ArticleG3 (Bethesda, Md.)2016
New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era.
Article in G3 (Bethesda, Md.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed.
- Presence of recombination hotspots throughout SLC6A3.PloS one · 2019Trial
- Evolution and domestication-trait associations of ultra-long centromere haplotypes in pepper plants.Nature ecology & evolution · 2026Article
- Spatial inference of ancestor locations suggests northern refugia for canopy-forming kelps in the Pacific Northwest.The New phytologist · 2026Article
- Constitution and function of intergenic genome regions in cultivated versus annual wild soybean in China.Journal of integrative plant biology · 2026Article
- Local adaptation sustains genetic differentiation between two varieties of Chinese walnut (Plant diversity · 2026Article
- Mapping structural variants in Populus tomentosa reveals adaptive signatures and improves prediction of wood properties.Nature communications · 2026Article
- Ultrarapid MC1R protein and associated plumage color evolution in the domestic chicken.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Ancient but dynamic: structural expansion, massive gene duplication, and transposable element colonization in a supergene controlling ant social organization.Molecular biology and evolution · 2026Article
- Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding.Nature communications · 2026Article
- Recombination shapes the diversification of theeLife · 2026Article
- Dynamic body size evolution during speciation of predatory cichlid fishes in the Lake Malawi superradiation.Genome research · 2026Article
- Population genomics reveals population structure, glacial divergence, and intertidal adaptation in the Chinese chiton (Liolophura sinensis).Communications biology · 2026Article
- Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding.The plant genome · 2026Article
- Unidirectional genomic introgression facilitates the colonization of an invasive orchid in arid, metal-enriched sedimentary habitats.Plant communications · 2026Article
- Mixed Outcomes in Recombination Rates After Domestication: Revisiting Theory and Data.Molecular ecology · 2025Review
- Genomic Insights into the Origin, High Fecundity and Environmental Adaptation of Hu Sheep.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Genomic introgression underlies environmental adaptation in three species of Chinese wingnuts,Plant diversity · 2025Article
- Standing genetic variation and introgression shape the cryptic radiation of Aquilegia in the mountains of Southwest China.Communications biology · 2025Article
- Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.Genetics · 2025Article
29 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Genetic recombination is a very important evolutionary mechanism that mixes parental haplotypes and produces new raw material for organismal evolution. As a result, information on recombination rates is critical for biological research. In this paper, we introduce a new extremely fast open-source software package (FastEPRR) that uses machine learning to estimate recombination rate [Formula: see text] (=[Formula: see text]) from intraspecific DNA polymorphism data. When [Formula: see text] and the number of sampled diploid individuals is large enough ([Formula: see text]), the variance of [Formula: see text] remains slightly smaller than that of [Formula: see text] The new estimate [Formula: see text] (calculated by averaging [Formula: see text] and [Formula: see text]) has the smallest variance of all cases. When estimating [Formula: see text], the finite-site model was employed to analyze cases with a high rate of recurrent mutations, and an additional method is proposed to consider the effect of variable recombination rates within windows. Simulations encompassing a wide range of parameters demonstrate that different evolutionary factors, such as demography and selection, may not increase the false positive rate of recombination hotspots. Overall, accuracy of FastEPRR is similar to the well-known method, LDhat, but requires far less computation time. Genetic maps for each human population (YRI, CEU, and CHB) extracted from the 1000 Genomes OMNI data set were obtained in less than 3 d using just a single CPU core. The Pearson Pairwise correlation coefficient between the [Formula: see text] and [Formula: see text] maps is very high, ranging between 0.929 and 0.987 at a 5-Mb scale. Considering that sample sizes for these kinds of data are increasing dramatically with advances in next-generation sequencing technologies, FastEPRR (freely available at http://www.picb.ac.cn/evolgen/) is expected to become a widely used tool for establishing genetic maps and studying recombination hotspots in the population genomic era.
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