ArticleGenetics2009
The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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Who cites it
99 citing papers in PubMed.
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- Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot.Systematic biology · 2024Article
- Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans.Genome biology and evolution · 2024Article
- Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.bioRxiv : the preprint server for biology · 2023Article
- Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates.Genome biology and evolution · 2023Article
- The design of mapping populations: Impacts of geographic scale on genetic architecture and mapping efficacy for defense and immunity.Current opinion in plant biology · 2023Review
- Recurrent mutation in the ancestry of a rare variant.Genetics · 2023Article
- Genetic decline and recovery of a demographically rebuilt fishery species.Molecular ecology · 2022Article
- Evolutionary Genomics of a Subdivided Species.Molecular biology and evolution · 2022Article
39 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using coalescent simulations, we study the impact of three different sampling schemes on patterns of neutral diversity in structured populations. Specifically, we are interested in two summary statistics based on the site frequency spectrum as a function of migration rate, demographic history of the entire substructured population (including timing and magnitude of specieswide expansions), and the sampling scheme. Using simulations implementing both finite-island and two-dimensional stepping-stone spatial structure, we demonstrate strong effects of the sampling scheme on Tajima's D (D(T)) and Fu and Li's D (D(FL)) statistics, particularly under specieswide (range) expansions. Pooled samples yield average D(T) and D(FL) values that are generally intermediate between those of local and scattered samples. Local samples (and to a lesser extent, pooled samples) are influenced by local, rapid coalescence events in the underlying coalescent process. These processes result in lower proportions of external branch lengths and hence lower proportions of singletons, explaining our finding that the sampling scheme affects D(FL) more than it does D(T). Under specieswide expansion scenarios, these effects of spatial sampling may persist up to very high levels of gene flow (Nm > 25), implying that local samples cannot be regarded as being drawn from a panmictic population. Importantly, many data sets on humans, Drosophila, and plants contain signatures of specieswide expansions and effects of sampling scheme that are predicted by our simulation results. This suggests that validating the assumption of panmixia is crucial if robust demographic inferences are to be made from local or pooled samples. However, future studies should consider adopting a framework that explicitly accounts for the genealogical effects of population subdivision and empirical sampling schemes.
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