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Resequencing Data Provide No Evidence for a Human Bottleneck in Africa during the Penultimate Glacial Period
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
2012 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 7, 1851-1860 p.Article in journal (Refereed) Published
Abstract [en]

Based on the accumulation of genetic, climatic, and fossil evidence, a central theory in paleoanthropology stipulates that a demographic bottleneck coincided with the origin of our species Homo Sapiens. This theory proposes that anatomically modern humans-which were only present in Africa at the time-experienced a drastic bottleneck during the penultimate glacial age (130-190 kya) when a cold and dry climate prevailed. Two scenarios have been proposed to describe the bottleneck, which involve either a fragmentation of the range occupied by humans or the survival of one small group of humans. Here, we analyze DNA sequence data from 61 nuclear loci sequenced in three African populations using Approximate Bayesian Computation and numerical simulations. In contrast to the bottleneck theory, we show that a simple model without any bottleneck during the penultimate ice age has the greatest statistical support compared with bottleneck models. Although the proposed bottleneck is ancient, occurring at least 130 kya, we can discard the possibility that it did not leave detectable footprints in the DNA sequence data except if the bottleneck involves a less than a 3-fold reduction in population size. Finally, we confirm that a simple model without a bottleneck is able to reproduce the main features of the observed patterns of genetic variation. We conclude that models of Pleistocene refugium for modern human origins now require substantial revision.

Place, publisher, year, edition, pages
2012. Vol. 29, no 7, 1851-1860 p.
Keyword [en]
human origins, African genetic diversity, penultimate glacial age, approximate Bayesian computation, African bottleneck, oxygen isotope 6
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-177576DOI: 10.1093/molbev/mss061ISI: 000305409000015OAI: oai:DiVA.org:uu-177576DiVA: diva2:541245
Available from: 2012-07-16 Created: 2012-07-16 Last updated: 2015-11-10Bibliographically approved
In thesis
1. Origins and Adaptation in Humans: A Case Study of Taste and Lifestyle
Open this publication in new window or tab >>Origins and Adaptation in Humans: A Case Study of Taste and Lifestyle
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, I use population genetics and statistical approaches to investigate early human demography, infer local adaptation in diverse sets of populations, and study the genetic basis for taste perception.

In the first paper, I examine the genomic evidence for a severe bottleneck, which has been suggested based on paleontological and climate studies to coincide with the emergence of anatomically modern humans. Using a Bayesian approach, I evaluate the genetic evidence of a bottleneck between 190,000 and 130,000 years ago and find that the data is in favor of a model without bottleneck at this time point.

I further develop a method to detect local adaptation based on frequencies of private haplotypes. I first show, using simulated data, that this method can detect local adaption. Applied to large-scale human genotype data, this method detects known signals of positive selection in human data such as the positive selection around the lactase gene in Europeans and East Africans. Also, this method permits to improve knowledge on potential adaptation events in humans as it finds several regions potentially selected that were not previously described. I further investigate patterns of adaptation in whole genome data based on a diverse set of African populations. The results from the regions potentially selected show that diet and pathogens are the common driving forces of adaptation in all studied populations.

There is evidence that taste perception have evolved in concert with diet, environment, and the organismal needs in humans. For this reason, I study taste perception in populations differing on lifestyle (hunter-gatherers, farmers and nomad herders). I present taste perception phenotypes for all tastes (sweet, bitter, sour, salty and umami) and relate them to high density genotype data. I show that taste and taste-involved genes have evolved with lifestyle. By performing an association study, I also show that variation in taste perception involves more genes than only the taste receptors genes.

In this thesis, by analyzing human genetic data with a population genetics approaches, I covered several topics of human ancient demography and adaptation and show the utility of using large-scale genetic data to better understand human history.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2015. 88 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1295
National Category
Evolutionary Biology
Research subject
Evolutionary Genetics
urn:nbn:se:uu:diva-263085 (URN)978-91-554-9350-9 (ISBN)
Public defence
2015-11-20, Salle informatique E1, 17 Place du Trocadéro, Paris, 14:00 (English)
Available from: 2015-10-29 Created: 2015-09-25 Last updated: 2016-01-28

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Sjödin, PerSjöstrand, Agnès E.Jakobsson, Mattias
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