ArticleMolecular biology and evolution2014
Genome scans for detecting footprints of local adaptation using a Bayesian factor model.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed.
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- The interplay among space, environment, and gene flow drives genetic differentiation in endemic Baja California Agave sobria subspecies.American journal of botany · 2025Article
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- Reversing the decline of threatened koala (Ecology and evolution · 2024Article
- Genome-environment association analyses reveal geographically restricted adaptive divergence across the range of the widespread Eurasian carnivoreEvolutionary applications · 2023Article
- Detection of the local adaptive and genome-wide associated loci in southeast Nigerian taro (Colocasia esculenta (L.) Schott) populations.BMC genomics · 2023Article
- Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad (Evolutionary applications · 2023Article
- Impact of roadside burning on genetic diversity in a high-biomass invasive grass.Evolutionary applications · 2022Article
- Parallel adaptation prompted core-periphery divergence ofFrontiers in plant science · 2022Article
- The genomes of ancient date palms germinated from 2,000 y old seeds.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Genome scans for selection and introgression based on k-nearest neighbour techniques.Molecular ecology resources · 2020Article
- Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis.Nature microbiology · 2020Article
- Global gene flow releases invasive plants from environmental constraints on genetic diversity.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Adaptive signals of flowering time pathways in wild barley from Israel over 28 generations.Heredity · 2020Article
- Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication.The Plant journal : for cell and molecular biology · 2019Article
- The Effect of Neutral Recombination Variation on Genome Scans for Selection.G3 (Bethesda, Md.) · 2019Article
- Partitioning genetic and species diversity refines our understanding of species-genetic diversity relationships.Ecology and evolution · 2018Article
- Whole-genome sequencing reveals new insights into age-related hearing loss: cumulative effects, pleiotropy and the role of selection.European journal of human genetics : EJHG · 2018Article
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3 authors.
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Abstract
There is a considerable impetus in population genomics to pinpoint loci involved in local adaptation. A powerful approach to find genomic regions subject to local adaptation is to genotype numerous molecular markers and look for outlier loci. One of the most common approaches for selection scans is based on statistics that measure population differentiation such as FST. However, there are important caveats with approaches related to FST because they require grouping individuals into populations and they additionally assume a particular model of population structure. Here, we implement a more flexible individual-based approach based on Bayesian factor models. Factor models capture population structure with latent variables called factors, which can describe clustering of individuals into populations or isolation-by-distance patterns. Using hierarchical Bayesian modeling, we both infer population structure and identify outlier loci that are candidates for local adaptation. In order to identify outlier loci, the hierarchical factor model searches for loci that are atypically related to population structure as measured by the latent factors. In a model of population divergence, we show that it can achieve a 2-fold or more reduction of false discovery rate compared with the software BayeScan or with an FST approach. We show that our software can handle large data sets by analyzing the single nucleotide polymorphisms of the Human Genome Diversity Project. The Bayesian factor model is implemented in the open-source PCAdapt software.
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