Camacho-Sanchez Miguel, Velo-Antón Guillermo, Hanson Jeffrey O, Veríssimo Ana, Martínez-Solano Íñigo, Marques Adam, Moritz Craig, Carvalho Sílvia B
CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal.
Museo Nacional de Ciencias Naturales CSIC Madrid Spain.
Ecol Evol. 2020 Sep 15;10(19):10353-10363. doi: 10.1002/ece3.6670. eCollection 2020 Oct.
Reduced representation genome sequencing has popularized the application of single nucleotide polymorphisms (SNPs) to address evolutionary and conservation questions in nonmodel organisms. Patterns of genetic structure and diversity based on SNPs often diverge from those obtained with microsatellites to different degrees, but few studies have explicitly compared their performance under similar sampling regimes in a shared analytical framework. We compared range-wide patterns of genetic structure and diversity in two amphibians endemic to the Iberian Peninsula: and based on microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci) datasets of comparable sample size and spatial extent. Model-based clustering analyses with STRUCTURE revealed minor differences in genetic structure between marker types, but inconsistent values of the optimal number of populations (K) inferred. SNPs yielded more repeatable and less admixed ancestries with increasing K compared to microsatellites. Genetic diversity was weakly correlated between marker types, with SNPs providing a better representation of southern refugia and of gradients of genetic diversity congruent with the demographic history of both species. Our results suggest that the larger number of loci in a SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset, at least at the spatial and temporal scales investigated.
简化基因组测序已使单核苷酸多态性（SNP）在解决非模式生物的进化和保护问题方面得到广泛应用。基于SNP的遗传结构和多样性模式往往在不同程度上与通过微卫星获得的模式有所不同，但很少有研究在共享分析框架下，在相似抽样方案下明确比较它们的性能。我们比较了伊比利亚半岛特有的两种两栖动物的全分布范围内的遗传结构和多样性模式：基于样本量和空间范围相当的微卫星（18个和14个位点）和SNP（15412个和33140个位点）数据集。使用STRUCTURE进行的基于模型的聚类分析显示，标记类型之间的遗传结构存在细微差异，但推断出的最优种群数量（K）值不一致。与微卫星相比，随着K值增加，SNP产生的可重复性更高且混合祖先更少。标记类型之间的遗传多样性呈弱相关，SNP能更好地反映南部避难所情况以及与两种物种种群历史一致的遗传多样性梯度。我们的结果表明，至少在所研究的空间和时间尺度上，SNP数据集中更多的位点能够比典型的微卫星数据集提供更可靠的遗传结构和多样性模式推断。
