Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

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dc.contributor.author Nazareno, Alison
dc.contributor.author Bemmels, Jordan B.
dc.contributor.author Dick, Christopher W
dc.contributor.author Lohmann, Lúcia G
dc.date.accessioned 2017-02-12T02:43:14Z
dc.date.available 2017-02-12T02:43:14Z
dc.date.issued 2017-01
dc.identifier.uri http://hdl.handle.net/2027.42/136081
dc.description.abstract High-throughput DNA sequencing facilitates the analysis of large portions of the genome in nonmodel organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double-digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a nonmodel plant species for which no reference genome is available. We used resampling techniques to construct simulated populations with a random subset of individuals and SNPs to determine how many individuals and biallelic markers should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We identified 3646 and 4900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than eight individuals has little impact on estimates of genetic diversity within A. longifolia populations, when 1000 SNPs or higher are used. Our results also show that even at a very small sample size (i.e. two individuals), accurate estimates of FST can be obtained with a large number of SNPs (≥1500). These results highlight the potential of high-throughput genomic sequencing approaches to address questions related to evolutionary biology in nonmodel organisms. Furthermore, our findings also provide insights into the optimization of sampling strategies in the era of population genomics. en_US
dc.language.iso en_US en_US
dc.publisher Elsevier en_US
dc.subject Amphirrhox longifolia, ddRADseq, genetic diversity, single nucleotide polymorphism, Violaceae en_US
dc.title Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species en_US
dc.type Article en_US
dc.subject.hlbsecondlevel Ecology and Evolutionary Biology
dc.subject.hlbtoplevel Science
dc.description.peerreviewed Peer Reviewed en_US
dc.contributor.affiliationum Department of Ecology and Evolutionary Biology, University of Michigan en_US
dc.contributor.affiliationumcampus Ann Arbor en_US
dc.description.bitstreamurl http://deepblue.lib.umich.edu/bitstream/2027.42/136081/1/Nazareno et al. 2017a.pdf
dc.identifier.doi 10.1111/1755-0998.12654
dc.identifier.source Molecular Ecology Resources en_US
dc.description.filedescription Description of Nazareno et al. 2017a.pdf : Main article
dc.owningcollname Ecology and Evolutionary Biology, Department of (EEB)
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