PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers

Molecular Ecology
Krystyna Nadachowska-BrzyskaHans Ellegren

Abstract

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 (Ne ) 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 Ne 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. Ne curves of Atlas, collared, pied and semicollared flycatcher converged 1-2 million years ago (Ma) at an Ne of ≈ 200 000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate Ne trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100-200 thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in Ne differed among species, and for pie...Continue Reading

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Nov 15, 2016·Nature Reviews. Genetics·Jochen B W Wolf, Hans Ellegren
Mar 21, 2017·Trends in Parasitology·Janneke Wit, John S Gilleard
Oct 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·Andrea BenazzoGiorgio Bertorelle
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Jan 18, 2019·Molecular Ecology·Krystyna Nadachowska-BrzyskaHans Ellegren
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Apr 22, 2020·ELife·Kira DelmoreMiriam Liedvogel
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Feb 26, 2019·Nature Ecology & Evolution·Patrick MonnahanLevi Yant

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Software Mentioned

fastq
PSMC
samtools
gatk

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