uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Alternative names
Publications (10 of 27) Show all publications
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
Lombard, M., Malmström, H., Schlebusch, C., Svensson, E., Günther, T., Munters, A. R., . . . Jakobsson, M. (2019). Genetic data and radiocarbon dating question Plovers Lake as a Middle Stone Age hominin-bearing site. Journal of Human Evolution, 131, 203-209
Open this publication in new window or tab >>Genetic data and radiocarbon dating question Plovers Lake as a Middle Stone Age hominin-bearing site
Show others...
2019 (English)In: Journal of Human Evolution, ISSN 0047-2484, E-ISSN 1095-8606, Vol. 131, p. 203-209Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
Plovers lake, Ancient DNA, Hominin-bearing site, South Africa, Middle Stone Age, C14 dating
National Category
Archaeology Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-390338 (URN)10.1016/j.jhevol.2019.03.014 (DOI)000472706300014 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 642-2013-8019Swedish Research Council, 621-2014-5211Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyWenner-Gren Foundations
Available from: 2019-08-09 Created: 2019-08-09 Last updated: 2019-08-09Bibliographically 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
Show others...
2019 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, no 1, article id 915Article in journal (Refereed) Published
Abstract [en]

Background

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

Results

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

Conclusions

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

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

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

Available from: 2020-01-03 Created: 2020-01-03 Last updated: 2020-03-05Bibliographically approved
Lombard, M., Jakobsson, M. & Schlebusch, C. (2018). Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history. South African Journal of Science, 114(1-2), Article ID a0253.
Open this publication in new window or tab >>Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history
2018 (English)In: South African Journal of Science, ISSN 0038-2353, E-ISSN 1996-7489, Vol. 114, no 1-2, article id a0253Article in journal, Editorial material (Other academic) Published
Keywords
human genome, hunter-gatherer, Homo sapiens, population split-time estimations
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-350207 (URN)10.17159/sajs.2018/a0253 (DOI)000423551800002 ()
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 642-2013-8019; 621-2014-5211Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of Technology
Available from: 2018-05-08 Created: 2018-05-08 Last updated: 2018-05-08Bibliographically approved
Naidoo, T., Sjödin, P., Schlebusch, C. & Jakobsson, M. (2018). Patterns of variation in cis-regulatory regions: examining evidence of purifying selection. BMC Genomics, 19, Article ID 95.
Open this publication in new window or tab >>Patterns of variation in cis-regulatory regions: examining evidence of purifying selection
2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 95Article in journal (Refereed) Published
Abstract [en]

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

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

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

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD, 2018
Keywords
Regulatory regions, Purifying selection, Selection efficacy, Non-coding DNA, Functional elements, Population genetics
National Category
Genetics Developmental Biology
Identifiers
urn:nbn:se:uu:diva-343792 (URN)10.1186/s12864-017-4422-y (DOI)000423443900002 ()29373957 (PubMedID)
Funder
Göran Gustafsson Foundation for Research in Natural Sciences and MedicineKnut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2018-03-05 Created: 2018-03-05 Last updated: 2018-09-28Bibliographically approved
Schlebusch, C. & Jakobsson, M. (2018). Tales of Human Migration, Admixture, and Selection in Africa. Annual review of genomics and human genetics (Print), 19, 405-428
Open this publication in new window or tab >>Tales of Human Migration, Admixture, and Selection in Africa
2018 (English)In: Annual review of genomics and human genetics (Print), ISSN 1527-8204, E-ISSN 1545-293X, Vol. 19, p. 405-428Article in journal (Refereed) Published
Abstract [en]

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

Place, publisher, year, edition, pages
ANNUAL REVIEWS, 2018
Keywords
Africa, human history, farming, human migration, admixture, population structure, human emergence
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-364846 (URN)10.1146/annurev-genom-083117-021759 (DOI)000443936800018 ()29727585 (PubMedID)
Available from: 2019-02-05 Created: 2019-02-05 Last updated: 2019-02-05Bibliographically approved
Owers, K. A., Sjödin, P., Schlebusch, C. M., Skoglund, P., Soodyall, H. & Jakobsson, M. (2017). Adaptation to infectious disease exposure in indigenous Southern African populations. Proceedings of the Royal Society of London. Biological Sciences, 284(1852), Article ID 20170226.
Open this publication in new window or tab >>Adaptation to infectious disease exposure in indigenous Southern African populations
Show others...
2017 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1852, article id 20170226Article in journal (Refereed) Published
Abstract [en]

Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the double dagger Khomani who had abundant contact with other people migrating into the region and the more isolated Ju vertical bar'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the double dagger Khomani than in the Ju vertical bar'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the double dagger Khomani, whereas in the Juj'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the double dagger Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.

Place, publisher, year, edition, pages
ROYAL SOC, 2017
Keywords
population genetics, human migrations, introduced diseases, immune genes, adaptation
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-322185 (URN)10.1098/rspb.2017.0226 (DOI)000399294100022 ()28381615 (PubMedID)
Funder
Wenner-Gren FoundationsGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyKnut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2017-05-17 Created: 2017-05-17 Last updated: 2017-05-17Bibliographically 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
Hollfelder, N., Schlebusch, C. M., Günther, T., Babiker, H., Hassan, H. Y. & Jakobsson, M. (2017). Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLOS Genetics, 13(8), Article ID e1006976.
Open this publication in new window or tab >>Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
Show others...
2017 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 8, article id e1006976Article in journal (Refereed) Published
Abstract [en]

Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gateway out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping similar to 3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2017
National Category
Genetics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-333162 (URN)10.1371/journal.pgen.1006976 (DOI)000408763800042 ()28837655 (PubMedID)
Available from: 2017-11-07 Created: 2017-11-07 Last updated: 2017-12-13Bibliographically 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
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
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-8160-9621

Search in DiVA

Show all publications