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 analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and seven microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from four overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), 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, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the two behaviorally distinct groups. 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 concatenated 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.

本研究基于线粒体细胞色素c氧化酶亚基I（mitochondrial cytochrome c oxidase subunit I, COI；658 bp）与亚基II（subunit II, COII；503 bp）基因片段，以及7个微卫星位点（microsatellite loci）的分析，对产自墨西哥的黑脉金斑蝶（Danaus plexippus (L.)）的种群遗传变异与种群历史动态展开了系统评估。
本次研究共纳入133个个体样本，涵盖两类群：主要采自墨西哥中部帝王蝶生物圈保护区（Monarch Butterfly Biosphere Reserve, MBBR）内4个越冬位点的迁飞型帝王蝶，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（h）与核苷酸多样性（π）相对偏低，平均值分别为0.466与0.00073；COII的对应多样性指标则分别为0.629与0.00245。
针对COI数据集（包含额外取自基因库[GenBank]的哥斯达黎加非迁飞型种群序列）开展的分子方差分析（Analysis of molecular variance, AMOVA）结果显示，墨西哥迁飞型帝王蝶与墨西哥、哥斯达黎加两地的非迁飞型帝王蝶之间存在显著种群结构，提示这两种行为模式迥异的类群间基因交流受限。
值得注意的是，尽管非迁飞型种群的COI单倍型频率与迁飞型种群存在显著差异，但两类非迁飞种群之间的单倍型频率却较为相似，即便二者地理间隔极为遥远。
然而，微卫星位点分析结果则表明两类群之间并无种群结构，这一现象可能源于多数位点均检测到显著的哈迪-温伯格平衡（Hardy Weinberg equilibrium）偏离，且偏离均由杂合子缺失所导致。
基于拼接得到的COI与COII联合数据集（样本量n=89）的错配分布（mismatch distribution）与贝叶斯天际线分析（Bayesian skyline analyses），研究人员对迁飞型帝王蝶MBBR种群的种群历史动态进行了估算，结果显示种群扩张事件发生于更新世晚期（距今约35000至40000年前），且在过去10000年间，有效雌性种群规模（effective female population size, Nef）稳定维持在约600万。