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Where our feet have taken us: Examples of human contact, migration, and adaptation as revealed by ancient DNA
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.ORCID iD: 0000-0002-1756-9469
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In spite of our extensive knowledge of the human past, certain key questions remain to be answered about human prehistory. One involves the nature of cultural change in material culture through time from the perspective of how different ancient human groups interacted with one another. The other is how humans have adapted to the different environments as they migrated and populated the rest of the world from their origin in Africa. For my thesis I have investigated examples of human evolutionary history using genetic information from ancient human remains. Chapter 1 focused on the nature of possible interaction between the Pitted Ware Culture (PWC) and Battle Axe Culture (BAC) on the island of Gotland, in the Baltic Sea. Through the analysis of 4500 year old human remains from three PWC burial sites, I found that the existence of BAC influences in these burial sites was the result of cultural and not demic influence from the BAC. In chapter 2, I investigated the ancestry of a Late Stone Age individual from the southwestern Cape of South Africa. Population genetic analyses revealed that this individual was genetically affiliated with Khoe groups in southern Africa, a genetic make-up that is today absent from the Cape. Chapter 3 investigated the genetic landscape of prehistoric individuals from southern Africa. Specifically, I explored frequencies of adaptive variants between Late Stone Age and Iron Age individuals. I found an increase in disease resistance alleles in Iron Age individuals and attributed this to the effects of the Bantu expansion. Chapter 4 incorporated a wider range of trait-associated variants among a greater number of modern-day populations and ancient individuals in Africa. I found that many allele frequency patterns found in modern populations follow the routes of major migrations which took place in the African Holocene. The thesis attests to the complexity of human demographic history in general, and how migration contributes to adaptation by dispersing novel adaptive variants to populations.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. , p. 78
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1880
Keywords [en]
Human demography, migration, adaptation, human contact, ancient DNA, human evolution, African prehistory, Scandinavian prehistory
National Category
Evolutionary Biology
Research subject
Biology with Specialisation in Human Evolution and Genetics
Identifiers
URN: urn:nbn:se:uu:diva-397222ISBN: 978-91-513-0815-9 (print)OAI: oai:DiVA.org:uu-397222DiVA, id: diva2:1371017
Public defence
2020-01-17, Lindahlsalen, Evolutionary Biology Centre EBC, Norbyvagen 18, 75236, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2019-12-16 Created: 2019-11-18 Last updated: 2020-01-13
List of papers
1. The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
Open this publication in new window or tab >>The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The 3rd millennium BCE was a period of marked cultural and demographic developments in Europe. Here we sequence genome data from human skeletal remains to study the interaction between two Scandinavian cultures; the hunter-gatherer Pitted Ware culture (PWC, 3400-2400 BCE) and the farmer/herder Battle Axe culture (BAC, 2800-2300 BCE), two cultures who have been found to be represented by distinct gene-pools in northern Europe. We focus on the Baltic island of Gotland that presents Scandinavia’s richest record of PWC gravesites where the majority of individuals are buried in typical PWC manner (supine position), but with some burials indicating BAC influences (either hocker position burial or burials with BAC associated artifacts). We sequenced and analyzed the genomes of 25 individuals of both types of burials excavated in three gravesites in order to determine if the different burial styles were associated with the different gene-pools (PWC or BAC) at the time. The genomic data show that all individuals belonged to one genetic population – that of the PWC – irrespective of the burial style. We conclude that the PWC communities on the island of Gotland were culturally influenced by the BAC society, without any signs of gene-flow.

National Category
Evolutionary Biology
Research subject
Biology with Specialisation in Human Evolution and Genetics
Identifiers
urn:nbn:se:uu:diva-397180 (URN)
Funder
Swedish Research Council, 2017-02503
Available from: 2019-11-17 Created: 2019-11-17 Last updated: 2019-11-18
2. Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
Open this publication in new window or tab >>Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting to arrive some 400 years ago and their descendants are today mixed with Europeans and Asians. Here we sequence and analyze the genome (1.01 times coverage) of a Later Stone Age individual, who lived about 200 years ago, obtained from a hair sample excavated at Vaalkrans Shelter southern Cape, South Africa. We analyzed this genome, along with genetic data from 10 prehistoric individuals from southern Africa spanning the last 2000 years. Our results show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherer populations, and ~20% to a mixed East African-Eurasian source. This genetic make-up is very similar to modern-day Khoekhoe individuals from South Africa and Namibia. The Vaalkrans man’s genome reveals how the Holocene pastoralist migration event shaped the genomic landscape of historic and current southern African populations and shows that Khoekhoe groups lived in the southern Cape as late as 200 years ago.

National Category
Evolutionary Biology
Research subject
Biology with Specialisation in Human Evolution and Genetics
Identifiers
urn:nbn:se:uu:diva-397032 (URN)
Available from: 2019-11-18 Created: 2019-11-18 Last updated: 2019-11-18
3. 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
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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: 2019-11-18Bibliographically approved
4. The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
Open this publication in new window or tab >>The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.

National Category
Evolutionary Biology
Research subject
Biology with Specialisation in Human Evolution and Genetics
Identifiers
urn:nbn:se:uu:diva-397169 (URN)
Available from: 2019-11-16 Created: 2019-11-16 Last updated: 2019-11-18

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