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. 2016 Mar;25(5):1058-72.
doi: 10.1111/mec.13540. Epub 2016 Feb 15.

PSMC Analysis of Effective Population Sizes in Molecular Ecology and Its Application to Black-And-White Ficedula Flycatchers

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Free PMC article

PSMC Analysis of Effective Population Sizes in Molecular Ecology and Its Application to Black-And-White Ficedula Flycatchers

Krystyna Nadachowska-Brzyska et al. Mol Ecol. .
Free PMC article

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 pied flycatcher, the temporal dynamics of Ne 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.

Keywords: Atlas flycatcher; PSMC; collared flycatcher; coverage; effective population size; pied flycatcher; semicollared flycatcher; whole-genome sequencing.

Figures

Figure 1
Figure 1
Range distributions of the four black‐and‐white Ficedula species: pied flycatcher (green), collared flycatcher (violet), semicollared flycatcher (red) and Atlas flycatcher (yellow). Black circles indicate sampling locations.
Figure 2
Figure 2
Influence of different per‐site filtering regimes on PSMC plots for example individuals with high (A; coverage 23) and low (B; coverage 8) mean genomewide coverage. Colours of the lines indicate filtering thresholds: no filtering (red), read depth ≥1/3 of the average read depth (green), read depth ≥6 (blue) and read depth ≥10 (violet). Note that each panel shows data from a single individual subject to different filtering thresholds.
Figure 3
Figure 3
PSMC results for a test population of collared flycatcher. The numbers in figure legend indicate mean genomewide coverage with percentage of missing data in brackets.
Figure 4
Figure 4
Correlations between maximum N e estimate and mean genomewide coverage (A), timing of the maximum N e estimate and mean coverage (B), maximum N e estimate and percentage of missing data (C), and percentage of missing data and mean coverage (D).
Figure 5
Figure 5
PSMC estimates of the changes in effective population size over time for four populations of collared flycatcher. Each line represents one individual and only individuals with no more than 25% of missing data and a mean genomewide coverage of ≥18X are included (Italy, n = 4; Hungary, n = 2; Czech Republic, n = 5; Baltic Sea, n = 8).
Figure 6
Figure 6
PSMC estimates of the changes in effective population size over time for four populations of pied flycatcher. Each line represents one individual and only individuals with no more than 25% of missing data and a mean genomewide coverage of ≥18X are included (Spain, n = 2; Sweden, n = 8; Czech Republic, n = 2; Baltic Sea, n = 1).
Figure 7
Figure 7
PSMC estimates of the changes in effective population size over time for four black‐and‐white Ficedula species.
Figure 8
Figure 8
PSMC estimates of changes in the effective population size over time for four Ficedula flycatcher species, with bootstrap results indicated with thin lines.

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