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

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 F 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.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

“…This was observed whatever the species and the panel of variants, and the effect was especially strong when measuring population differentiation and linkage disequilibrium, even greater than the effect of variant density. Our findings disagree with Nazareno, Bemmels, Dick, and Lohmann () who showed that accurate estimates of F ST between two Violaceae populations could be obtained with down to two individuals and about 1,500 SNPs. In our case the sample size effects reported could also be associated to the finescale structure of wild samples (i.e., substructures in Asiatic mouflon and Bezoar ibex groups that do not correspond to true populations) illustrated by high inbreeding between some individuals (Table ) and sNMF results (Figure S16).…”

Tangled banks: A landscape genomic evaluation of Wallace's Riverine barrier hypothesis for three Amazon plant species

“…Specifically, leaves from six individuals were obtained per sampling location. The typical limitations of small sample sizes are offset by large numbers of SNPs (Nazareno, Dick, et al., ; Willing, Dreyer, & van Oosterhout, ; Senn et al., ), which permit high‐resolution identification of genetic structure (Brown et al, ; Puckett et al, ; Trucchi et al, ; Kotsakiozi et al, ; Nazareno, Bemmels, Dick, & Lohmann, ). For example, in a previous study of Amphirrhox longifolia , Nazareno, Dick, et al.…”

“…Four genomic libraries were created using a double digest RADseq protocol (Peterson et al., ), with the modifications proposed by Nazareno, Bemmels, et al. () to minimize variance in the number of reads per individual within each pool. Double‐stranded DNA concentrations were quantified before digestion reactions using the Qubit dsDNA Assay Kit (Invitrogen).…”

“…A total of 96 EcoRI double‐stranded barcodes with a unique 10 base pair sequence were created using Python; for further details on the barcodes and the MseI oligos sequences, see Nazareno, Bemmels, et al. ().…”

Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards

“…Genetic material is both easy and inexpensive to sample (Schwartz, Luikart, & Waples, ), and recent advances in sequencing technology and bioinformatics allow researchers to harvest information from across the genome at low cost. Furthermore, reliable estimates of both genetic diversity and past population size have been recovered from sample sizes as small as a single individual (Li & Durbin, ; Nazareno, Bemmels, Dick, & Lohmann, ). However, historical signals of demographic processes can weaken the relationship between census and effective population size, and thus the relationship between abundance and heterozygosity (Frankham, ).…”