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Vicente, M., Jakobsson, M., Ebbesen, P. & Schlebusch, C. (2019). Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations. Molecular biology and evolution, 36(9), 1849-1861
Öppna denna publikation i ny flik eller fönster >>Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations
2019 (Engelska)Ingår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, nr 9, s. 1849-1861Artikel i tidskrift (Refereegranskat) 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.

Nyckelord
Khoe-San, southern Africa, population structure, isolation-by-distance, adaptive gene-flow
Nationell ämneskategori
Genetik
Identifikatorer
urn:nbn:se:uu:diva-397127 (URN)10.1093/molbev/msz089 (DOI)000493043800001 ()31288264 (PubMedID)
Forskningsfinansiär
Knut och Alice Wallenbergs StiftelseVetenskapsrådet, 621-2014-5211Vetenskapsrådet, 6422013-8019EU, Europeiska forskningsrådet, 759933Göran Gustafssons stiftelse för naturvetenskaplig och medicinsk forskning (KVA)
Tillgänglig från: 2019-11-29 Skapad: 2019-11-29 Senast uppdaterad: 2019-11-29Bibliografiskt granskad
Vicente, M., Priehodova, E., Diallo, I., Podgorna, E., Poloni, E. S., Cerny, V. & Schlebusch, C. (2019). Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait. BMC Genomics, 20(1), Article ID 915.
Öppna denna publikation i ny flik eller fönster >>Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait
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2019 (Engelska)Ingår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, nr 1, artikel-id 915Artikel i tidskrift (Refereegranskat) 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.

Nyckelord
Fulani people, Pastoralism, Lactase persistence, Adaptive gene-flow, GWAS
Nationell ämneskategori
Medicinsk genetik
Identifikatorer
urn:nbn:se:uu:diva-400745 (URN)10.1186/s12864-019-6296-7 (DOI)000501323300001 ()31791255 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 621-2014-5211EU, Europeiska forskningsrådet, 759933
Anmärkning

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

Tillgänglig från: 2020-01-03 Skapad: 2020-01-03 Senast uppdaterad: 2020-01-03Bibliografiskt granskad
Günther, T., Malmström, H., Svensson, E., Omrak, A., Sanchez-Quinto, F., Kilinc, G. M., . . . Jakobsson, M. (2018). Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. PLoS biology, 16(1), Article ID e2003703.
Öppna denna publikation i ny flik eller fönster >>Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
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2018 (Engelska)Ingår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 16, nr 1, artikel-id e2003703Artikel i tidskrift (Refereegranskat) Published
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.

Nationell ämneskategori
Biologiska vetenskaper Arkeologi
Identifikatorer
urn:nbn:se:uu:diva-346367 (URN)10.1371/journal.pbio.2003703 (DOI)000423830300009 ()29315301 (PubMedID)
Forskningsfinansiär
EU, Europeiska forskningsrådetThe Wenner-Gren FoundationKnut och Alice Wallenbergs StiftelseRiksbankens JubileumsfondVetenskapsrådet, 421-2013-730; 2013-1905Forskningsrådet Formas, 2011-1138
Tillgänglig från: 2018-03-26 Skapad: 2018-03-26 Senast uppdaterad: 2018-03-26Bibliografiskt granskad
Vicente, M., Ebbesen, P., Jakobsson, M. & Schlebusch, C. (2017). Genetic variation of southern Africa hunter-gatherers and the impact of admixture with farming and pastoralist populations. Paper presented at 86th Annual Meeting of the American-Association-of-Physical-Anthropologists (AAPA), APR 19-22, 2017, New Orleans, LA. American Journal of Physical Anthropology, 162(S64), 395-395
Öppna denna publikation i ny flik eller fönster >>Genetic variation of southern Africa hunter-gatherers and the impact of admixture with farming and pastoralist populations
2017 (Engelska)Ingår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, nr S64, s. 395-395Artikel i tidskrift, Meeting abstract (Övrigt vetenskapligt) Published
Nationell ämneskategori
Arkeologi
Identifikatorer
urn:nbn:se:uu:diva-350219 (URN)10.1002/ajpa.23210 (DOI)000423063104279 ()
Konferens
86th Annual Meeting of the American-Association-of-Physical-Anthropologists (AAPA), APR 19-22, 2017, New Orleans, LA
Tillgänglig från: 2018-05-18 Skapad: 2018-05-18 Senast uppdaterad: 2018-05-18Bibliografiskt granskad
Schlebusch, C., Malmström, H., Günther, T., Sjödin, P., Coutinho, A., Edlund, H., . . . Jakobsson, M. (2017). Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science, 358(6363), 652-655
Öppna denna publikation i ny flik eller fönster >>Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
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2017 (Engelska)Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, nr 6363, s. 652-655Artikel i tidskrift (Refereegranskat) 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.

Nationell ämneskategori
Arkeologi Evolutionsbiologi Genetik
Identifikatorer
urn:nbn:se:uu:diva-334636 (URN)10.1126/science.aao6266 (DOI)000414240500038 ()28971970 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 642-2013-8019; 621-2014-5211Knut och Alice Wallenbergs StiftelseGöran Gustafssons Stiftelse för främjande av vetenskaplig forskning vid Uppsala universitet och Kungl tekniska högskolan (UU/KTH)The Wenner-Gren Foundation
Anmärkning

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

Tillgänglig från: 2017-11-24 Skapad: 2017-11-24 Senast uppdaterad: 2019-11-18Bibliografiskt granskad
Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M. A., Järve, M., Talas, U. G., . . . Kivisild, T. (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture.. Genome Research, 25(4)
Öppna denna publikation i ny flik eller fönster >>A recent bottleneck of Y chromosome diversity coincides with a global change in culture.
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2015 (Engelska)Ingår i: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, nr 4Artikel i tidskrift (Refereegranskat) Published
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.

Nationell ämneskategori
Naturvetenskap
Identifikatorer
urn:nbn:se:uu:diva-270875 (URN)10.1101/gr.186684.114 (DOI)25770088 (PubMedID)
Tillgänglig från: 2016-03-21 Skapad: 2016-01-04 Senast uppdaterad: 2017-11-30
Clemente, F. J., Cardona, A., Inchley, C. E., Peter, B. M., Jacobs, G., Pagani, L., . . . Kivisild, T. (2014). A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.. American Journal of Human Genetics, 95(5)
Öppna denna publikation i ny flik eller fönster >>A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.
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2014 (Engelska)Ingår i: American Journal of Human Genetics, ISSN 0002-9297, E-ISSN 1537-6605, Vol. 95, nr 5Artikel i tidskrift (Refereegranskat) Published
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.

Nationell ämneskategori
Medicin och hälsovetenskap
Identifikatorer
urn:nbn:se:uu:diva-270876 (URN)10.1016/j.ajhg.2014.09.016 (DOI)25449608 (PubMedID)
Tillgänglig från: 2016-03-21 Skapad: 2016-01-04 Senast uppdaterad: 2017-11-30Bibliografiskt granskad
Barbieri, C., Vicente, M., Oliveira, S., Bostoen, K., Rocha, J., Stoneking, M. & Pakendorf, B. (2014). Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.. PLoS ONE, 9(6)
Öppna denna publikation i ny flik eller fönster >>Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.
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2014 (Engelska)Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 6Artikel i tidskrift (Refereegranskat) Published
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.

Nationell ämneskategori
Naturvetenskap
Identifikatorer
urn:nbn:se:uu:diva-281222 (URN)
Tillgänglig från: 2016-03-21 Skapad: 2016-03-21 Senast uppdaterad: 2017-11-30
Barbieri, C., Vicente, M., Rocha, J., Mpoloka, S. W., Stoneking, M. & Pakendorf, B. (2013). Ancient substructure in early mtDNA lineages of southern Africa.. American Journal of Human Genetics, 92(2)
Öppna denna publikation i ny flik eller fönster >>Ancient substructure in early mtDNA lineages of southern Africa.
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2013 (Engelska)Ingår i: American Journal of Human Genetics, ISSN 0002-9297, E-ISSN 1537-6605, Vol. 92, nr 2Artikel i tidskrift (Refereegranskat) Published
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.

Nationell ämneskategori
Naturvetenskap
Identifikatorer
urn:nbn:se:uu:diva-270878 (URN)10.1016/j.ajhg.2012.12.010 (DOI)23332919 (PubMedID)
Tillgänglig från: 2016-03-21 Skapad: 2016-01-04 Senast uppdaterad: 2017-11-30
Naidoo, T., Xu, J., Vicente, M., Malmström, H., Soodyall, H., Jakobsson, M. & Schlebusch, C.Full genomic Y chromosomal variation in southern African Khoe-San populations.
Öppna denna publikation i ny flik eller fönster >>Full genomic Y chromosomal variation in southern African Khoe-San populations
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(Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
Nationell ämneskategori
Genetik Evolutionsbiologi
Identifikatorer
urn:nbn:se:uu:diva-361124 (URN)
Tillgänglig från: 2018-09-20 Skapad: 2018-09-20 Senast uppdaterad: 2018-09-20
Organisationer
Identifikatorer
ORCID-id: ORCID iD iconorcid.org/0000-0002-9122-4530

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