Data from: Characterizing genic and non-genic molecular markers: comparison of microsatellites and SNPs

The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between-lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within-lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad-scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine-scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions.

诸多群体遗传学研究已探讨了从微卫星标记（microsatellite markers, MSs）转向单核苷酸多态性（single nucleotide polymorphism, SNPs）的应用意义，但基因组位置对两类标记所携带信息量的影响尚未得到深入探究。本研究在三刺鱼（threespine stickleback）基因组中，针对13个基因区域内（基因内部或距基因<1 kb）及13个非基因区域内（距注释基因>10 kb）的微卫星标记侧翼1 kb区域开发了新型单核苷酸多态性标记，以获取两类标记的可比数据。我们将各基因组区域内的单核苷酸多态性位点转化为单体型（haplotype）后，分析了不同地理尺度下的遗传多样性与分化模式。标记类型（单核苷酸多态性单体型或微卫星标记）与基因组位置（基因区域或非基因区域）对多数群体多样性与分化评估指标均具有显著影响。谱系间分化在单核苷酸多态性单体型（基因区域及非基因区域）中显著更高，但两类标记的谱系内分化水平相近。多数分化与多样性指标在两类标记间无相关性，但群体分化指标例外：微卫星标记与单核苷酸多态性单体型（无论基因区域还是非基因区域）的群体分化结果显著相关。两类标记均可较好解析大尺度群体结构与个体归属，但仅微卫星标记能够界定小尺度群体结构，尤其在结合基因区域与非基因区域标记时效果更显著。本研究结果表明，群体间遗传变异与分化的评估结果会受到标记类型、标记相对于基因的基因组位置，以及二者交互作用的强烈影响。这凸显了明晰不同分子工具的固有优势与局限性的重要性，以便选择最适方法精准解答各类生态学与进化学问题。