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  • 1.
    Ausmees, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Sanchez-Quinto, Federico
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    An empirical evaluation of genotype imputation of ancient DNA2019Report (Other academic)
  • 2.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Where our feet have taken us: Examples of human contact, migration, and adaptation as revealed by ancient DNA2019Doctoral thesis, comprehensive summary (Other academic)
    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.

    List of papers
    1. The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
    Open this publication in new window or tab >>The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The 3rd millennium BCE was a period of marked cultural and demographic developments in Europe. Here we sequence genome data from human skeletal remains to study the interaction between two Scandinavian cultures; the hunter-gatherer Pitted Ware culture (PWC, 3400-2400 BCE) and the farmer/herder Battle Axe culture (BAC, 2800-2300 BCE), two cultures who have been found to be represented by distinct gene-pools in northern Europe. We focus on the Baltic island of Gotland that presents Scandinavia’s richest record of PWC gravesites where the majority of individuals are buried in typical PWC manner (supine position), but with some burials indicating BAC influences (either hocker position burial or burials with BAC associated artifacts). We sequenced and analyzed the genomes of 25 individuals of both types of burials excavated in three gravesites in order to determine if the different burial styles were associated with the different gene-pools (PWC or BAC) at the time. The genomic data show that all individuals belonged to one genetic population – that of the PWC – irrespective of the burial style. We conclude that the PWC communities on the island of Gotland were culturally influenced by the BAC society, without any signs of gene-flow.

    National Category
    Evolutionary Biology
    Research subject
    Biology with Specialisation in Human Evolution and Genetics
    Identifiers
    urn:nbn:se:uu:diva-397180 (URN)
    Funder
    Swedish Research Council, 2017-02503
    Available from: 2019-11-17 Created: 2019-11-17 Last updated: 2019-11-18
    2. Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
    Open this publication in new window or tab >>Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting to arrive some 400 years ago and their descendants are today mixed with Europeans and Asians. Here we sequence and analyze the genome (1.01 times coverage) of a Later Stone Age individual, who lived about 200 years ago, obtained from a hair sample excavated at Vaalkrans Shelter southern Cape, South Africa. We analyzed this genome, along with genetic data from 10 prehistoric individuals from southern Africa spanning the last 2000 years. Our results show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherer populations, and ~20% to a mixed East African-Eurasian source. This genetic make-up is very similar to modern-day Khoekhoe individuals from South Africa and Namibia. The Vaalkrans man’s genome reveals how the Holocene pastoralist migration event shaped the genomic landscape of historic and current southern African populations and shows that Khoekhoe groups lived in the southern Cape as late as 200 years ago.

    National Category
    Evolutionary Biology
    Research subject
    Biology with Specialisation in Human Evolution and Genetics
    Identifiers
    urn:nbn:se:uu:diva-397032 (URN)
    Available from: 2019-11-18 Created: 2019-11-18 Last updated: 2019-11-18
    3. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
    Open this publication in new window or tab >>Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
    Show others...
    2017 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, no 6363, p. 652-655Article in journal (Refereed) 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.

    National Category
    Archaeology Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-334636 (URN)10.1126/science.aao6266 (DOI)000414240500038 ()28971970 (PubMedID)
    Funder
    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 TechnologyThe Wenner-Gren Foundation
    Note

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

    Available from: 2017-11-24 Created: 2017-11-24 Last updated: 2020-03-05Bibliographically approved
    4. The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
    Open this publication in new window or tab >>The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
    (English)Manuscript (preprint) (Other academic)
    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.

    National Category
    Evolutionary Biology
    Research subject
    Biology with Specialisation in Human Evolution and Genetics
    Identifiers
    urn:nbn:se:uu:diva-397169 (URN)
    Available from: 2019-11-16 Created: 2019-11-16 Last updated: 2019-11-18
  • 3.
    Coutinho, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Henshilwood, Christopher
    Institutt for arkeologi, historie, kultur- og religionsvitenskap, Universitetet i Bergen.
    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 University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groupsManuscript (preprint) (Other academic)
    Abstract [en]

    The indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting to arrive some 400 years ago and their descendants are today mixed with Europeans and Asians. Here we sequence and analyze the genome (1.01 times coverage) of a Later Stone Age individual, who lived about 200 years ago, obtained from a hair sample excavated at Vaalkrans Shelter southern Cape, South Africa. We analyzed this genome, along with genetic data from 10 prehistoric individuals from southern Africa spanning the last 2000 years. Our results show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherer populations, and ~20% to a mixed East African-Eurasian source. This genetic make-up is very similar to modern-day Khoekhoe individuals from South Africa and Namibia. The Vaalkrans man’s genome reveals how the Holocene pastoralist migration event shaped the genomic landscape of historic and current southern African populations and shows that Khoekhoe groups lived in the southern Cape as late as 200 years ago.

  • 4.
    Coutinho, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Munters, Arielle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Svensson, Emma
    Area Offices, Office of Technology and Science; The Student Service Unit.
    Götherström, Anders
    Department of Archaeology and Classical Studies, Stockholm University.
    Storå, Jan
    Department of Archaeology and Classical Studies, Stockholm University.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herdersManuscript (preprint) (Other academic)
    Abstract [en]

    The 3rd millennium BCE was a period of marked cultural and demographic developments in Europe. Here we sequence genome data from human skeletal remains to study the interaction between two Scandinavian cultures; the hunter-gatherer Pitted Ware culture (PWC, 3400-2400 BCE) and the farmer/herder Battle Axe culture (BAC, 2800-2300 BCE), two cultures who have been found to be represented by distinct gene-pools in northern Europe. We focus on the Baltic island of Gotland that presents Scandinavia’s richest record of PWC gravesites where the majority of individuals are buried in typical PWC manner (supine position), but with some burials indicating BAC influences (either hocker position burial or burials with BAC associated artifacts). We sequenced and analyzed the genomes of 25 individuals of both types of burials excavated in three gravesites in order to determine if the different burial styles were associated with the different gene-pools (PWC or BAC) at the time. The genomic data show that all individuals belonged to one genetic population – that of the PWC – irrespective of the burial style. We conclude that the PWC communities on the island of Gotland were culturally influenced by the BAC society, without any signs of gene-flow.

  • 5.
    Coutinho, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan AfricaManuscript (preprint) (Other academic)
    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.

  • 6.
    Cubas, Miriam
    et al.
    University of York, York, UK; Sociedad de Ciencias Aranzadi, Donostia, San Sebastian, Spain.
    Peyroteo Stjerna, Rita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human 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 perspective2019In: Archaeological and Anthropological Sciences, ISSN 1866-9557, E-ISSN 1866-9565, Vol. 11, no 8, p. 3825-3836Article in journal (Refereed)
    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.

  • 7.
    Fortes-Lima, Cesar A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Evolutionary Biology Centre, Uppsala University.
    Unraveling African diversity from a cross‐disciplinary perspective2019In: Evolutionary AnthropologyArticle in journal (Refereed)
  • 8.
    Fraser, Magdalena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human 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 University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Knutsson, Kjel
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    New insights on cultural dualism and population structure in the MiddleNeolithic Funnel Beaker culture on the island of Gotland2018In: Journal of Archaeological Science: Reports, ISSN 2352-409X, E-ISSN 2352-4103, Vol. 17, p. 325-334Article in journal (Refereed)
    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.

  • 9.
    Fraser, Magdalena
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Evans, Jane
    Natural Environment Research Council, Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK.
    Svedjemo, Gustaf
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Knutsson, Kjel
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Wallin, Paul
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    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 Gotland2018In: Journal of Archaeological Science: Reports, ISSN 2352-409X, E-ISSN 2001-1199, Vol. 20, p. 324-337Article in journal (Refereed)
    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.

  • 10.
    Goldberg, Amy
    et al.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Rosenberg, Noah A.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Neolithic familial migration contrasts Bronze Age male migration inferred from ancient X chromosomes2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 196-196Article in journal (Other academic)
  • 11.
    Gummesson, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human 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 Sweden2019In: Journal of field archaeology, ISSN 0093-4690, E-ISSN 2042-4582, Vol. 44, no 3, p. 165-179Article in journal (Refereed)
    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.

  • 12.
    Günther, Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Svensson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Omrak, Ayca
    Stockholm Univ, Dept Archaeol & Class Studies.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Kilinc, Gülsah Merve
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.; Middle East Tech Univ, Dept Biol Sci, Ankara.
    Krzewińska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Eriksson, Gunilla
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Fraser, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Munters, Arielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Simões, Luciana G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjölander, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sellevold, Berit Jansen
    Norwegian Inst Cultural Heritage Res, Oslo.
    Jørgensen, Roger
    Arctic Univ Norway, Univ Tromsø, Tromsø Univ Museum, Tromsø.
    Claes, Peter
    Katholieke Univ Leuven, Dept Elect Engn, Ctr Proc Speech & Images, Leuven.
    Shriver, Mark D.
    Penn State Univ, Dept Anthropol, State Coll, Pennsylvania.
    Valdiosera, Cristina
    La Trobe Univ, Dept Archaeol & Hist, Melbourne.
    Netea, Mihai G.
    Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, Nijmegen; Radboud Univ Nijmegen, Med Ctr, Radboud Ctr Infect Dis, Nijmegen.
    Apel, Jan
    Lund Univ, Dept Archaeol & Ancient Hist, Lund.
    Liden, Kerstin
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Skar, Birgitte
    Norwegian Univ Sci & Technol Univ Museum, Trondheim.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Götherström, Anders
    Uppsala University, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.; SciLifeLab, Stockholm.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. SciLifeLab, Stockholm.
    Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation2018In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 16, no 1, article id e2003703Article in journal (Refereed)
    Abstract [en]

    Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

  • 13.
    Günther, Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The presence and impact of reference bias on population genomic studies of prehistoric human populations2019In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 7, article id e1008302Article in journal (Refereed)
  • 14.
    Jeong, Choongwon
    et al.
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA.
    Ozga, Andrew T.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Witonsky, David B.
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala Univ, Dept Organismal Biol, SE-75236 Uppsala, Sweden.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala Univ, Dept Organismal Biol, SE-75236 Uppsala, Sweden.
    Hofman, Courtney A.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Hagan, Richard W.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala Univ, Dept Organismal Biol, SE-75236 Uppsala, Sweden.
    Lewis, Cecil M.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Aldenderfer, Mark S.
    Univ Calif Merced, Sch Social Sci Humanities & Arts, Merced, CA 95343 USA.
    Di Rienzo, Anna
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA.
    Warinner, Christina
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA;Univ Zurich, Inst Evolut Med, CH-8057 Zurich, Switzerland.
    Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 27, p. 7485-7490Article in journal (Refereed)
    Abstract [en]

    The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04x-7.25x, mean 2.16x) and mitochondrial genomes (20.8x-1,311.0x, mean 482.1x) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.

  • 15.
    Juras, Anna
    et al.
    Adam Mickiewicz Univ, Dept Human Evolutionary Biol, Inst Anthropol, Fac Biol, Umultowska 89, PL-61614 Poznan, Poland..
    Chylenski, Maciej
    Adam Mickiewicz Univ, Inst Archaeol, Fac Hist, Umultowska 89D, PL-61614 Poznan, Poland..
    Ehler, Edvard
    Adam Mickiewicz Univ, Dept Human Evolutionary Biol, Inst Anthropol, Fac Biol, Umultowska 89, PL-61614 Poznan, Poland.;ASCR, Lab Genom & Bioinformat, Inst Mol Genet, Vvi, Videnska 1083, Prague 14220 4, Czech Republic..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zurkiewicz, Danuta
    Adam Mickiewicz Univ, Inst Archaeol, Fac Hist, Umultowska 89D, PL-61614 Poznan, Poland..
    Wlodarczak, Piotr
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska Str 17, PL-31016 Krakow, Poland..
    Wilk, Stanislaw
    Jagiellonian Univ, Inst Archaeol, Golebia 11, PL-31007 Krakow, Poland..
    Peska, Jaroslav
    Archaeol Ctr Olomouc, U Hradiska 42-6, Olomouc 77900, Czech Republic.;Palacky Univ Olomouc, Philosoph Fac, Sect Archaeol, Dept Hist, Hrade 5, Olomouc 77180, Czech Republic..
    Fojtik, Pavel
    Inst Archaeol Heritage Brno, Vvi, Kaloudova 30, Brno 61400, Czech Republic..
    Kralik, Miroslav
    Masaryk Univ, Fac Sci, Lab Morphol & Forens Anthropol LaMorFA, Dept Anthropol, Kotlarska 267-2, CS-61137 Brno, Czech Republic..
    Libera, Jerzy
    Marie Curie Sklodowska Univ, Inst Archaeol, Maria Curie Sklodowska Sq 4, PL-20031 Lublin, Poland..
    Baginska, Jolanta
    Muzeum Reg Janusza Petera, Ul Zamojska 2, PL-22600 Tomaszow Lubelski, Poland..
    Tunia, Krzysztof
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska Str 17, PL-31016 Krakow, Poland..
    Klochko, Viktor I.
    Natl Univ Kyiv Mohyla Acad, Inst Archaeol, Hryhoriya Skovorody St 2, UA-04655 Kiev, Ukraine..
    Dabert, Miroslawa
    Adam Mickiewicz Univ, Fac Biol, Mol Biol Tech Lab, Umultowska 89, PL-61614 Poznan, Poland..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Ctr Anthropol Res, Auckland Pk, ZA-2006 Johannesburg, South Africa..
    Kosko, Aleksander
    Adam Mickiewicz Univ, Inst Archaeol, Fac Hist, Umultowska 89D, PL-61614 Poznan, Poland..
    Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11603Article in journal (Refereed)
    Abstract [en]

    From around 4,000 to 2,000 BC the forest-steppe north-western Pontic region was occupied by people who shared a nomadic lifestyle, pastoral economy and barrow burial rituals. It has been shown that these groups, especially those associated with the Yamnaya culture, played an important role in shaping the gene pool of Bronze Age Europeans, which extends into present-day patterns of genetic variation in Europe. Although the genetic impact of these migrations from the forest-steppe Pontic region into central Europe have previously been addressed in several studies, the contribution of mitochondrial lineages to the people associated with the Corded Ware culture in the eastern part of the North European Plain remains contentious. In this study, we present mitochondrial genomes from 23 Late Eneolithic and Bronze Age individuals, including representatives of the north-western Pontic region and the Corded Ware culture from the eastern part of the North European Plain. We identified, for the first time in ancient populations, the rare mitochondrial haplogroup X4 in two Bronze Age Catacomb culture-associated individuals. Genetic similarity analyses show close maternal genetic affinities between populations associated with both eastern and Baltic Corded Ware culture, and the Yamnaya horizon, in contrast to larger genetic differentiation between populations associated with western Corded Ware culture and the Yamnaya horizon. This indicates that females with steppe ancestry contributed to the formation of populations associated with the eastern Corded Ware culture while more local people, likely of Neolithic farmer ancestry, contributed to the formation of populations associated with western Corded Ware culture.

  • 16.
    Kilinc, Gulsah Merve
    et al.
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Kashuba, Natalija
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden;Univ Oslo, Museum Cultural Hist, N-0164 Oslo, Norway.
    Yaka, Reyhan
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Sumer, Arev Pelin
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Yuncu, Eren
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Shergin, Dmitrij
    Ivanov, Grigorij Leonidovich
    Irkutsk Museum Reg Studies, Irkutsk 664003, Irkutsk Oblast, Russia.
    Kichigin, Dmitrii
    Irkutsk State Univ, Lab Archaeol & Ethnog, Fac Hist & Methods, Dept Humanitarian & Aesthet Educ,Pedag Inst, Irkutsk 664011, Irkutsk Oblast, Russia;Irkutsk State Tech Univ, Irkutsk Natl Res Tech Univ, Lab Archaeol Paleoecol & Subsistence Strategies P, Irkutsk 664074, Irkutsk Oblast, Russia.
    Pestereva, Kjunnej
    MK Ammosov North Eastern Fed Univ NEFU, Fed State Autonomous Educ Inst Higher Educ, Yakutsk 677000, Sakha Republic, Russia.
    Volkov, Denis
    Ctr Preservat Hist & Cultural Heritage Amur Reg, Blagoveshchensk 675000, Amur Oblast, Russia.
    Mandryka, Pavel
    Siberian Fed Univ, Krasnoyarsk 660041, Krasnoyarskiy K, Russia.
    Kharinskii, Artur
    Irkutsk State Tech Univ, Irkutsk Natl Res Tech Univ, Lab Archaeol Paleoecol & Subsistence Strategies P, Irkutsk 664074, Irkutsk Oblast, Russia.
    Tishkin, Alexey
    Altai State Univ, Dept Archaeol Ethnog & Museol, Lab Interdisciplinary Studies Archaeol Western Si, Barnaul, Altaiskiy Kray, Russia.
    Ineshin, Evgenij
    Irkutsk State Univ, Lab Archaeol & Ethnog, Fac Hist & Methods, Dept Humanitarian & Aesthet Educ,Pedag Inst, Irkutsk 664011, Irkutsk Oblast, Russia.
    Kovychev, Evgeniy
    Transbaikal State Univ, Fac Hist, Chita 672039, Zabaykalsky Kra, Russia.
    Stepanov, Aleksandr
    MK Ammosov North Eastern Fed Univ NEFU, Fed State Autonomous Educ Inst Higher Educ, Yakutsk 677000, Sakha Republic, Russia.
    Alekseev, Aanatolij
    Acad Sci Sakha Republ, Inst Humanities Res & Indigenous Studies IHRISN, Yakutsk 677000, Sakha Republic, Russia.
    Fedoseeva, Svetlana Aleksandrovna
    Russian Acad Sci, Inst Arctic Archaeol & Paleoecol, Yakutsk 677000, Sakha Republic, Russia.
    Somel, Mehmet
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Krzewinska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Investigating Holocene human population history in North Asia using ancient mitogenomes2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 8969Article in journal (Refereed)
    Abstract [en]

    Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c. 13,790 BP and c. 1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.

  • 17.
    Krzewinska, Maja
    et al.
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Kilinc, Gulsah Merve
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Juras, Anna
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.
    Koptekin, Dilek
    Middle East Tech Univ, Dept Hlth Informat, TR-06800 Ankara, Turkey.
    Chylenski, Maciej
    Adam Mickiewicz Univ, Fac Hist, Inst Archaeol, Umultowska 89D, PL-61614 Poznan, Poland.
    Nikitin, Alexey G.
    Grand Valley State Univ, Biol Dept, 1 Campus Dr, Allendale, MI 49401 USA.
    Shcherbakov, Nikolai
    Bashkir State Pedag Univ, Lab Methodol & Methods Humanitarian Res, Octyabrskoy Revolutsii 3A, Ufa 450007, Russia.
    Shuteleva, Iia
    Bashkir State Pedag Univ, Lab Methodol & Methods Humanitarian Res, Octyabrskoy Revolutsii 3A, Ufa 450007, Russia;Bashkir State Univ, Inst Hist & State Management, Zaki Validy St 32, Ufa 450076, Russia.
    Leonova, Tatiana
    Bashkir State Pedag Univ, Lab Methodol & Methods Humanitarian Res, Octyabrskoy Revolutsii 3A, Ufa 450007, Russia.
    Kraeva, Liudmila
    Orenburg State Pedag Univ, Archaeol Lab, Orenburg, Russia.
    Sungatov, Flarit A.
    Bashkir State Univ, Archaeol Lab, Str Validi Z 32, Ufa, Russia.
    Sultanova, Alfija N.
    Bashkir State Univ, Archaeol Lab, Str Validi Z 32, Ufa, Russia.
    Potekhina, Inna
    Natl Acad Sci Ukraine, Inst Archaeol, Kiev, Ukraine.
    Lukasik, Sylwia
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.
    Krenz-Niedbala, Marta
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.
    Dalen, Love
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, POB 50007, S-10405 Stockholm, Sweden.
    Sinika, Vitaly
    Taras Shevchenko Univ Tiraspol, October St 25, Tiraspol 3300, Moldova;Nizhnevartovsk State Univ, Lenin St 56, Khanty Mansi Autonomous 628605, Yugra, Russia.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Ctr Anthropol Res, POB 524, ZA-2006 Auckland Pk, South Africa;Univ Johannesburg, Dept Anthropol & Dev Studies, POB 524, ZA-2006 Auckland Pk, South Africa.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Classical Studies, Osteoarchaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads2018In: Science Advances, E-ISSN 2375-2548, Vol. 4, no 10, article id eaat4457Article in journal (Refereed)
    Abstract [en]

    For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

  • 18.
    Krzewinska, Maja
    et al.
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Kjellstrom, Anna
    Univ Stockholm, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Hedenstierna-Jonson, Charlotte
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Zachrisson, Torun
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Omrak, Ayca
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Yaka, Reyhan
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Kilinc, Gulsah Merve
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Somel, Mehmet
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Sobrado, Veronica
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Evans, Jane
    British Geol Survey, NERC Isotope Geosci Lab, Nottingham NG12 5GG, England.
    Knipper, Conine
    Curt Engelhorn Zentrum Archaometrie, D6,3, D-68159 Mannheim, Germany.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden.
    Stora, Jan
    Univ Stockholm, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Gotherstrom, Anders
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden;Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden.
    Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town2018In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 28, no 17, p. 2730-2738.e10Article in journal (Refereed)
    Abstract [en]

    The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.

  • 19.
    Kuhn, Jose Manuel Monroy
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Estimating genetic kin relationships in prehistoric populations2018In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 4, article id e0195491Article in journal (Refereed)
    Abstract [en]

    Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data. READ is publicly available from https://bitbucket.org/tguenther/read.

  • 20.
    Lombard, Marlize
    et al.
    University of Johannesburg, Centre for Anthropological Research, Johannesburg, South Africa; University of Johannesburg, Department of Anthropology and Development Studies, Johannesburg, South Africa.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. University of Johannesburg, Centre for Anthropological Research, Johannesburg, South Africa; University of Johannesburg, Department of Anthropology and Development Studies, Johannesburg, South Africa; .
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. University of Johannesburg, Centre for Anthropological Research, Johannesburg, South Africa; University of Johannesburg, Department of Anthropology and Development Studies, Johannesburg, South Africa.
    Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history2018In: South African Journal of Science, ISSN 0038-2353, E-ISSN 1996-7489, Vol. 114, no 1-2, article id a0253Article in journal (Other academic)
  • 21.
    Lombard, Marlize
    et al.
    Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Svensson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Zipfel, Bernhard
    Univ Witwatersrand, Evolutionary Studies Inst, Johannesburg, South Africa;Univ Witwatersrand, Sch Geosci, Johannesburg, South Africa.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Genetic data and radiocarbon dating question Plovers Lake as a Middle Stone Age hominin-bearing site2019In: Journal of Human Evolution, ISSN 0047-2484, E-ISSN 1095-8606, Vol. 131, p. 203-209Article in journal (Refereed)
    Abstract [en]

    We have sampled five out of the eleven previously identified human specimens and some faunal remains from the Plovers Lake site in the Cradle of Humankind, South Africa, for ancient DNA. We were successful in obtaining positive results for three of the human individuals and three 'buffalo' teeth. Based on ages obtained for flowstone and one bovid tooth, the site was interpreted previously as a hominin-bearing Middle Stone Age site of more than 60 000 years old. Our work, however, revealed that not all the material accumulated during the Pleistocene. Instead, the sampled humans and bovids most likely represent a Bantu-speaking Iron Age population (mtDNA haplogroup L3d) and their Nguni cattle. Newly obtained radiocarbon dates confirmed that these remains are probably no older than the last 500 years bp. This study demonstrates the usefulness of inter-disciplinary investigation into the human past, and the depositional and stratigraphic complexities that researchers in the Cradle of Humankind need to contend with before interpreting their assemblages.

  • 22.
    Lona-Durazo, Frida
    et al.
    Univ Toronto, Dept Anthropol, Hlth Sci Complex,Room 352, Mississauga, ON L5L 1C6, Canada.
    Hernandez-Pacheco, Natalia
    Univ La Laguna, Res Unit, Hosp Univ NS de Candelaria, Santa Cruz De Tenerife, Spain;Univ La Laguna, Genom & Hlth Grp, Dept Biochem Microbiol Cell Biol & Genet, Tenerife, Spain.
    Fan, Shaohua
    Univ Penn, Dept Genet, Perelman Sch Med, Philadelphia, PA 19104 USA.
    Zhang, Tongwu
    NCI, Lab Translat Genom, Div Canc Epidemiol & Genet, NIH, Bethesda, MD 20892 USA.
    Choi, Jiyeon
    NCI, Lab Translat Genom, Div Canc Epidemiol & Genet, NIH, Bethesda, MD 20892 USA.
    Kovacs, Michael A.
    NCI, Lab Translat Genom, Div Canc Epidemiol & Genet, NIH, Bethesda, MD 20892 USA.
    Loftus, Stacie K.
    NHGRI, Genet Dis Res Branch, NIH, Bethesda, MD 20892 USA.
    Le, Phuong
    Edwards, Melissa
    Univ Toronto, Dept Anthropol, Hlth Sci Complex,Room 352, Mississauga, ON L5L 1C6, Canada.
    Fortes-Lima, Cesar A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Paris Diderot, Evolutionary Anthropol Team, Lab Ecoanthropol & Ethnobiol UMR7206, CNRS,MNHN,Musee Homme, Paris, France.
    Eng, Celeste
    Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA.
    Huntsman, Scott
    Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA.
    Hu, Donglei
    Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA.
    Javier Gomez-Cabezas, Enrique
    Ctr Sociol & Psychol Res, Havana, Cuba.
    Caridad Marin-Padron, Lilia
    Med Univ Havana, Natl Ctr Med Genet, Havana, Cuba.
    Grauholm, Jonas
    Statens Serum Inst, Dept Congenital Disorders, Copenhagen, Denmark.
    Mors, Ole
    Aarhus Univ, Translat Neuropsychiat Unit, Dept Clin Med, Aarhus, Denmark;Aarhus Univ, Lundbeck Fdn Initiat Integrat Psychiat Res, Aarhus, Denmark;Aarhus Univ Hosp, Psychiat Dept, Aarhus, Denmark.
    Burchard, Esteban G.
    Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA.
    Norton, Heather L.
    Univ Cincinnati, Dept Anthropol, Cincinnati, OH USA.
    Pavan, William J.
    NHGRI, Genet Dis Res Branch, NIH, Bethesda, MD 20892 USA.
    Brown, Kevin M.
    NCI, Lab Translat Genom, Div Canc Epidemiol & Genet, NIH, Bethesda, MD 20892 USA.
    Tishkoff, Sarah
    Univ Penn, Dept Genet, Perelman Sch Med, Philadelphia, PA 19104 USA;Univ Penn, Dept Biol, Sch Arts & Sci, Philadelphia, PA 19104 USA.
    Pino-Yanes, Maria
    Univ La Laguna, Genom & Hlth Grp, Dept Biochem Microbiol Cell Biol & Genet, Tenerife, Spain;Inst Salud Carlos III, CIBER Enfermedades Resp, Madrid, Spain;Univ La Laguna, ITB, Santa Cruz De Tenerife, Spain.
    Beleza, Sandra
    Univ Leicester, Dept Genet & Genome Biol, Coll Life Sci, Leicester, Leics, England.
    Marcheco-Teruel, Beatriz
    Med Univ Havana, Natl Ctr Med Genet, Havana, Cuba.
    Parra, Esteban J.
    Univ Toronto, Dept Anthropol, Hlth Sci Complex,Room 352, Mississauga, ON L5L 1C6, Canada.
    Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations2019In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 20, article id 59Article in journal (Refereed)
    Abstract [en]

    Background: Association studies in recently admixed populations are extremely useful to identify the genetic architecture of pigmentation, due to their high genotypic and phenotypic variation. However, to date only four Genome-Wide Association Studies (GWAS) have been carried out in these populations.

    Results: We present a GWAS of skin pigmentation in an admixed sample from Cuba (N=762). Additionally, we conducted a meta-analysis including the Cuban sample, and admixed samples from Cape Verde, Puerto Rico and African-Americans from San Francisco. This meta-analysis is one of the largest efforts so far to characterize the genetic basis of skin pigmentation in admixed populations (N=2,104). We identified five genome-wide significant regions in the meta-analysis, and explored if the markers observed in these regions are associated with the expression of relevant pigmentary genes in human melanocyte cultures. In three of the regions identified in the meta-analysis (SLC24A5, SLC45A2, and GRM5/TYR), the association seems to be driven by non-synonymous variants (rs1426654, rs16891982, and rs1042602, respectively). The rs16891982 polymorphism is strongly associated with the expression of the SLC45A2 gene. In the GRM5/TYR region, in addition to the rs1042602 non-synonymous SNP located on the TYR gene, variants located in the nearby GRM5 gene have an independent effect on pigmentation, possibly through regulation of gene expression of the TYR gene. We also replicated an association recently described near the MFSD12 gene on chromosome 19 (lead variant rs112332856). Additionally, our analyses support the presence of multiple signals in the OCA2/HERC2/APBA2 region on chromosome 15. A clear causal candidate is the HERC2 intronic variant rs12913832, which has a profound influence on OCA2 expression. This variant has pleiotropic effects on eye, hair, and skin pigmentation. However, conditional and haplotype-based analyses indicate the presence of other variants with independent effects on melanin levels in OCA2 and APBA2. Finally, a follow-up of genome-wide signals identified in a recent GWAS for tanning response indicates that there is a substantial overlap in the genetic factors influencing skin pigmentation and tanning response.

    Conclusions: Our meta-analysis of skin pigmentation GWAS in recently admixed populations provides new insights about the genetic architecture of this complex trait.

  • 23.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Ctr Anthropol Res, Dept Anthropol & Dev Studies, ZA-2006 Auckland Pk, South Africa.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Juras, Anna
    Adam Mickiewia Univ Poznan, Dept Human Evolutionary Biol, Inst Anthropol, Fac Biol, Ul Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland.
    Fraser, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History.
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Pospieszny, Lukasz
    Univ Bristol, Dept Anthropol & Archaeol, Bristol BS8 1UU, Avon, England;Polish Acad Sci, Inst Archaeol & Ethnol, Ctr Studies Late Antiqu & Early Medieval Times, PL-61612 Poznan, Poland.
    Tõrv, Mari
    Univ Tartu, Dept Archaeol, Inst Hist & Archaeol, EE-50090 Tartu, Estonia.
    Lindström, Jonathan
    Linneaus Univ, Grad Sch Contract Archaeol, Dept Archaeol, S-39182 Kalmar, Sweden.
    Götherström, Anders
    Stockholm Univ, Archaeol Res Lab, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Storå, Jan
    Stockholm Univ, Osteoarchaeol Res Lab, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Ctr Anthropol Res, Dept Anthropol & Dev Studies, ZA-2006 Auckland Pk, South Africa.
    The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1912, article id 20191528Article in journal (Refereed)
    Abstract [en]

    The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24x coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.

  • 24.
    Naidoo, Thijessen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Population Genetics of Human Genomic Elements2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The genomes of living organisms are composed of a multitude of functional units, which interact with each other and their environment in a highly regulated fashion, to facilitate the expression of an enduring (and evolving) phenotype. Several approaches have emerged in the effort to identify these functional units and explore their activities. In this thesis, I have taken a population genetics approach; evaluating how the distribution of genetic variation in the human genome has been shaped through the actions of natural selection on functional genomic elements. In the first paper, I interrogate a catalogue of elements derived from biochemical signatures for signals of selection; finding significant signals of purifying selection on regulatory elements, independent of linked-purifying selection. In the second paper, I explore the pseudogene class of genomic elements, and find that a large proportion of a particular subclass, transcribed duplicated pseudogenes, has experienced significant amounts of positive selection. In the third paper, I focus on protein coding genes and variants that disrupt their open reading frames. Specifically, I examine the distribution of loss-of-function variants in the Khoe-San population; gauging their functional significance and exploring the biological roles of affected genes. In the final paper, instead of using population genetics to uncover and explore genomic elements, I use a major genomic element – the Y chromosome – as an effective tool to study the evolutionary history of a human population.

    List of papers
    1. Patterns of variation in cis-regulatory regions: examining evidence of purifying selection
    Open this publication in new window or tab >>Patterns of variation in cis-regulatory regions: examining evidence of purifying selection
    2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 95Article in journal (Refereed) Published
    Abstract [en]

    Background: With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the assessment of functionality is a complex task, the presence of selection acting on a genomic region is a strong indicator of importance. In this study, we apply population genetic methods to investigate signals overlaying several classes of regulatory elements.

    Results: We disentangle signals of purifying selection acting directly on regulatory elements from the confounding factors of demography and purifying selection linked to e.g. nearby protein coding regions. We confirm the importance of regulatory regions proximal to coding sequence, while also finding differential levels of selection at distal regions. We note differences in purifying selection among transcription factor families. Signals of constraint at some genomic classes were also strongly dependent on their physical location relative to coding sequence. In addition, levels of selection efficacy across genomic classes differed between African and non-African populations.

    Conclusions: In order to assign a valid signal of selection to a particular class of genomic sequence, we show that it is crucial to isolate the signal by accounting for the effects of demography and linked-purifying selection. Our study highlights the intricate interplay of factors affecting signals of selection on functional elements.

    Place, publisher, year, edition, pages
    BIOMED CENTRAL LTD, 2018
    Keywords
    Regulatory regions, Purifying selection, Selection efficacy, Non-coding DNA, Functional elements, Population genetics
    National Category
    Genetics Developmental Biology
    Identifiers
    urn:nbn:se:uu:diva-343792 (URN)10.1186/s12864-017-4422-y (DOI)000423443900002 ()29373957 (PubMedID)
    Funder
    Göran Gustafsson Foundation for Research in Natural Sciences and MedicineKnut and Alice Wallenberg FoundationSwedish Research Council
    Available from: 2018-03-05 Created: 2018-03-05 Last updated: 2018-09-28Bibliographically approved
    2. Selective sweeps among transcribed pseudogenes underline their utility in the human genome
    Open this publication in new window or tab >>Selective sweeps among transcribed pseudogenes underline their utility in the human genome
    (English)Manuscript (preprint) (Other academic)
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-361122 (URN)
    Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20
    3. Loss-of-function variants among Khoe and San individuals
    Open this publication in new window or tab >>Loss-of-function variants among Khoe and San individuals
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-361123 (URN)
    Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20
    4. Full genomic Y chromosomal variation in southern African Khoe-San populations
    Open this publication in new window or tab >>Full genomic Y chromosomal variation in southern African Khoe-San populations
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-361124 (URN)
    Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-09-20
  • 25.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    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..
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Loss-of-function variants among Khoe and San individualsManuscript (preprint) (Other academic)
  • 26.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Patterns of variation in cis-regulatory regions: examining evidence of purifying selection2018In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 95Article in journal (Refereed)
    Abstract [en]

    Background: With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the assessment of functionality is a complex task, the presence of selection acting on a genomic region is a strong indicator of importance. In this study, we apply population genetic methods to investigate signals overlaying several classes of regulatory elements.

    Results: We disentangle signals of purifying selection acting directly on regulatory elements from the confounding factors of demography and purifying selection linked to e.g. nearby protein coding regions. We confirm the importance of regulatory regions proximal to coding sequence, while also finding differential levels of selection at distal regions. We note differences in purifying selection among transcription factor families. Signals of constraint at some genomic classes were also strongly dependent on their physical location relative to coding sequence. In addition, levels of selection efficacy across genomic classes differed between African and non-African populations.

    Conclusions: In order to assign a valid signal of selection to a particular class of genomic sequence, we show that it is crucial to isolate the signal by accounting for the effects of demography and linked-purifying selection. Our study highlights the intricate interplay of factors affecting signals of selection on functional elements.

  • 27.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Selective sweeps among transcribed pseudogenes underline their utility in the human genomeManuscript (preprint) (Other academic)
  • 28.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Xu, Jingzi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    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.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Full genomic Y chromosomal variation in southern African Khoe-San populationsManuscript (preprint) (Other academic)
  • 29.
    Peyroteo Stjerna, Rita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Arqueotanatologia e coleções museológicas: Estratégias e desafios para o estudo das práticas funerárias do passado2017In: Arqueologia em Portugal: 2017-Estado da Questão / [ed] José Morais Arnaud, Andreia Martins, Lisbon, 2017, p. 447-459Conference paper (Other academic)
    Abstract [en]

    Archaeothanatology is a method based on the knowledge of human anatomy and taphonomic theory, developed to analyse archaeological contexts with human remains. The method emerged in the context of field archaeology and its application to museum colections can be problematic. In this paper, I present the principles of archaeothanatology and show its flexibility for the study of archaeological documentation in archive.Through the presentation of a case study I aim to demonstrate the potential of the method for the reconstructionof the chaîne operátoire of funerary gestures, which remains were documented in archaeological excavations several decades ago.

  • 30.
    Peyroteo Stjerna, Rita
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Roots of Death: origins of human burial and the research on early Holocene mortuary practices in the Iberian Peninsula2016In: Mesolithic burials: Rites, symbols and social organisation of early postglacial communities. / [ed] Judith M. Grünberg, Bernhard Gramsch, Lars Larsson, Jörg Orschiedt and Harald Meller, 2016, Vol. Band 13/II, p. 629-643Conference paper (Other academic)
    Abstract [en]

    In the context of postglacial environmental changes, the new form of settlement known to exist in the Late Mesolithic seems to be followed by a different relationship to death. In the archaeological record, this is well observed in the shell midden sites known in both the Tagus and Sado valleys in Portugal, with ca. 374 human burials of both sexes and ages, mostly individual primary depositions. This concentration of human remains and the regular practice of funerary burial are in apparent contrast with the archaeological record for previous phases, at least in the Iberian Peninsula.

    Here, I present a review of the archaeological data available for the mortuary practices of the Early Holocene, i.e. Early Mesolithic, in the Iberian Peninsula, prior to these Late Mesolithic cemeteries in the Tagus and Sado valleys, and attempt to trace back in time the possible origins of this behaviour in the hunter-gatherer mortuary tradition.

  • 31.
    Peyroteo Stjerna, Rita
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Portugal.
    Araújo, Ana Cristina
    UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Portugal.
    Diniz, Mariana
    UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Portugal.
    The dead at Escoural Cave (Montemor-o-Novo, Portugal): Early farmer's interactions in south-western Iberian Peninsula2018In: De Gibraltar aos Pirenéus: Megalitismo, Vida e Morte na Fachada Atlântica Peninsular / [ed] João Carlos de Sena Martinez, Mariana Diniz, António Faustino Carvalho, Nelas, 2018, p. 65-83Conference paper (Other academic)
    Abstract [en]

    The arrival of farmers to the south-western Iberian Peninsula was followed by a period of complex human interaction after 5500 BCE. This marked the arrival of new technologies and subsistence practices such as pottery, husbandry and domestication of plants, but also the co-existence of diverse social structures and world-views in a territory populated by hunter-gatherers. Biological and sociocultural interactions between local and migrant groups at the onset and establishment of the Neolithic in Atlantic Europe are poorly understood. The Neolithic funerary context in the Escoural cave, Montemor-o-Novo,Portugal, offers a research opportunity to examine these processes because it is uniquely well preserved and its use intersects key periods to understand multilayered human interaction. In this paper we present a synthesis of what is known about the Neolithic use ofthe cave complemented by new observations in the scope of a multidisciplinary project centred on the Escoural Cave started in 2018.

  • 32.
    Pilloud, Marin A.
    et al.
    Univ Nevada, Anthropol, Reno, NV, USA.
    Somel, Mehmet
    Middle East Tech Univ, Ankara, Turkey.
    Haddow, Scott D.
    Univ Bordeaux, PACEA UMR, Bordeaux, France.
    Knusel, Christopher J.
    Univ Bordeaux, PACEA UMR, Bordeaux, France.
    Larsen, Clark Spencer
    Ohio State Univ, Anthropol, Columbus, OH, USA.
    Ozbasaran, Mihriban
    Istanbul Univ, Archaeol Dept, Istanbul, Turkey.
    Erdal, Omur Dilek
    Hacettepe Univ, Dept Anthropol, Ankara, Turkey.
    Baird, Douglas
    Univ Liverpool, Dept Archaeol Class & Egyptol, Liverpool, Merseyside, England.
    Pearson, Jessica
    Univ Liverpool, Dept Archaeol Class & Egyptol, Liverpool, Merseyside, England.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Kilinc, Gulsah Merve
    Middle East Tech Univ, Ankara, Turkey.
    Ozer, Fusun
    Middle East Tech Univ, Ankara, Turkey.
    Koptekin, Dilek
    Middle East Tech Univ, Ankara, Turkey.
    Dagtas, Nihan Dilsad
    Middle East Tech Univ, Ankara, Turkey.
    Mobility in Neolithic Central Anatolia: A Comparison of Dental Morphometrics and aDNA2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 316-316Article in journal (Other academic)
  • 33.
    Price, Neil
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Hedenstierna-Jonson, Charlotte
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Zachrisson, Torun
    Upplandsmuseet, Uppsala, Sweden.
    Kjellström, Anna
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Krzewińska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sobrado, Verónica
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Götherström, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Viking warrior women?: Reassessing Birka chamber grave Bj.5812019In: Antiquity, ISSN 0003-598X, E-ISSN 1745-1744, Vol. 93, no 367, p. 181-198Article in journal (Refereed)
    Abstract [en]

    The warrior woman has long been part of the Viking image, with a pedigree that extends from the Valkyries of Old Norse prose and poetry to modern media entertainment. Until recently, however, actual Viking Age evidence for such individuals has been sparse. This article addresses research showing that the individual buried at Birka in an 'archetypal' high-status warrior grave-always assumed to be male since its excavation in 1878-is, in fact, biologically female. Publication, in 2017, of the genomic data led to unprecedented public debate about this individual. Here, the authors address in detail the interpretation of the burial, discussing source-critical issues and parallels.

  • 34.
    Sanchez-Quinto, Federico
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Dept Anthropol & Dev Studies, Ctr Anthropol Res, ZA-2006 Auckland Pk, South Africa.
    Fraser, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Girdland-Flink, Linus
    Liverpool John Moores Univ, Sch Nat Sci & Psychol, Res Ctr Evolutionary Anthropol & Paleoecol, Liverpool L3 3AF, Merseyside, England.
    Svensson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Simões, Luciana G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    George, Robert
    Royal Prince Alfred Hosp, Dept Surg, Sydney, NSW 2050, Australia;Stockholm Univ, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, SE-10691 Stockholm, Sweden.
    Hollfelder, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Burenhult, Göran
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History.
    Noble, Gordon
    Univ Aberdeen, Sir Duncan Rice Lib, Museums & Special Collect, Aberdeen AB24 3AA, Scotland.
    Britton, Kate
    Univ Aberdeen, Sir Duncan Rice Lib, Museums & Special Collect, Aberdeen AB24 3AA, Scotland;Max Planck Inst Evolutionary Anthropol, Dept Human Evolut, D-04103 Leipzig, Germany.
    Talamo, Sahra
    Max Planck Inst Evolutionary Anthropol, Dept Human Evolut, D-04103 Leipzig, Germany.
    Curtis, Neil
    Univ Aberdeen, Sir Duncan Rice Lib, Museums & Special Collect, Aberdeen AB24 3AA, Scotland.
    Brzobohata, Hana
    Czech Acad Sci, Inst Archaeol, Dept Prehist Archaeol, CZ-11801 Prague, Czech Republic.
    Sumberova, Radka
    Czech Acad Sci, Inst Archaeol, Dept Prehist Archaeol, CZ-11801 Prague, Czech Republic.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, SE-10691 Stockholm, Sweden.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, SE-10691 Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Dept Anthropol & Dev Studies, Ctr Anthropol Res, ZA-2006 Auckland Pk, South Africa.
    Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 19, p. 9469-9474Article in journal (Refereed)
    Abstract [en]

    Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic facade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.

  • 35.
    Schlebusch, Carina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Ctr Anthropol Res, ZA-2006 Johannesburg, South Africa;Univ Johannesburg, Dept Anthropol & Dev Studies, ZA-2006 Johannesburg, South Africa;SciLifeLab, SE-75123 Uppsala, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Ctr Anthropol Res, ZA-2006 Johannesburg, South Africa;Univ Johannesburg, Dept Anthropol & Dev Studies, ZA-2006 Johannesburg, South Africa;SciLifeLab, SE-75123 Uppsala, Sweden.
    Tales of Human Migration, Admixture, and Selection in Africa2018In: Annual review of genomics and human genetics (Print), ISSN 1527-8204, E-ISSN 1545-293X, Vol. 19, p. 405-428Article in journal (Refereed)
    Abstract [en]

    In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000-350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is complex and includes demographic events that influenced patterns of genetic variation across the continent. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter-gatherers, as the world's deepest population divergences occur among these groups, and that the deepest population divergence dates to 300,000 years before present. However, the spread of pastoralism and agriculture in the last few thousand years has shaped the geographic distribution of present-day Africans and their genetic diversity. With today's sequencing technologies, we can obtain full genome sequences from diverse sets of extant and prehistoric Africans. The coming years will contribute exciting new insights toward deciphering human evolutionary history in Africa.

  • 36.
    Semo, Armando
    et al.
    Univ Porto, CIBIO Ctr Invest Biodiversidade & Recursos Genet, Vairao, Portugal.
    Gaya-Vidal, Magdalena
    Univ Porto, CIBIO Ctr Invest Biodiversidade & Recursos Genet, Vairao, Portugal.
    Fortes-Lima, Cesar A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Alard, Berenice
    Univ Porto, CIBIO Ctr Invest Biodiversidade & Recursos Genet, Vairao, Portugal.
    Oliveira, Sandra
    Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany.
    Almeida, Joao
    Univ Porto, CIBIO Ctr Invest Biodiversidade & Recursos Genet, Vairao, Portugal.
    Prista, Antonio
    Univ Pedagog Mocambique, Fac Educ Fis & Desporto, Maputo, Mozambique.
    Damasceno, Albertino
    Univ Eduardo Mondlane, Fac Med, Maputo, Mozambique.
    Fehn, Anne-Maria
    Univ Porto, CIBIO Ctr Invest Biodiversidade & Recursos Genet, Vairao, Portugal;Max Planck Inst Sci Human Hist, Dept Linguist & Cultural Evolut, Jena, Germany.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, Auckland Pk, South Africa.
    Rocha, Jorge
    Univ Porto, CIBIO Ctr Invest Biodiversidade & Recursos Genet, Vairao, Portugal;Univ Porto, Fac Ciencias, Dept Biol, Porto, Portugal.
    Along the Indian Ocean Coast: Genomic Variation in Mozambique Provides New Insights into the Bantu Expansion2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 2, p. 406-416Article in journal (Refereed)
    Abstract [en]

    The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using similar to 1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a "late split" between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North-South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North-South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.

  • 37.
    Shebanits, Kateryna
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Larhammar: Pharmacology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johansson, Anna C. V.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Maqbool, Khurram
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Feuk, Lars
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Larhammar, Dan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Larhammar: Pharmacology.
    Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.2019In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 19, article id 31Article in journal (Refereed)
    Abstract [en]

    Background: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.

    Results: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split.

    Conclusions: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation.

  • 38.
    Terrinoni, Manuela
    et al.
    Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Microbiol & Immunol, SE-40530 Gothenburg, Sweden;Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Univ Gothenburg Vaccine Res Inst GUVAX, SE-40530 Gothenburg, Sweden.
    Holmgren, Jan
    Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Microbiol & Immunol, SE-40530 Gothenburg, Sweden;Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Univ Gothenburg Vaccine Res Inst GUVAX, SE-40530 Gothenburg, Sweden.
    Lebens, Michael
    Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Microbiol & Immunol, SE-40530 Gothenburg, Sweden;Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Univ Gothenburg Vaccine Res Inst GUVAX, SE-40530 Gothenburg, Sweden.
    Larena, Maximilian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Dept Microbiol & Immunol, SE-40530 Gothenburg, Sweden;Univ Gothenburg, Sahlgrenska Acad, Inst Biomed, Univ Gothenburg Vaccine Res Inst GUVAX, SE-40530 Gothenburg, Sweden.
    Proteomic analysis of cholera toxin adjuvant-stimulated human monocytes identifies Thrombospondin-1 and Integrin-beta 1 as strongly upregulated molecules involved in adjuvant activity2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 2812Article in journal (Refereed)
    Abstract [en]

    Cholera Toxin (CT) as well as its related non-toxic mmCT and dmLT mutant proteins have been shown to be potent adjuvants for mucosally administered vaccines. Their adjuvant activity involves activation of cAMP/protein kinase A (PKA) signaling and inflammasome/IL-1 beta pathways in antigen presenting cells (APC). To get a further understanding of the signal transduction and downstream pathways activated in APCs by this group of adjuvants we have, employing quantitative proteomic analytic tools, investigated human monocytes at various time points after treatment with CT. We report the activation of three main biological pathways among upregulated proteins, peaking at 16 hours of CT treatment: cellular organization, metabolism, and immune response. Specifically, in the further analyzed immune response pathway we note a strong upregulation of thrombospondin 1 (THBS1) and integrin beta 1 (ITGB1) in response to CT as well as to mmCT and dmLT, mediated via cAMP/PKA and NFKB signaling. Importantly, inhibition in vitro of THSB1 and ITGB1 in monocytes or primary dendritic cells using siRNA abrogated the ability of the treated APCs to promote an adjuvant-stimulated Th17 cell response when co-cultured with peripheral blood lymphocytes indicating the involvement of these molecules in the adjuvant action on APCs by CT, mmCT and dmLT.

  • 39.
    Terrinoni, Manuela
    et al.
    Univ Gothenburg, Sahlgrenska Acad, Univ Gothenburg Vaccine Res Inst GUVAX, Dept Microbiol & Immunol,Inst Biomed, Gothenburg, Sweden.
    Holmgren, Jan
    Univ Gothenburg, Sahlgrenska Acad, Univ Gothenburg Vaccine Res Inst GUVAX, Dept Microbiol & Immunol,Inst Biomed, Gothenburg, Sweden.
    Lebens, Michael
    Univ Gothenburg, Sahlgrenska Acad, Univ Gothenburg Vaccine Res Inst GUVAX, Dept Microbiol & Immunol,Inst Biomed, Gothenburg, Sweden.
    Larena, Maximilian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Gothenburg, Sahlgrenska Acad, Univ Gothenburg Vaccine Res Inst GUVAX, Dept Microbiol & Immunol,Inst Biomed, Gothenburg, Sweden.
    Requirement for Cyclic AMP/Protein Kinase A-Dependent Canonical NFκB Signaling in the Adjuvant Action of Cholera Toxin and Its Non-toxic Derivative mmCT2019In: Frontiers in Immunology, ISSN 1664-3224, E-ISSN 1664-3224, Vol. 10, article id 269Article in journal (Refereed)
    Abstract [en]

    Cholera toxin (CT) is widely used as an effective adjuvant in experimental immunology for inducing mucosal immune responses; yet its mechanisms of adjuvant action remain incompletely defined. Here, we demonstrate that mice lacking NFκB, compared to wild-type (WT) mice, had a 90% reduction in their systemic and mucosal immune responses to oral immunization with a model protein antigen [Ovalbumin (OVA)] given together with CT. Further, NFκB−/− mouse dendritic cells (DCs) stimulated in vitro with CT showed reduced expression of MHCII and co-stimulatory molecules, such as CD80 and CD86, as well as of IL-1β, and other pro-inflammatory cytokines compared to WT DCs. Using a human monocyte cell line THP1 with an NFκB activation reporter system, we show that CT induced NFκB signaling in human monocytes, and that inhibition of the cyclic AMP—protein kinase A (cAMP-PKA) pathway abrogated the activation and nuclear translocation of NFκB. In a human monocyte-CD4+ T cell co-culture system we further show that the strong Th17 response induced by CT treatment of monocytes was abolished by blocking the classical but not the alternative NFκB signaling pathway of monocytes. Our results indicate that activation of classical (canonical) NFκB pathway signaling in antigen-presenting cells (APCs) by CT is important for CT's adjuvant enhancement of Th17 responses. Similar findings were obtained using the almost completely detoxified mmCT mutant protein as adjuvant. Altogether, our results demonstrate that activation of the classical NFκB signal transduction pathway in APCs is important for the adjuvant action of both CT and mmCT.

  • 40.
    Tournebize, Rémi
    et al.
    Univ Montpellier, IRD, UMR DIADE, BP 64501, Montpellier 5, France.
    Poncet, Valérie
    Univ Montpellier, IRD, UMR DIADE, BP 64501, Montpellier 5, France.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Dept Anthropol & Dev Studies, Ctr Anthropol Res, Auckland Pk, South Africa.
    Vigouroux, Yves
    Univ Montpellier, IRD, UMR DIADE, BP 64501, Montpellier 5, France.
    Manel, Stéphanie
    Univ Montpellier, PSL Res Univ, CNRS, EPHE,IRD,INRA,UMR 5175 CEFE,Montpellier SupAgro, Montpellier, France.
    McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes2019In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 19, no 1, p. 283-295Article in journal (Refereed)
    Abstract [en]

    Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here, we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic models that include selection. McSwan demonstrated high power (high sensitivity and specificity) in capturing hard selective sweep events without requiring haplotype phasing. It performed slightly better than SweeD when the recent effective population size was low and the genomic region was small. We then applied our method to a European (CEU) and an African (LWK) human re-sequencing data set. Most hard sweeps were detected in the CEU population (96%). Moreover, hard sweeps in the African population were estimated to have occurred further back in time (mode: 43,625 years BP) compared to those of Europeans (mode: 24,850 years BP). Most of the estimated ages of hard sweeps in Europeans were associated with the Last Glacial Maximum and were enriched in immunity-associated genes.

  • 41.
    Valdiosera, Cristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. La Trobe Univ, Dept Archaeol & Hist, Melbourne, Vic 3086, Australia.; Univ Complutense Madrid, Inst Salud Carlos III Evoluc & Comportamiento Hum, Ctr Mixto, Madrid 28029, Spain..
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Carlos Vera-Rodriguez, Juan
    Univ Huelva, Dept Hist Geog & Antropol, Ctr Invest Patrimonio Hist Cultural & Nat, Huelva 21071, Spain..
    Urena, Irene
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. Univ Complutense Madrid, Inst Salud Carlos III Evoluc & Comportamiento Hum, Ctr Mixto, Madrid 28029, Spain..
    Iriarte, Eneko
    Univ Burgos, Dept Hist Geog & Comunicac, Lab Evoluc Humana, Burgos 09001, Spain..
    Rodriguez-Varela, Ricardo
    Univ Complutense Madrid, Inst Salud Carlos III Evoluc & Comportamiento Hum, Ctr Mixto, Madrid 28029, Spain.;Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden..
    Simões, Luciana G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Martinez-Sanchez, Rafael M.
    Univ Granada, Fac Filosofia & Letras, Dept Prehist & Arqueol, E-18071 Granada, Spain..
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Rodriguez, Laura
    Univ Burgos, Dept Hist Geog & Comunicac, Lab Evoluc Humana, Burgos 09001, Spain.;Univ Isabel 1, Fac Humanidades, Burgos 09003, Spain..
    Bermudez de Castro, Jose-Maria
    Ctr Nacl Invest Evoluc Humana, Burgos 09002, Spain..
    Carbonell, Eudald
    Inst Catala Paleoecol Humana & Evolucio Social, Tarragona 43007, Spain..
    Alday, Alfonso
    Univ Basque Country, Dept Geog Prehist & Arqueol, Lejona 48940, Vizcaya, Spain..
    Hernandez Vera, Jose Antonio
    Univ Zaragoza, Dept Ciencias Antiguedad, E-50009 Zaragoza, Spain..
    Götherström, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden..
    Carretero, Jose-Miguel
    Univ Complutense Madrid, Inst Salud Carlos III Evoluc & Comportamiento Hum, Ctr Mixto, Madrid 28029, Spain.;Univ Burgos, Dept Hist Geog & Comunicac, Lab Evoluc Humana, Burgos 09001, Spain..
    Luis Arsuaga, Juan
    Univ Complutense Madrid, Inst Salud Carlos III Evoluc & Comportamiento Hum, Ctr Mixto, Madrid 28029, Spain..
    Smith, Colin I.
    La Trobe Univ, Dept Archaeol & Hist, Melbourne, Vic 3086, Australia..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Ctr Anthropol Res, ZA-2006 Johannesburg, South Africa..
    Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 13, p. 3428-3433Article in journal (Refereed)
    Abstract [en]

    Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500-3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

  • 42.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Demographic History and Adaptation in African Populations2020Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Africa is the continent where modern humans originated and yet, African demographic history remains largely unknown. Through analyzing the genetic composition of extant and extinct individuals, it is possible to reveal signals of past demographic history and adaptation. In this thesis, I applied population genetic methods to investigate both deep African history and demographic changes associated with the migrations of farmers in Africa. While Paper I and II assess the genomic landscape before the arrival farming groups, Paper III, IV and V focus on the demographic patterns associated with the emergence of various African agro-pastoral societies and how shifts in ways of subsistence resulted in different selective pressures on the genomic level. The genomes from Southern African San hunter-gatherers harbor the earliest diverging lineages and represent the first population divergence event within the modern human phylogeny. However, gene-flow from farming groups has complicated the investigation of genetic relationships between different San groups. In Paper I, I established that Southern African hunter-gatherer genetic diversity fitted an isolation-by-distance model when genomic segments that trace their ancestry to farming groups were excluded. Paper II confirmed that all extant Southern African hunter-gatherers received admixture from farming groups, through comparison with ancient DNA data from three 2,000-year-old southern African Stone Age individuals. New date estimates for the first population divergence event in the modern human phylogeny, based on the Stone Age individuals, coincided with a period in the fossil record associated with transition between archaic humans into anatomically modern humans. Paper III assesses the genetic variation of four ancient Iron Age women from current-day South Africa. I was able to further refine their genetic profiles, which were closest related to southeast Bantu-speaking farmers from current-day South Africa. In Paper IV, I propose that the emergence of pastoralism in Southern Africa arrived through a male-driven migration of East African Afro-Asiatic related groups, who introduced their pastoral subsistence practices and livestock into Southern Africa. In Paper V, I investigated the history of the Fulani population and demonstrated how a shift in subsistence practice triggered different selective pressures in the Fulani. The pastoral Fulani from the Western Sahel show relatively high frequencies of the European-associated Lactase Persistence (LP) variant. Here, I propose that the LP mutation were introduced into Fulani genomes through contact with a North African group(s) who themselves carried European admixture. Additionally, by performing the first genome wide association study (GWAS) on the lactose digestion phenotype, I confirmed the association with the MCM6/LCT locus and identified a possible association between glycemic levels after lactose intake and the SPRY2 gene. Furthermore, in addition to the LP trait, I also identified other potential signals of local adaption related to the pastoralism lifeway of the Fulani. This thesis provided further insights on how the African genomic landscape was shaped through time, influenced by the environment, interactions between different groups and adaptations to different lifeways.

    List of papers
    1. Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait
    Open this publication in new window or tab >>Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait
    Show others...
    2019 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, no 1, article id 915Article in journal (Refereed) Published
    Abstract [en]

    Background

    Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt.

    Results

    Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake.

    Conclusions

    Our findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

    Keywords
    Fulani people, Pastoralism, Lactase persistence, Adaptive gene-flow, GWAS
    National Category
    Medical Genetics
    Identifiers
    urn:nbn:se:uu:diva-400745 (URN)10.1186/s12864-019-6296-7 (DOI)000501323300001 ()31791255 (PubMedID)
    Funder
    Swedish Research Council, 621-2014-5211EU, European Research Council, 759933
    Note

    Mário Vicente, Edita Priehodová, ViktorČerný and Carina M. Schlebusch contributed equally to this work.

    Available from: 2020-01-03 Created: 2020-01-03 Last updated: 2020-03-05Bibliographically approved
    2. Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations
    Open this publication in new window or tab >>Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations
    2019 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 9, p. 1849-1861Article in journal (Refereed) Published
    Abstract [en]

    Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as "Khoe-San" populations and have a long history in southern Africa. Their ancestors were largely isolated up until similar to 2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx'a-language family (double dagger Hoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.

    Keywords
    Khoe-San, southern Africa, population structure, isolation-by-distance, adaptive gene-flow
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-397127 (URN)10.1093/molbev/msz089 (DOI)000493043800001 ()31288264 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2014-5211Swedish Research Council, 6422013-8019EU, European Research Council, 759933Göran Gustafsson Foundation for Research in Natural Sciences and Medicine
    Available from: 2019-11-29 Created: 2019-11-29 Last updated: 2020-03-05Bibliographically approved
    3. Male-biased migration from East Africa introduced pastoralism into southern Africa
    Open this publication in new window or tab >>Male-biased migration from East Africa introduced pastoralism into southern Africa
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Hunter-gatherer lifestyles dominated the southern African landscape up to ~2,000 years ago, when herding and farming groups started to arrive into the area. First, herding and livestock of (possible) East African origin appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agropastoral expansion. Modern-day Khoekhoe speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most of the other historical Khoekhoe populations have, however, disappeared over the last few centuries. In our study we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking herder groups from the southern Cape region of current-day South Africa. With the help of comparative data, we were able to align genetic date estimates and admixture proportions to archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We also identified several Afro-Asiatic speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. Furthermore, we detect that the East African pastoralist expansion was heavily male-biased. We propose that pastoralism in southern Africa arrived through a male-biased migration of an East African Afro-Asiatic related group(s) who introduced the new subsistence practice to local southern African hunter-gatherers.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-406232 (URN)
    Available from: 2020-03-05 Created: 2020-03-05 Last updated: 2020-03-05
    4. Four Iron Age women from KwaZulu-Natal: biological anthropology, genetics and archaeological context
    Open this publication in new window or tab >>Four Iron Age women from KwaZulu-Natal: biological anthropology, genetics and archaeological context
    Show others...
    2019 (English)In: Southern African Humanities, ISSN 1681-5564, Vol. 32, no 1, p. 23-56Article in journal (Refereed) Published
    Abstract [en]

    We report further details on four partial human skeletons from KwaZulu-Natal previously selected for genetic analysis. Dating and genetic results indicate that they derived from agriculturist communities of the mid-second millennium AD. Morphological and genetic analysis shows that three individuals were female; identification of the fourth as female comes from genetic analysis only. All four were adults at death, three older adults and one younger. Genetically, all four individuals cluster strongly with Bantu-speaking populations with West African roots, a result supported by craniometric data for the one individual with a complete and well-preserved cranium. All nevertheless display some admixture with Khoe-San populations. We show that three of the women, and probably the fourth, carried genetic resistance to the Plasmodium vivax malaria parasite, while two had some protection against Trypanosoma brucei gambiense-induced sleeping sickness. The unusual rock-shelter burial locations of three of the women suggest that their deaths required ritual ‘cooling’. Lightning and violence are possible causes. We argue that this multipronged approach is necessary for the development of detailed and nuanced understandings of the past and of the individuals who lived in the region centuries ago.

    Place, publisher, year, edition, pages
    South Africa: Council of the Natal Museum, 2019
    Keywords
    Ancient DNA, Bantu-speaker expansion, Palaeopathology, Physical anthropology, Iron Age
    National Category
    Genetics Archaeology
    Identifiers
    urn:nbn:se:uu:diva-406231 (URN)
    Available from: 2020-03-05 Created: 2020-03-05 Last updated: 2020-03-05
    5. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
    Open this publication in new window or tab >>Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
    Show others...
    2017 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, no 6363, p. 652-655Article in journal (Refereed) 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.

    National Category
    Archaeology Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-334636 (URN)10.1126/science.aao6266 (DOI)000414240500038 ()28971970 (PubMedID)
    Funder
    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 TechnologyThe Wenner-Gren Foundation
    Note

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

    Available from: 2017-11-24 Created: 2017-11-24 Last updated: 2020-03-05Bibliographically approved
  • 43.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Male-biased migration from East Africa introduced pastoralism into southern AfricaManuscript (preprint) (Other academic)
    Abstract [en]

    Hunter-gatherer lifestyles dominated the southern African landscape up to ~2,000 years ago, when herding and farming groups started to arrive into the area. First, herding and livestock of (possible) East African origin appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agropastoral expansion. Modern-day Khoekhoe speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most of the other historical Khoekhoe populations have, however, disappeared over the last few centuries. In our study we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking herder groups from the southern Cape region of current-day South Africa. With the help of comparative data, we were able to align genetic date estimates and admixture proportions to archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We also identified several Afro-Asiatic speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. Furthermore, we detect that the East African pastoralist expansion was heavily male-biased. We propose that pastoralism in southern Africa arrived through a male-biased migration of an East African Afro-Asiatic related group(s) who introduced the new subsistence practice to local southern African hunter-gatherers.

  • 44.
    Vicente, Mário
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Ebbesen, Peter
    Aalborg Univ, Dept Hlth Sci & Technol, Aalborg, Denmark.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Genetic variation of southern Africa hunter-gatherers and the impact of admixture with farming and pastoralist populations2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 395-395Article in journal (Other academic)
  • 45.
    Vicente, Mário
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, Auckland Pk, South Africa.
    Ebbesen, Peter
    Aalborg Univ, Dept Hlth Sci & Technol, Aalborg, Denmark.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, Auckland Pk, South Africa.
    Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 9, p. 1849-1861Article in journal (Refereed)
    Abstract [en]

    Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as "Khoe-San" populations and have a long history in southern Africa. Their ancestors were largely isolated up until similar to 2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx'a-language family (double dagger Hoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.

  • 46.
    Vicente, Mário
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Priehodova, Edita
    Acad Sci Czech Republ, Inst Archaeol, Archaeogenet Lab, Prague, Czech Republic.
    Diallo, Issa
    CNRST, Inst Sci Soc, Dept Linguist & Langues Natl, Ouagadougou, Burkina Faso.
    Podgorna, Eliska
    Acad Sci Czech Republ, Inst Archaeol, Archaeogenet Lab, Prague, Czech Republic.
    Poloni, Estella S.
    Univ Geneva, Dept Genet & Evolut, Anthropol Unit, Geneva, Switzerland;Inst Genet & Genom Geneva IGE3, Geneva, Switzerland.
    Cerny, Viktor
    Acad Sci Czech Republ, Inst Archaeol, Archaeogenet Lab, Prague, Czech Republic.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait2019In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, no 1, article id 915Article in journal (Refereed)
    Abstract [en]

    Background

    Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending throughout the African Sahel/Savannah belt.

    Results

    Based on genome-wide analyses we propose that ancestors of the Fulani population experienced admixture between a West African group and a group carrying both European and North African ancestries. This admixture was likely coupled with newly adopted herding practices, as it resulted in signatures of genetic adaptation in contemporary Fulani genomes, including the control element of the LCT gene enabling carriers to digest lactose throughout their lives. The lactase persistence (LP) trait in the Fulani is conferred by the presence of the allele T-13910, which is also present at high frequencies in Europe. We establish that the T-13910 LP allele in Fulani individuals analysed in this study lies on a European haplotype background thus excluding parallel convergent evolution. We furthermore directly link the T-13910 haplotype with the Lactase Persistence phenotype through a Genome Wide Association study (GWAS) and identify another genomic region in the vicinity of the SPRY2 gene associated with glycaemic measurements after lactose intake.

    Conclusions

    Our findings suggest that Eurasian admixture and the European LP allele was introduced into the Fulani through contact with a North African population/s. We furthermore confirm the link between the lactose digestion phenotype in the Fulani to the MCM6/LCT locus by reporting the first GWAS of the lactase persistence trait. We also explored other signals of recent adaptation in the Fulani and identified additional candidates for selection to adapt to herding life-styles.

1 - 46 of 46
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