Journal article
Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population
Molecular ecology, Vol.23(1), pp.136-150
01/2014
Handle:
https://hdl.handle.net/2376/107017
PMID: 24237665
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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Details
- Title
- Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population
- Creators
- Rajiv C McCoy - Rocky Mountain Biological LaboratoryNandita R Garud - Stanford UniversityJoanna L Kelley - Washington State UniversityCarol L Boggs - University of South CarolinaDmitri A Petrov - Stanford University
- Publication Details
- Molecular ecology, Vol.23(1), pp.136-150
- Academic Unit
- Kelley Lab; Biological Sciences, School of
- Number of pages
- 15
- Grant note
- NSF GRFP NIH (RO1GM100366; RO1GM097415)
- Identifiers
- 99900546531801842
- Language
- English
- Resource Type
- Journal article