Ryynänen Heikki J, Tonteri Anni, Vasemägi Anti, Primmer Craig R
Department of Biological and Environmental Sciences, University of Helsinki, PO Box 65, FIN-00014 University of Helsinki, Finland.
J Hered. 2007 Nov-Dec;98(7):692-704. doi: 10.1093/jhered/esm093. Epub 2007 Nov 5.
Biallelic markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms have become increasingly popular markers for various population genetics applications. However, the effort required to develop biallelic markers in nonmodel organisms is still substantial. In this study, we compared the estimation of various population genetic parameters (genetic divergence and structuring, isolation-by-distance, genetic diversity) using a limited number of biallelic markers (in total 7 loci) to those estimated with 14 microsatellite loci in 21 Atlantic salmon (Salmo salar) populations from northern Europe. Pairwise FST values were significantly correlated between biallelic loci and microsatellite datasets, as was overall heterozygosity when both anadromous and nonanadromous populations were analyzed together. However, when the anadromous and nonanadromous samples were analyzed separately, only genetic divergence correlations remained significant. Biallelic markers alone were not sufficient for reliable neighbor-joining clustering of populations but gave highly similar isolation-by-distance signals when compared with microsatellites. Finally, although several population prioritization measures for conservation exhibited significant correlation between different marker types, the specific populations highlighted as being most valuable for conservation purposes varied depending on the marker type and conservation criteria applied. This study demonstrates that a relatively small set of biallelic markers can be sufficient for obtaining concordant results in most of the analyses compared with microsatellites, although estimates of genetic distance are generally more concordant than estimates of genetic diversity. This suggests that a relatively small number of biallelic markers can provide useful information for various population genetic applications. However, we emphasize that the use of much higher number of loci is preferable, especially when the genetic differences between populations are subtle or individual multilocus genotype-based analyses are to be performed.
双等位基因标记，如单核苷酸多态性（SNP）和插入/缺失多态性，已成为各种群体遗传学应用中越来越受欢迎的标记。然而，在非模式生物中开发双等位基因标记所需的工作量仍然很大。在本研究中，我们比较了使用有限数量的双等位基因标记（总共7个位点）与使用14个微卫星位点对21个来自北欧的大西洋鲑（Salmo salar）种群估计的各种群体遗传参数（遗传分化和结构、距离隔离、遗传多样性）。双等位基因位点和微卫星数据集之间的成对FST值显著相关，当溯河洄游和非溯河洄游种群一起分析时，总体杂合度也是如此。然而，当分别分析溯河洄游和非溯河洄游样本时，只有遗传分化相关性仍然显著。仅双等位基因标记不足以对种群进行可靠的邻接法聚类，但与微卫星相比，给出了高度相似的距离隔离信号。最后，尽管几种保护种群优先级措施在不同标记类型之间表现出显著相关性，但根据标记类型和应用的保护标准，被突出显示为对保护最有价值的特定种群有所不同。这项研究表明，与微卫星相比，相对较少的一组双等位基因标记在大多数分析中足以获得一致的结果，尽管遗传距离估计通常比遗传多样性估计更一致。这表明相对较少数量的双等位基因标记可以为各种群体遗传学应用提供有用信息。然而，我们强调使用更多数量位点是更可取的，特别是当种群之间的遗传差异细微或要进行基于个体多位点基因型的分析时。
