ArticleMolecular ecology2016
PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers.
Article in Molecular ecology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
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Who cites it
147 citing papers in PubMed.
- Article
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- Long-term small effective population size, inbreeding, and a recessive lethal haplotype drive premature death in the endangered Devils Hole pupfish (bioRxiv : the preprint server for biology · 2026Article
- Assembled and annotated reference genome and demographic history of the eastern chipmunk (Tamias striatus).Molecular genetics and genomics : MGG · 2026Article
- Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii).Genome biology and evolution · 2026Article
- PSMC-FAC: Automated Optimization of False-Negative Rate Corrections for Low-Coverage PSMC-Based Demographic Inference.Biology · 2026Article
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea.Molecular ecology · 2025Article
- Genome-Wide Population Structure in a Marine Keystone Species, the European Flat Oyster (Ostrea edulis).Molecular ecology · 2025Article
- Genome assembly and insights into globally invasive Red-vented Bulbul (Pycnonotus cafer).DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Whole genome sequencing and resequencing provide insight into the genetic structure of wild Ophiocordyceps sinensis.BMC genomics · 2025Article
- Museum genomics suggests long-term population decline in a putatively extinct bumble bee.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Conservation genomics of two endangered buntings reveal genetic diversity before and after severe population declines.BMC biology · 2025Article
- Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers.Molecular ecology · 2025Article
- Chromosome-level genome assembly of Ulmus parvifolia identifies genomic signatures and transcriptional profiling underlying Dutch elm disease resistance.BMC plant biology · 2025Article
- Mismatch in reindeer resilience to past and future warming signals ongoing declines.Science advances · 2025Article
- A genomic test of sex-biased dispersal in white sharks.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Inter-Island Whole-Genome Comparison Reveals Micro-Evolutionary Dynamics of the Red Fox, Stimulated Through Post-Glacial Sea-Level Alterations.Genome biology and evolution · 2025Article
- Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species.Molecular ecology · 2025Article
- Article
87 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
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.
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