Data from: Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus)

Deciphering patterns of genetic variation within a species is essential for understanding population structure, local adaptation and differences in diversity between populations. Whilst neutrally evolving genetic markers can be used to elucidate demographic processes and genetic structure, they are not subject to selection and therefore are not informative about patterns of adaptive variation. As such, assessments of pertinent adaptive loci, such as the immunity genes of the Major Histocompatibility Complex (MHC), are increasingly being incorporated into genetic studies. In this study we combined neutral (microsatellite, mtDNA) and adaptive (MHC class II DLA-DRB1 locus) markers to elucidate the factors influencing patterns of genetic variation in the African wild dog (Lycaon pictus); an endangered canid that has suffered extensive declines in distribution and abundance. Our genetic analyses found all extant wild dog populations to be relatively small (Ne < 30). Furthermore, through coalescent modelling, we detected a genetic signature of a recent and substantial demographic decline, which correlates with human expansion, but contrasts with findings in some other African mammals. We found strong structure of wild dog populations, indicating the negative influence of extensive habitat fragmentation and loss of gene flow between habitat patches. Across populations we found that the spatial and temporal structure of microsatellite and MHC diversity were correlated, and strongly influenced by demographic stability and population size, indicating the effects of genetic drift in these small populations. Despite this correlation, we detected signatures of selection at the MHC, implying that selection has not been completely overwhelmed by genetic drift.

解析物种内的遗传变异模式，对于阐明种群结构、局部适应性及种群间多样性差异均至关重要。尽管中性进化的遗传标记可用于解析种群动态过程与遗传结构，但这类标记不受选择压力作用，因此无法反映适应性变异的分布模式。有鉴于此，针对主要组织相容性复合体（Major Histocompatibility Complex, MHC）这类免疫相关基因的关键适应性位点开展评估，正日益被纳入遗传学研究范畴。本研究结合中性标记（微卫星、线粒体DNA（mtDNA））与适应性标记（MHC II类DLA-DRB1基因座），以解析影响非洲野犬（Lycaon pictus，一种曾经历分布范围与种群规模大幅缩减的濒危犬科动物）遗传变异模式的相关因素。遗传分析结果显示，所有现存非洲野犬种群的有效种群规模均较小（Ne<30）。此外，通过溯祖模型分析，我们检测到近期发生大规模种群衰退的遗传信号，该信号与人类扩张进程高度契合，但与部分其他非洲哺乳动物的相关研究结果相悖。研究发现非洲野犬种群存在显著的遗传结构，这表明广泛的栖息地碎片化以及栖息地斑块间基因流丧失对种群连通性产生了负面影响。跨种群分析显示，微卫星与MHC多样性的时空结构呈现显著相关性，且二者均受种群动态稳定性与种群规模的强烈影响，这体现了遗传漂变在这些小型种群中的作用。尽管存在上述相关性，我们仍在MHC区域检测到选择信号，这意味着选择作用并未完全被遗传漂变所掩盖。