Seddon J M, Parker H G, Ostrander E A, Ellegren H
Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
Mol Ecol. 2005 Feb;14(2):503-11. doi: 10.1111/j.1365-294X.2005.02435.x.
Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.
单核苷酸多态性（SNPs）有潜力成为自然种群生态学和保护研究中首选的遗传标记，因为它们能够获取全基因组的变异性。在本研究中，我们首次展示了在野生种群中发现SNP，以解决重新定殖的斯堪的纳维亚及邻近芬兰狼（Canis lupus）种群在生态学和保护方面的典型重要问题。利用针对犬类的细菌人工染色体（BAC）克隆的末端序列，我们设计了24个SNP位点的检测方法，其中20个位点先前已证实在家犬中具有多态性，另外4个位点是在狼中新鉴定出的多态性位点。在检测的24个位点中，发现22个SNP在斯堪的纳维亚种群内具有变异性，重要的是，这些位点能够区分不同的狼个体（无偏个体识别概率为4.33×10⁻⁸），这与对同一种群中12个可变微卫星进行基因分型得到的结果相当。一项归位测试显示斯堪的纳维亚和邻近芬兰狼种群之间存在分化，尽管并非所有已知的迁入个体都能被准确识别。对关系识别中错误分类率的探索表明，22个SNP位点和20个微卫星位点都无法区分一阶关系。尽管在非模式生物中发现SNP仍存在障碍，但大规模筛选方法的出现鼓励了在生态学和保护研究中使用SNP。此外，扩增极小片段的能力使得SNP特别适用于种群监测，在种群监测中粪便和其他非侵入性样本经常被使用。
