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PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers
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, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, 1058-1072 p.Article, review/survey (Refereed) PublishedText
Abstract [en]

Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have previously been hindered by a lack of means and genetic data to model changes in effective population size (N-e) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in N-e over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black-and-white flycatchers. N-e curves of Atlas, collared, pied and semicollared flycatcher converged 1-2million years ago (Ma) at an N-e of approximate to 200000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate N-e trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100-200thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in N-e differed among species, and for pied flycatcher, the temporal dynamics of N-e differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of 18X, a per-site filter of 10 reads and no more than 25% of missing data.

Place, publisher, year, edition, pages
2016. Vol. 25, no 5, 1058-1072 p.
Keyword [en]
Atlas flycatcher, collared flycatcher, coverage, effective population size, pied flycatcher, PSMC, semicollared flycatcher, whole-genome sequencing
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-294812DOI: 10.1111/mec.13540ISI: 000371433400004PubMedID: 26797914OAI: oai:DiVA.org:uu-294812DiVA: diva2:954060
Funder
Swedish Research Council, 2007-8731 2010-5650 2013-8271Knut and Alice Wallenberg FoundationEU, European Research Council, AdG 249976
Available from: 2016-08-19 Created: 2016-05-27 Last updated: 2016-08-19Bibliographically approved

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Nadachowska-Brzyska, KrystynaSmeds, LinneaEllegren, Hans
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