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Vicente, M. (2020). Demographic History and Adaptation in African Populations. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Demographic History and Adaptation in African Populations
2020 (English)Doctoral 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.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2020. p. 60
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1911
Keywords
African demography, human evolutionary genetics, population structure, population admixture, genetic adaptation
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-406233 (URN)978-91-513-0889-0 (ISBN)
Public defence
2020-04-24, Ekmansalen, EBC, Norbyvägen 14, Uppsala, 10:15 (English)
Opponent
Supervisors
Available from: 2020-04-03 Created: 2020-03-05 Last updated: 2020-05-19
Hollfelder, N., Erasmus, J. C., Hammarén, R., Vicente, M., Jakobsson, M., Greeff, J. M. & Schlebusch, C. (2020). Patterns of African and Asian admixture in the Afrikaner population of South Africa. BMC Biology, 18(1), Article ID 16.
Open this publication in new window or tab >>Patterns of African and Asian admixture in the Afrikaner population of South Africa
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2020 (English)In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 18, no 1, article id 16Article in journal (Refereed) Published
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.

Keywords
Afrikaner, South Africa, Admixture, Slave trade, Colonial times
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-335377 (URN)10.1186/s12915-020-0746-1 (DOI)000518016100001 ()32089133 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2014-5211; 642-2013-8019
Available from: 2017-12-04 Created: 2017-12-04 Last updated: 2020-04-16Bibliographically approved
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
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
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.
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
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.
Open this publication in new window or tab >>Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
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2018 (English)In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 16, no 1, article id e2003703Article in journal (Refereed) 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.

National Category
Biological Sciences Archaeology
Identifiers
urn:nbn:se:uu:diva-346367 (URN)10.1371/journal.pbio.2003703 (DOI)000423830300009 ()29315301 (PubMedID)
Funder
EU, European Research CouncilThe Wenner-Gren FoundationKnut and Alice Wallenberg FoundationRiksbankens JubileumsfondSwedish Research Council, 421-2013-730; 2013-1905Swedish Research Council Formas, 2011-1138
Available from: 2018-03-26 Created: 2018-03-26 Last updated: 2018-03-26Bibliographically approved
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
Open this publication in new window or tab >>Genetic variation of southern Africa hunter-gatherers and the impact of admixture with farming and pastoralist populations
2017 (English)In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 395-395Article in journal, Meeting abstract (Other academic) Published
National Category
Archaeology
Identifiers
urn:nbn:se:uu:diva-350219 (URN)10.1002/ajpa.23210 (DOI)000423063104279 ()
Conference
86th Annual Meeting of the American-Association-of-Physical-Anthropologists (AAPA), APR 19-22, 2017, New Orleans, LA
Available from: 2018-05-18 Created: 2018-05-18 Last updated: 2018-05-18Bibliographically approved
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
Open this publication in new window or tab >>Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago
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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
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)
Open this publication in new window or tab >>A recent bottleneck of Y chromosome diversity coincides with a global change in culture.
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2015 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, no 4Article in journal (Refereed) 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.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-270875 (URN)10.1101/gr.186684.114 (DOI)25770088 (PubMedID)
Available from: 2016-03-21 Created: 2016-01-04 Last updated: 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)
Open this publication in new window or tab >>A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations.
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2014 (English)In: American Journal of Human Genetics, ISSN 0002-9297, E-ISSN 1537-6605, Vol. 95, no 5Article in journal (Refereed) 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.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-270876 (URN)10.1016/j.ajhg.2014.09.016 (DOI)25449608 (PubMedID)
Available from: 2016-03-21 Created: 2016-01-04 Last updated: 2017-11-30Bibliographically approved
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)
Open this publication in new window or tab >>Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.
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2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 6Article in journal (Refereed) 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.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-281222 (URN)
Available from: 2016-03-21 Created: 2016-03-21 Last updated: 2017-11-30
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9122-4530

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