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.

从微卫星标记（microsatellite markers, MSs）转向单核苷酸多态性（single nucleotide polymorphism, SNPs）的相关影响，已在多项群体遗传学研究中得到探讨，但基因组位置对两类标记所揭示的信息量的具体作用尚未得到细致探究。本研究针对三棘刺鱼（threespine stickleback）基因组中13个基因相关（genic，即基因内或距注释基因小于1kb）及13个基因间（nongenic，即距注释基因大于10kb）的微卫星标记侧翼1kb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。研究人员将每个基因组区域内的单核苷酸多态性位点转换为单倍型后，分析了不同地理尺度下的遗传多样性与遗传分化模式。标记类型（单核苷酸多态性单倍型或微卫星标记）以及基因组位置（基因相关或基因间），对绝大多数群体多样性与分化评估指标均产生了显著影响。谱系间的遗传分化在单核苷酸多态性单倍型（无论基因相关还是基因间）中显著更高，而谱系内的遗传分化在两类标记间并无显著差异。绝大多数分化与多样性指标在两类标记间均无相关性，但群体分化指标在微卫星标记与单核苷酸多态性单倍型（无论基因相关还是基因间）之间均呈显著相关。两类标记均可类似地解析大尺度群体结构与个体归属分析结果，但仅微卫星标记能够界定精细尺度的群体结构，尤其是在结合基因相关与基因间标记时。本研究结果表明，群体间的遗传变异与分化评估结果，会显著受到标记类型、标记相对于基因的基因组位置，以及这两个因素的交互作用的影响。这凸显了充分认识不同分子工具的固有优势与局限性的重要性，以便选择最恰当的方法，准确解答各类生态学与进化学问题。