Data from: Shaping species with ephemeral boundaries: the distribution and genetic structure of the desert tortoise (Gopherus morafkai) in the Sonoran Desert region

Aim: We examine the role biogeographical features played in the evolution of Morafka's desert tortoise (Gopherus morafkai) and test the hypothesis that G. morafkai maintains genetically distinct lineages associated with different Sonoran Desert biomes. Increased knowledge of the past and present distribution of the Sonoran Desert region's biota provides insight into the forces that drive and maintain its biodiversity. Location: Sonoran Desert biogeographical region; Sonora and Sinaloa, Mexico and Arizona, USA. Methods: We examined wild tortoises from Mexico (n = 155) and Arizona (n = 78), spanning their known distribution. We used mtDNA sequences to reconstruct matrilineal relationships and 25 microsatellite (STR) loci for Bayesian analyses of gene flow. We performed clinal analyses on both mtDNA and STR loci to determine the position and amount of introgression where lineages co-occur. We used GIS to assess the association of genetic structuring with ecological features. We used these data in a hypothesis-driven approach to assess different models of how genetic diversity is maintained and distributed in G. morafkai. Results: Gopherus morafkai was found to comprise genetically and geographically distinct ‘Sonoran’ and ‘Sinaloan’ lineages. Both lineages occurred in a relatively narrow zone of overlap in Sinaloan thornscrub, where it transitions into Sonoran desertscrub. Limited introgression occurred at the contact zone. The best-fit model suggests that these lineages diverged in parapatry where the distribution of genotypes is environment-dependent and introgression is inhibited by exogenous selection. Main conclusions: The historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.

研究目的：本研究探讨生物地理特征在莫拉卡沙漠陆龟（Gopherus morafkai）演化过程中的作用，并检验如下假说：G. morafkai保有与不同索诺兰沙漠生物群系相关的遗传分化支系。加深对索诺兰沙漠地区生物类群过去与当前分布的认知，有助于解析驱动并维持其生物多样性的核心动力。
研究区域：索诺兰沙漠生物地理区域，涵盖墨西哥索诺拉州、锡那罗亚州以及美国亚利桑那州。
研究方法：本研究采集覆盖该物种已知分布范围的野生陆龟样本，其中墨西哥种群155只，亚利桑那种群78只。通过线粒体DNA（mtDNA）序列重建母系亲缘关系，并利用25个微卫星（STR）位点开展基因流的贝叶斯分析。针对线粒体DNA及微卫星位点开展渐变群分析，以确定支系共存区域的基因渐渗位置与程度。借助地理信息系统（GIS）评估遗传结构与生态特征的关联。本研究采用假说驱动的研究框架，基于上述数据检验关于G. morafkai遗传多样性维持与分布模式的多种假说。
研究结果：本研究发现，莫拉卡沙漠陆龟可划分为遗传与地理均存在分化的“索诺兰支系”与“锡那罗亚支系”。两个支系在锡那罗亚灌丛向索诺兰荒漠灌丛过渡的狭窄重叠带内共存。该接触区仅发生有限的基因渐渗。最优拟合模型表明，这些支系以邻域模式发生分化，其基因型分布依赖于环境，且外源选择抑制了基因渐渗。
主要结论：热带落叶林与索诺兰荒漠灌丛之间历史上动态变化的生态交错带，可能是推动陆龟邻域支系分化的关键边界。两个支系间显著的遗传渐变群表明，更新世气候旋回导致的临时避难所隔离期，对支系分化产生了重要影响。尽管二者尚未形成完全的生殖隔离，但G. morafkai的索诺兰支系与锡那罗亚支系已走上独立的演化路径。