ArticleGenetics2010
Optimal neutrality tests based on the frequency spectrum.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Maternal haplotype diversity and phylogenetic relationships of Damascus, Kilis, Hatay, and Kil goat breeds: insight from mtDNA D-loop sequences in the Fertile Crescent.Archives animal breeding · 2025Article
- Statistical summaries of unlabelled evolutionary trees.Biometrika · 2024Article
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- Approximations to the expectations and variances of ratios of tree properties under the coalescent.G3 (Bethesda, Md.) · 2022Article
- A compendium of covariances and correlation coefficients of coalescent tree properties.Theoretical population biology · 2022Article
- Genomic Diversity and Evolution of Quasispecies in Newcastle Disease Virus Infections.Viruses · 2020Article
- Chromoblastomycosis in an Endemic Area of Brazil: A Clinical-Epidemiological Analysis and a Worldwide Haplotype Network.Journal of fungi (Basel, Switzerland) · 2020Article
- Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.PLoS computational biology · 2019Article
- Evolutionary and functional impact of common polymorphic inversions in the human genome.Nature communications · 2019Article
- Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree.Genetics · 2018Article
- The Site Frequency/Dosage Spectrum of Autopolyploid Populations.Frontiers in genetics · 2018Article
- Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.Genetics · 2018Article
- Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests.Genetics · 2017Article
- The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.G3 (Bethesda, Md.) · 2015Article
- Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation.PLoS computational biology · 2013Article
- Neutrality tests for sequences with missing data.Genetics · 2012Article
Corrections and comments
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The ascertainment of the demographic and selective history of populations has been a major research goal in genetics for decades. To that end, numerous statistical tests have been developed to detect deviations between expected and observed frequency spectra, e.g., Tajima's D, Fu and Li's F and D tests, and Fay and Wu's H. Recently, Achaz developed a general framework to generate tests that detect deviations in the frequency spectrum. In a further development, we argue that the results of these tests should be as independent on the sample size as possible and propose a scale-free form for them. Furthermore, using the same framework as that of Achaz, we develop a new family of neutrality tests based on the frequency spectrum that are optimal against a chosen alternative evolutionary scenario. These tests maximize the power to reject the standard neutral model and are scalable with the sample size. Optimal tests are derived for several alternative evolutionary scenarios, including demographic processes (population bottleneck, expansion, contraction) and selective sweeps. Within the same framework, we also derive an optimal general test given a generic evolutionary scenario as a null model. All formulas are relatively simple and can be computed very fast, making it feasible to apply them to genome-wide sequence data. A simulation study showed that, generally, the tests proposed are more consistently powerful than standard tests like Tajima's D. We further illustrate the method with real data from a QTL candidate region in pigs.
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