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

High throughput DNA sequencing facilitates the analysis of large portions of the genome in non-model 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 non-model 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 bi-allelic markers should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We identified 3,646 and 4,900 polymorphic SNPs for the two populations of A. longifolia, respectively. Our simulations show that, overall, a sample size greater than ei...

高通量DNA测序（High throughput DNA sequencing）可促进非模式生物（non-model organisms）基因组大片段的分析，确保种群遗传参数（population genetic parameters）的高准确性。然而，针对此类研究评估适宜样本量（sample size）的实证研究（empirical studies）仍较为匮乏。本研究采用双酶切限制性相关DNA测序（ddRADseq）技术，对无参考基因组（reference genome）的非模式植物物种——长叶Amphirrhox longifolia（堇菜科）的两个地理隔离种群，检测到数千个单核苷酸多态性（SNP）位点。我们采用重采样技术（resampling techniques），通过随机选取个体和SNP的子集构建模拟种群（simulated populations），以确定需采样多少个体和双等位基因标记（bi-allelic markers），才能准确估计种群内及种群间遗传多样性（intra- and interpopulation genetic diversity）。我们在长叶A. longifolia的两个种群中分别鉴定出3646个和4900个多态性SNP位点。模拟结果表明，总体而言，样本量大于ei...