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  • 1. Barbieri, Chiara
    et al.
    Vicente, Mário
    Oliveira, Sandra
    Bostoen, Koen
    Rocha, Jorge
    Stoneking, Mark
    Pakendorf, Brigitte
    Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 6Article in journal (Refereed)
    Abstract [en]

    Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000-5000 years, reaching different parts of southern Africa 1200-2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speakers. During their expansion, Bantu speakers would have come into contact with diverse local populations, such as the Khoisan hunter-gatherers and pastoralists of southern Africa, with whom they may have intermarried. In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia, and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations. Only the pastoralist Himba and Herero stand out due to high frequencies of particular L3f and L3d lineages; the latter are also found in the neighboring Damara, who speak a Khoisan language and were foragers and small-stock herders. In contrast, the close cultural and linguistic relatives of the Herero and Himba, the Kuvale, are genetically similar to other Bantu-speakers. Nevertheless, as demonstrated by resampling tests, the genetic divergence of Herero, Himba, and Kuvale is compatible with a common shared ancestry with high levels of drift, while the similarity of the Herero, Himba, and Damara probably reflects admixture, as also suggested by linguistic analyses.

  • 2. Barbieri, Chiara
    et al.
    Vicente, Mário
    Rocha, Jorge
    Mpoloka, Sununguko W
    Stoneking, Mark
    Pakendorf, Brigitte
    Ancient substructure in early mtDNA lineages of southern Africa.2013In: American Journal of Human Genetics, ISSN 0002-9297, E-ISSN 1537-6605, Vol. 92, no 2Article in journal (Refereed)
    Abstract [en]

    Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.

  • 3. Clemente, Florian J
    et al.
    Cardona, Alexia
    Inchley, Charlotte E
    Peter, Benjamin M
    Jacobs, Guy
    Pagani, Luca
    Lawson, Daniel J
    Antão, Tiago
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Mitt, Mario
    DeGiorgio, Michael
    Faltyskova, Zuzana
    Xue, Yali
    Ayub, Qasim
    Szpak, Michal
    Mägi, Reedik
    Eriksson, Anders
    Manica, Andrea
    Raghavan, Maanasa
    Rasmussen, Morten
    Rasmussen, Simon
    Willerslev, Eske
    Vidal-Puig, Antonio
    Tyler-Smith, Chris
    Villems, Richard
    Nielsen, Rasmus
    Metspalu, Mait
    Malyarchuk, Boris
    Derenko, Miroslava
    Kivisild, Toomas
    A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.2014In: American Journal of Human Genetics, ISSN 0002-9297, E-ISSN 1537-6605, Vol. 95, no 5Article in journal (Refereed)
    Abstract [en]

    Arctic populations live in an environment characterized by extreme cold and the absence of plant foods for much of the year and are likely to have undergone genetic adaptations to these environmental conditions in the time they have been living there. Genome-wide selection scans based on genotype data from native Siberians have previously highlighted a 3 Mb chromosome 11 region containing 79 protein-coding genes as the strongest candidates for positive selection in Northeast Siberians. However, it was not possible to determine which of the genes might be driving the selection signal. Here, using whole-genome high-coverage sequence data, we identified the most likely causative variant as a nonsynonymous G>A transition (rs80356779; c.1436C>T [p.Pro479Leu] on the reverse strand) in CPT1A, a key regulator of mitochondrial long-chain fatty-acid oxidation. Remarkably, the derived allele is associated with hypoketotic hypoglycemia and high infant mortality yet occurs at high frequency in Canadian and Greenland Inuits and was also found at 68% frequency in our Northeast Siberian sample. We provide evidence of one of the strongest selective sweeps reported in humans; this sweep has driven this variant to high frequency in circum-Arctic populations within the last 6-23 ka despite associated deleterious consequences, possibly as a result of the selective advantage it originally provided to either a high-fat diet or a cold environment.

  • 4.
    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.

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  • 5.
    Hollfelder, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Erasmus, Johannes Christoff
    Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
    Hammarén, Rickhard
    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.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
    Greeff, Jaco M.
    Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 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. Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
    Patterns of African and Asian admixture in the Afrikaner population of South Africa2020In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 18, no 1, article id 16Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. RESULTS: To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. CONCLUSIONS: While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.

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  • 6. Karmin, Monika
    et al.
    Saag, Lauri
    Vicente, Mário
    Wilson Sayres, Melissa A
    Järve, Mari
    Talas, Ulvi Gerst
    Rootsi, Siiri
    Ilumäe, Anne-Mai
    Mägi, Reedik
    Mitt, Mario
    Pagani, Luca
    Puurand, Tarmo
    Faltyskova, Zuzana
    Clemente, Florian
    Cardona, Alexia
    Metspalu, Ene
    Sahakyan, Hovhannes
    Yunusbayev, Bayazit
    Hudjashov, Georgi
    DeGiorgio, Michael
    Loogväli, Eva-Liis
    Eichstaedt, Christina
    Eelmets, Mikk
    Chaubey, Gyaneshwer
    Tambets, Kristiina
    Litvinov, Sergei
    Mormina, Maru
    Xue, Yali
    Ayub, Qasim
    Zoraqi, Grigor
    Korneliussen, Thorfinn Sand
    Akhatova, Farida
    Lachance, Joseph
    Tishkoff, Sarah
    Momynaliev, Kuvat
    Ricaut, François-Xavier
    Kusuma, Pradiptajati
    Razafindrazaka, Harilanto
    Pierron, Denis
    Cox, Murray P
    Sultana, Gazi Nurun Nahar
    Willerslev, Rane
    Muller, Craig
    Westaway, Michael
    Lambert, David
    Skaro, Vedrana
    Kovačevic, Lejla
    Turdikulova, Shahlo
    Dalimova, Dilbar
    Khusainova, Rita
    Trofimova, Natalya
    Akhmetova, Vita
    Khidiyatova, Irina
    Lichman, Daria V
    Isakova, Jainagul
    Pocheshkhova, Elvira
    Sabitov, Zhaxylyk
    Barashkov, Nikolay A
    Nymadawa, Pagbajabyn
    Mihailov, Evelin
    Seng, Joseph Wee Tien
    Evseeva, Irina
    Migliano, Andrea Bamberg
    Abdullah, Syafiq
    Andriadze, George
    Primorac, Dragan
    Atramentova, Lubov
    Utevska, Olga
    Yepiskoposyan, Levon
    Marjanovic, Damir
    Kushniarevich, Alena
    Behar, Doron M
    Gilissen, Christian
    Vissers, Lisenka
    Veltman, Joris A
    Balanovska, Elena
    Derenko, Miroslava
    Malyarchuk, Boris
    Metspalu, Andres
    Fedorova, Sardana
    Eriksson, Anders
    Manica, Andrea
    Mendez, Fernando L
    Karafet, Tatiana M
    Veeramah, Krishna R
    Bradman, Neil
    Hammer, Michael F
    Osipova, Ludmila P
    Balanovsky, Oleg
    Khusnutdinova, Elza K
    Johnsen, Knut
    Remm, Maido
    Thomas, Mark G
    Tyler-Smith, Chris
    Underhill, Peter A
    Willerslev, Eske
    Nielsen, Rasmus
    Metspalu, Mait
    Villems, Richard
    Kivisild, Toomas
    A recent bottleneck of Y chromosome diversity coincides with a global change in culture.2015In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, no 4Article in journal (Refereed)
    Abstract [en]

    It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

  • 7.
    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)
  • 8.
    Schlebusch, Carina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Steyn, Maryna
    Human Variation and Identification Research Unit, School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, South Africa..
    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..
    Lombard, Marlize
    Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa.; Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, 7600, South Africa. .
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago2017In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, no 6363, p. 652-655Article in journal (Refereed)
    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.

  • 9.
    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
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    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
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  • 10.
    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.

  • 11.
    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)
  • 12.
    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.

    Download full text (pdf)
    fulltext
  • 13.
    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, Bur