Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1949

Human demographic history

Insights on the human past based on genomes from Southern through Central Africa

GWENNA BRETON

ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-0979-8 UPPSALA urn:nbn:se:uu:diva-416653 2020 Dissertation presented at Uppsala University to be publicly examined in Ekmansalen, EBC, Norbyvägen 14, Uppsala, Friday, 18 September 2020 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor David Comas (Universitat Pompeu Fabra, Barcelona, Spain).

Abstract Breton, G. 2020. Human demographic history. Insights on the human past based on genomes from Southern through Central Africa. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1949. 112 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0979-8.

Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming. I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution. I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-like. The estimated times for the admixture between a presumably local hunter-gatherer population and incoming agropastoralist groups are consistent with archaeological records. In this thesis, I investigated questions related to human history in Sub-Saharan Africa, from the emergence of modern humans ~300 kya to recent events related to the expansion of farming.

Keywords: high-coverage genomes, Sub-Saharan Africa, demography, genetic admixture, population genetics, human evolutionary genetics, Khoe-San, rainforest hunter-gatherers

Gwenna Breton, Department of Organismal Biology, Human Evolution, Norbyvägen 18 A, Uppsala University, SE-752 36 Uppsala, Sweden.

© Gwenna Breton 2020

ISSN 1651-6214 ISBN 978-91-513-0979-8 urn:nbn:se:uu:diva-416653 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416653) 3RXU $PDQGLQH TX¶LO PH WDUGH GH UHQFRQWUHU HW SRXU PD 0DPLH TX¶LO PH WDUGH GH UHYRLU

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Second axis of variance population Describe genetic diversity population populations and First axis of variance

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Bi.Aka Mbati + Biaka Speakers of Bangu C10. Both populations live in association with the Mbati-farmers, but the Bi.Aka Mbati, or Mbati-hunter gatherers, are closer. Hypothesis: more gene
ow in the Bi.Aka Mbati?

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Scenario 1b Scenario 1c

tKPNP >>>tPNP tK1 tP1 tKPNP >>tK1 tPNP >tP1 Time Time

N A NA

tKPNP tKPNP

tadAK-APNP tadAK-APNP

NAPNP NAPNP Rainforest hunter- NAK NAK t gatherer neighbours tPNP K1 Western rainforest NAP tad AK-NP tad hunter-gatherers Eastern rainforest SK-APNP tadAK-AP tadNK-APNP tad hunter-gatherers NP-AP

NNP tPNP

tadNP-AP tK1

tadSK-NP N AP tadSK-NP Northern tad NK-NP tadNK-NP

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Southern tadNP-EP tadNP-EP

tadWP-EP Khoe-San tadWP-EP

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Acta Universitatis Upsaliensis Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1949 Editor: The Dean of the Faculty of Science and Technology

A doctoral dissertation from the Faculty of Science and Technology, Uppsala University, is usually a summary of a number of papers. A few copies of the complete dissertation are kept at major Swedish research libraries, while the summary alone is distributed internationally through the series Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology. (Prior to January, 2005, the series was published under the title “Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology”.)

ACTA UNIVERSITATIS UPSALIENSIS Distribution: publications.uu.se UPPSALA urn:nbn:se:uu:diva-416653 2020