Data from: Range-wide and regional patterns of population structure and genetic diversity in the gopher tortoise

The gopher tortoise (Gopherus polyphemus) has experienced dramatic population declines throughout its distribution in the southeastern United States and is federally listed as threatened in the area west of the Tombigbee-Mobile Rivers. While there is molecular support for recognizing the listed portion of the range as genetically distinct, other research has suggested that additional population structure exists at both range-wide and regional scales. In this study, we sought to comprehensively define structure at both spatial scales by doubling the data available in terms of the number of sampling sites, individuals and microsatellite loci compared to previously published work. Patterns of genetic diversity, gene flow and demographic history were also compared across the range. We collected 933 individuals from 47 sampling sites across the range and genotyped them for 20 microsatellite loci. Our range-wide analyses supported the recognition of five genetic groups (or regions) delineated by the Tombigbee-Mobile Rivers, Apalachicola-Chattahoochee Rivers, and the transitional areas between several physiographic province sections of the Coastal Plains (i.e., Eastern Gulf, Sea Island, and Floridian). Genetic admixture was found at sampling sites along the boundaries of these genetically defined groups. We detected some degree of additional genetic structure within each of the five regions. Notably, within the federally listed portion of the range, we found some support for two additional genetic groups loosely delineated by the Pascagoula-Chickasawhay Rivers, and we detected four more genetic groups within the Florida region that seemed to reflect the influence of the local physiography. Additionally, our range-wide analysis found the periphery of the range had lower levels of genetic diversity relative to the core. We suggest that the five main genetic groups delineated in our study warrant recognition as management units in terms of conservation planning. Intraregional population structure also points to the potential importance of other barriers to gene flow at finer spatial scales, although additional work is needed to better delineate these genetic groups.哥法地鼠龟（Gopherus polyphemus）在美国东南部的整个自然分布范围内种群数量均出现大幅下降，其中汤比格比-莫比尔河（Tombigbee-Mobile Rivers）以西区域被美国联邦政府列为受威胁物种。尽管已有分子生物学证据支持将该受威胁分布区域认定为独立遗传类群，但其他研究表明，在全分布范围及区域尺度上均存在额外的种群遗传结构。本研究旨在全面解析这两类空间尺度下的种群遗传结构，相较于已发表的相关研究，本研究的采样位点、个体数量及微卫星位点（microsatellite loci）的数量均提升了一倍。本研究还对全分布范围内的遗传多样性、基因流及种群历史动态模式进行了比较分析。我们从全分布范围的47个采样位点中共采集933只个体，并对其20个微卫星位点进行了基因分型。全分布范围分析结果支持划分5个遗传类群（或区域），其分界分别为汤比格比-莫比尔河、阿巴拉契科拉-查特胡奇河，以及沿海平原（Coastal Plains）多个地貌省分区之间的过渡区域（即东海湾、海岛及佛罗里达分区）。在上述遗传类群的边界沿线采样位点中，均检测到了遗传混合现象。我们在5个区域内部均检测到了一定程度的额外遗传结构。值得注意的是，在被联邦列为受威胁的分布区域内，我们发现有证据支持存在另外两个由帕斯卡古拉-奇克索黑河（Pascagoula-Chickasawhay Rivers）大致划定的遗传类群；而在佛罗里达区域内，我们还检测到另外4个遗传类群，其分布似乎受当地地貌特征影响。此外，全分布范围分析显示，分布范围边缘区域的遗传多样性水平相较于核心区域更低。我们建议，本研究划定的5个主要遗传类群应被认定为保护规划中的管理单元。区域内的种群遗传结构也表明，在更精细的空间尺度下，其他基因流障碍可能具有重要作用，但仍需开展更多研究以更精准地划定这些遗传类群。