ArticleMolecular ecology2014
Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population.
Article in Molecular ecology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 47 citations in OpenAlex.
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- The role of neutral and adaptive evolutionary processes on patterns of genetic diversity across small cave-dwelling populations of Icelandic Arctic charr (Ecology and evolution · 2024Article
- Balancing selection and the functional effects of shared polymorphism in crypticbioRxiv : the preprint server for biology · 2024Article
- Go west: Population genomics reveals unexpected population fluctuations and little gene flow in Western hemisphere populations of the predatory lady beetle,Evolutionary applications · 2024Article
- The genomic footprint of whaling and isolation in fin whale populations.Nature communications · 2023Article
- Genetic decline and recovery of a demographically rebuilt fishery species.Molecular ecology · 2022Article
- Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene).Molecular ecology · 2020Article
- Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection.Heredity · 2020Article
- GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.GigaScience · 2020Article
- Estimation of contemporary effective population size and population declines using RAD sequence data.Heredity · 2018Article
- Article
- Genomic data reveal a loss of diversity in two species of tuco-tucos (genus Ctenomys) following a volcanic eruption.Scientific reports · 2017Article
- Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories.G3 (Bethesda, Md.) · 2017Article
- Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex.Molecular ecology · 2017Article
- Patterns of Genome-Wide Diversity and Population Structure in the Drosophila athabasca Species Complex.Molecular biology and evolution · 2017Article
- Partner-Drug Resistance and Population Substructuring of Artemisinin-Resistant Plasmodium falciparum in Cambodia.Genome biology and evolution · 2017Article
- Fast diffusion of domesticated maize to temperate zones.Scientific reports · 2017Article
- Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations.Molecular ecology resources · 2015Article
- Sampling strategies for frequency spectrum-based population genomic inference.BMC evolutionary biology · 2014Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
The analysis of molecular data from natural populations has allowed researchers to answer diverse ecological questions that were previously intractable. In particular, ecologists are often interested in the demographic history of populations, information that is rarely available from historical records. Methods have been developed to infer demographic parameters from genomic data, but it is not well understood how inferred parameters compare to true population history or depend on aspects of experimental design. Here, we present and evaluate a method of SNP discovery using RNA sequencing and demographic inference using the program δaδi, which uses a diffusion approximation to the allele frequency spectrum to fit demographic models. We test these methods in a population of the checkerspot butterfly Euphydryas gillettii. This population was intentionally introduced to Gothic, Colorado in 1977 and has as experienced extreme fluctuations including bottlenecks of fewer than 25 adults, as documented by nearly annual field surveys. Using RNA sequencing of eight individuals from Colorado and eight individuals from a native population in Wyoming, we generate the first genomic resources for this system. While demographic inference is commonly used to examine ancient demography, our study demonstrates that our inexpensive, all-in-one approach to marker discovery and genotyping provides sufficient data to accurately infer the timing of a recent bottleneck. This demographic scenario is relevant for many species of conservation concern, few of which have sequenced genomes. Our results are remarkably insensitive to sample size or number of genomic markers, which has important implications for applying this method to other nonmodel systems.
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