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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Nazareno, Alison G. [1] ; Bemmels, Jordan B. [2] ; Dick, Christopher W. [2] ; Lohmann, Lucia G. [1]
Total Authors: 4
[1] Univ Sao Paulo, Dept Bot, Rua Matao 277, Cidade Univ, BR-05508900 Sao Paulo, SP - Brazil
[2] Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 - USA
Total Affiliations: 2
Document type: Journal article
Source: MOLECULAR ECOLOGY RESOURCES; v. 17, n. 6, p. 1136-1147, NOV 2017.
Web of Science Citations: 37

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 F-ST 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. (AU)

FAPESP's process: 12/50260-6 - Structure and evolution of the Amazonian biota and its environment: an integrative approach
Grantee:Lúcia Garcez Lohmann
Support type: BIOTA-FAPESP Program - Thematic Grants
FAPESP's process: 13/12633-8 - Comparative phylogeography of plants in the Central Amazonia
Grantee:Alison Gonçalves Nazareno
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 15/07141-4 - A test of the riverine barrier hypothesis for Amazonian plants
Grantee:Alison Gonçalves Nazareno
Support type: Scholarships abroad - Research Internship - Post-doctor