Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms
Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms
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DOI：
10.1111/j.1365-294x.2008.03851.x
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发表时间：
2008-08-01
影响因子：
4.9
通讯作者：
Garza, J. C.
中科院分区：
文献类型：
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作者：
Narum, S. R.;Banks, M.;Garza, J. C.
单核苷酸多态(SNPs)具有多种有益的遗传标记，是一种很有吸引力的遗传标记，但对于有多少双等位基因标记才能有足够的能力区分种群仍然存在不确定性，这项任务现在通常使用高度多态的微卫星标记来完成。在这项研究中，我们测试了37个SNPs和13个微卫星对29个广泛分布的Chinook鲑鱼种群(n=2783)的区分能力。所有座位的信息量均由In和决定，其中In排序的前12个标记为微卫星，最高的6个标记和前10个标记中的7个为SNPs。随机SNPs与随机微卫星的平均比率在3.9至4.1之间，但当只包括信息量最大的基因座时，这一比率一直在下降。微卫星的个体分配测试准确率(73.1%)高于SNPs(66.6%)，其中综合50个标记的准确率最高(83.2%)。当标记类型组合在一起时，只有15个排名靠前的基因座比单独使用微卫星或SNPs提供更高的分配准确率。邻接树状图显示相似的聚类模式，群体分化的配对测试对每组标记都有几乎相同的结果。统计检验和模拟表明，与SNPs相比，微卫星能更好地区分密切相关的群体。我们的结果表明，这两种类型的标记很可能在群体遗传学研究中有用，在某些情况下，SNPs和微卫星的组合可能是最有效的一套基因座。
Single nucleotide polymorphisms ( SNPs) are appealing genetic markers due to several beneficial attributes, but uncertainty remains about how many of these bi-allelic markers are necessary to have sufficient power to differentiate populations, a task now generally accomplished with highly polymorphic microsatellite markers. In this study, we tested the utility of 37 SNPs and 13 microsatellites for differentiating 29 broadly distributed populations of Chinook salmon (n = 2783). Information content of all loci was determined by In and, and the top 12 markers ranked by In were microsatellites, but the 6 highest, and 7 of the top 10 ranked markers, were SNPs. The mean ratio of random SNPs to random microsatellites ranged from 3.9 to 4.1, but this ratio was consistently reduced when only the most informative loci were included. Individual assignment test accuracy was higher for microsatellites (73.1%) than SNPs (66.6%), and pooling all 50 markers provided the highest accuracy (83.2%). When marker types were combined, as few as 15 of the top ranked loci provided higher assignment accuracy than either microsatellites or SNPs alone. Neighbour-joining dendrograms revealed similar clustering patterns and pairwise tests of population differentiation had nearly identical results with each suite of markers. Statistical tests and simulations indicated that closely related populations were better differentiated by microsatellites than SNPs. Our results indicate that both types of markers are likely to be useful in population genetics studies and that, in some cases, a combination of SNPs and microsatellites may be the most effective suite of loci.