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Human Demographic History 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 /LVW RI SDSHUV 7KLV WKHVLV LV EDVHG RQ WKH IROORZLQJ SDSHUV ZKLFK DUH UHIHUUHG WR LQ WKH WH[W E\ WKHLU 5RPDQ QXPHUDOV , 6FKOHEXVFK &0 6M|GLQ 3 %UHWRQ * *QWKHU 7 1DLGRR 7 +ROOIHOGHU 1 6M|VWUDQG $( ;X - *DWWHSDLOOH /0 9LFHQWH 0 6FRILHOG '* 0DOPVWU|P + GH -RQJK 0 /RPEDUG 0 6RRG\DOO + -DNREVVRQ 0 .KRH6DQ *HQRPHV 5HYHDO 8QLTXH 9DULDWLRQ DQG &RQILUP WKH 'HHSHVW 3RSXODWLRQ 'LYHUJHQFH LQ +RPR VDSLHQV 0ROHFXODU %LRORJ\ DQG (YROXWLRQ LQ SUHVV ,, %UHWRQ * -RKDQVVRQ $ 6M|GLQ 3 6FKOHEXVFK &0 -DNREVVRQ 0 &RPSDULVRQ RI VHTXHQFLQJ GDWD SURFHVVLQJ SLSHOLQHV DQG DSSOLFDWLRQ WR XQGHUUHSUHVHQWHG KXPDQ SRSXODWLRQV 8QGHU UHYLHZ ,,, %UHWRQ * 6M|GLQ 3 =HUYDNLV 3, /DXUHQW 5 6M|VWUDQG $( +HZOHWW %6 %DUUHLUR /% 3HUU\ *+ 6RRG\DOO + +H\HU ( 6FKOHEXVFK &0 9HUGX 3 -DNREVVRQ 0 'HFLSKHULQJ HDUO\ KXPDQ KLVWRU\ XVLQJ $SSUR[LPDWH %D\HVLDQ &RPSXWDWLRQ DQG ZKROH JHQRPHV IURP &HQWUDO DQG 6RXWKHUQ $IULFD 0DQXVFULSW ,9 %UHWRQ * %DUKDP / 0XGHQGD * 6RRG\DOO + 6FKOHEXVFK &0 -DNREVVRQ 0 7KH ³%D7ZD´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±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pVXPp HQ IUDQoDLV $FNQRZOHGJPHQWV 5HIHUHQFHV $EEUHYLDWLRQV $%& $SSUR[LPDWH %D\HVLDQ &RPSXWDWLRQ $' $QQR GRPLQL D'1$ DQFLHQW '1$ $0+ $QDWRPLFDOO\ PRGHUQ KXPDQV ES %DVH SDLU %465 %DVH TXDOLW\ VFRUH UHFDOLEUDWLRQ &$5 &HQWUDO $IULFDQ 5HSXEOLF &19 &RS\QXPEHU YDULDWLRQ '5& 'HPRFUDWLF 5HSXEOLF RI WKH &RQJR *$7. *HQRPH $QDO\VLV 7RRONLW +*'3 +XPDQ *HQRPH 'LYHUVLW\ 3URMHFW +76 +LJKWKURXJKSXW VHTXHQFLQJ +:( +DUG\:HLQEHUJ HTXLOLEULXP .6 .
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