Data from: Mitochondrial DNA assessment of the phylogeography of the gopher tortoise

Identifying geographic barriers that define genetic structure within a species is crucial in formulating an effective conservation plan. The identification of appropriate management units is critical for the protection and recovery of the gopher tortoise Gopherus polyphemus, which have declined across their entire range. Previous molecular work at various spatial scales has identified distinct population assemblages of the gopher tortoise. The goal of this study was to assess the genetic structure in gopher tortoises through a more complete sampling of the federally listed as threatened portion of the range and evaluate the extent of genetic isolation imposed by several potential geographic barriers. We sequenced a 712–base-pair portion of a mitochondrial gene (NADH dehydrogenase 4) for 322 individuals from 42 sites across the range. We found two major assemblages of haplotypes separated by a modest phylogenetic break (average uncorrected p distance  =  0.015). The biogeographic barrier that best explained the geographic partitioning of genetic variation was the Apalachicola–Chattahoochee rivers and not the one used to delimit the federally listed as threatened portion of the range (Tombigbee–Mobile). However, the presence of distinct (group 1 and 2) haplotypes on either side of Apalachicola–Chattahoochee rivers indicates that the two lineages experienced historical isolation and divergence, after which they came back into contact. If one were to define genetic units of conservation for gopher tortoises, then the Apalachicola–Chattahoochee rivers delineation would be the most appropriate based on the analysis of molecular variance of the mitochondrial sequence data. However, a model that combines the Apalachicola–Chattahoochee and Tombigbee–Mobile rivers as geographic breaks was the second-best model in this analysis, which suggests that the federally listed as threatened portion of the range also contains important geographic structure. Thus, we recommend that making management decisions on the basis of mitochondrial data alone is premature, and that prior to any status review additional work that examines finer scale patterns of genetic structure by using microsatellite loci is required.

识别界定物种内遗传结构的地理屏障，是制定高效物种保护方案的关键所在。针对分布范围遍及全境且种群数量持续下降的哥法地鼠龟（Gopherus polyphemus）而言，明确合理的管理单元对其保护与种群恢复至关重要。此前在不同空间尺度开展的分子生物学研究，已识别出哥法地鼠龟的多个独特种群类群。本研究的目标是：通过对该物种分布范围内被联邦列为受威胁的种群区段开展更全面的采样，解析哥法地鼠龟的遗传结构，并评估若干潜在地理屏障所造成的遗传隔离程度。我们对分布范围内42个采样点的322个个体的线粒体基因（烟酰胺腺嘌呤二核苷酸脱氢酶4，NADH dehydrogenase 4）的712碱基对区段进行了测序。研究发现两类主要的单倍型集群，二者间存在适度的系统发育分化（平均未校正p遗传距离为0.015）。最能解释遗传变异地理分布格局的生物地理屏障是阿巴拉契科拉-查特胡奇河，而非此前用于界定该物种受威胁分布区段的汤比格比-莫比尔河。不过，阿巴拉契科拉-查特胡奇河两岸存在截然不同的单倍型类群（类群1与类群2），这表明两个谱系曾经历历史隔离与分化，随后再度发生接触。若要为哥法地鼠龟划定保护遗传单元，基于线粒体序列数据的分子方差分析结果显示，以阿巴拉契科拉-查特胡奇河作为划分边界最为合理。然而，本研究中第二优的模型将阿巴拉契科拉-查特胡奇河与汤比格比-莫比尔河共同作为地理断裂带，这提示该联邦列为受威胁的分布区段内同样存在重要的地理遗传结构。因此，我们建议仅基于线粒体数据制定管理决策尚为时过早；在开展任何物种现状评估前，还需要利用微卫星位点开展进一步研究，以解析更精细尺度的遗传结构格局。