Archaeological Science: Reports, 42, Article ID 103370.
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7840-7853

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