Data from: Genetic diversity and population structure of Mesoamerican jaguars (Panthera onca): implications for conservation and management

Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of understanding levels of genetic diversity and connectivity to making informed management and conservation decisions with the goal to maintain functional connectivity across the region.中美洲美洲豹（Panthera onca）已在其历史分布范围内超77%的区域中局部灭绝，当前栖息于破碎化景观中，种群规模或已缩减。维持与恢复受人类改造景观内的遗传多样性及种群连通性，已成为首要的保护优先级工作；但针对野生种群的大规模遗传监测仍属罕见。本研究是首个主要利用在伯利兹、哥斯达黎加、危地马拉、洪都拉斯及墨西哥这五个中美洲国家野外采集的粪便样本开展的美洲豹区域保护遗传学研究。我们对445份美洲豹粪便样本进行了基因分型，并利用12个微卫星位点（microsatellite loci）的遗传数据，对115只独立美洲豹个体的遗传多样性与连通性模式展开了分析。整体而言，本次检测到中等水平的遗传变异（等位基因数NA=4.50±1.05、等位基因丰富度AR=3.43±0.22、期望杂合度HE=0.59±0.04）；其中墨西哥的遗传多样性最低，其次依次为洪都拉斯、危地马拉、伯利兹与哥斯达黎加。种群水平的基因流参数（FST=0.09至0.15，Dest=0.09至0.21）、主成分分析以及分层框架下的贝叶斯聚类分析均揭示，中美洲美洲豹存在显著的遗传结构，个体大致可被划分为4个具有不同程度遗传混合的遗传簇。玛雅丛林（Selva Maya）区域的美洲豹种群间基因流水平最高，而其余所有采样点之间的遗传分化均处于中等水平。玛雅丛林与洪都拉斯美洲豹种群间的遗传分化最为显著，表明这两个地理距离较近的区域间美洲豹的扩散活动有限，最终驳斥了当代随机交配（panmixia）的假说。为维持美洲豹在中美洲景观中扩散所需的关键连通廊道，并保障这一近危物种的长期种群存续，我们建议持续开展美洲豹保护廊道的管理与维护工作。本研究提供的基础遗传数据，凸显了厘清遗传多样性与连通性水平的重要性，可为制定科学合理的管理与保护决策提供依据，以维持整个区域的功能性种群连通性。