Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of STRUCTURE-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates, impact the estimation of the optimal number of population clusters Kopt that best describe the observed data. Domestic horses are suited as a test case as there is extensive knowledge of the history of many breeds, extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (DAPC, FLOCK, PCoA and STRUCTURE with different run scenarios) all revealed the general, broad-scale relationships among the breeds that largely reflect known breed histories but...

STRUCTURE是目前应用最为广泛的工具，旨在从观测得到的微卫星数据或其他遗传标记中还原真实但未知的种群结构。2012年Gilbert等人的研究显示，约30%基于STRUCTURE开展的研究无法被复现。本研究利用一套涵盖93个家马品种的2323份样本以及普氏野马的大规模数据集，所有样本均通过15个微卫星标记完成基因分型，以此评估程序参数设置——尤其是迄今尚未得到充分探究的重复运行次数——对最优种群聚类数K_opt估计的影响，该聚类数为最契合观测数据的种群划分参数。家马适合作为本次测试案例，因为学界对诸多马品种的演化历史拥有充分认知，且已有大量系统发育分析成果。基于不同遗传假设与统计流程的多种方法（包括DAPC、FLOCK、PCoA以及设置不同运行场景的STRUCTURE）均揭示了各品种间大体的广谱亲缘关系，这些关系在很大程度上呼应已知的品种演化历史，但……