Data from: Population genetics of overwintering monarch butterflies, Danaus plexippus (Linnaeus), from central Mexico inferred from mitochondrial DNA and microsatellite markers

Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) and seven microsatellite loci. The sample of 133 individuals included migratory monarchs, from four overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico, and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance (AMOVA) of the COI data set, including additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from Mexico and Costa Rica, suggesting limited gene flow. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the two groups, possibly owing to the number of significant deviations from Hardy Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35,000 to 40,000 years before present) followed by a stable effective female population size (Nef) of about six million over the last 10,000 years.

本研究以采自墨西哥的黑脉金斑蝶（Danaus plexippus (L.)）为研究对象，基于线粒体细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I, COI；658 bp）、亚基II（cytochrome c oxidase subunit II, COII；503 bp）以及7个微卫星位点，对其种群遗传变异与种群历史动态展开评估。本次研究共纳入133个个体样本，其中包括采自墨西哥中部君主蝶生物圈保护区（Monarch Butterfly Biosphere Reserve, MBBR）内4个越冬位点的迁飞型黑脉金斑蝶，以及来自瓜纳华托州伊拉普阿托的非迁飞型种群。COI的单倍型多样性（haplotype diversity, h）与核苷酸多样性（nucleotide diversity, π）均处于较低水平，均值分别为0.466和0.00073；COII的对应值则分别为0.629和0.00245。对包含额外来自哥斯达黎加非迁飞种群的GenBank序列的COI数据集进行分子方差分析（analysis of molecular variance, AMOVA）结果显示，墨西哥迁飞型黑脉金斑蝶与墨西哥、哥斯达黎加的非迁飞型种群间存在显著的种群遗传结构，提示二者间基因交流有限。有趣的是，非迁飞种群的COI单倍型频率虽与迁飞种群存在显著差异，但二者尽管地理距离悬殊，其单倍型频率却彼此相近。然而微卫星分析结果则显示两类种群间不存在明显遗传结构，这一现象可能源于多数位点检测到的杂合子缺失（heterozygote deficiencies）导致其显著偏离哈迪-温伯格平衡（Hardy Weinberg equilibrium）。基于合并后的MBBR迁飞型黑脉金斑蝶种群（n=89）的COI与COII数据集，通过错配分布分析与贝叶斯天际线分析对其种群历史动态进行估算，结果显示该种群曾在更新世晚期（距今约3.5万至4万年）发生种群扩张，且在过去1万年中维持着约600万的稳定雌性有效种群数量（effective female population size, Nef）。