Olah George, Waples Robin S, Stojanovic Dejan
Fenner School of Environment and Society Australian National University Canberra Australian Capital Territory Australia.
King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine King's College London London UK.
Ecol Evol. 2024 Mar 24;14(3):e11102. doi: 10.1002/ece3.11102. eCollection 2024 Mar.
Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, , and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower than . We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size ( ) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.
遗传学是一个快速发展的领域，对于保护从业者或生态学家来说，它可能令人困惑。研究中使用的标记物选择至关重要；在文献中，最近的偏好已从微卫星转向单核苷酸多态性（SNP）位点。了解标记物类型如何影响种群遗传参数的估计在保护背景下很重要，特别是因为估计的准确性关系到为保护濒危物种而采取的行动。我们比较了针对完全相同的324只纯色吸蜜鹦鹉，七个微卫星、3761个SNP位点以及100个SNP的随机子集之间的参数估计，并且还使用了后续年份的另外457个样本比较SNP估计。两种标记物类型估计的 都低于 。我们表明，微卫星和SNP主要表明缺乏空间遗传结构，除非在主成分判别分析（DAPC）中对SNP数据使用先验收集位置。100个SNP的子集给出了与使用完整数据集时相当的结果。当考虑相同个体时，标记物之间有效种群大小（ ）的估计相当，但SNP的置信区间更窄。这令人放心，因为依赖基于少数微卫星的种群遗传估计的保护评估不太可能因文献中普遍转向SNP而无效。然而，当仅考虑成年样本时，标记物和数据集之间的估计差异很大；因此，建议在有可用样本时使用包括所有年龄组的样本。完整SNP数据集（2010 - 2019年）估计的 高于较小的比较数据（2010 - 2015年），这可能更好地反映了物种状况。微卫星较低的精度不一定是大多数保护应用的障碍；然而，SNP将提高置信限度，这对从业者可能有用。
