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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.

  • 5. 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.

  • 6.
    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)
  • 7.
    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.

  • 8.
    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)
1 - 8 of 8
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