1. Long‐term evolutionary history and demographic processes shape current patterns of genetic variation in natural populations. Genetic diversity is of prime importance for the long‐term survival of species, especially those threatened or endangered, which can be lost in a few generations and can take hundreds to recover. Notably, turtles are among the most endangered vertebrate taxa in the world. The Coahuilan box turtle Terrapene coahuila is the only aquatic species within the genus, microendemic to the desert‐spring ecosystem of the Cuatrociénegas Basin (CCB). The CCB has experienced significant habitat changes during recent decades, fragmenting otherwise interconnected wetlands systems. We aimed to perform a detailed evaluation of the evolutionary and genetic patterns of T. coahuila, both historical and contemporary, linked to the biogeography of the CCB and processes governing the species distribution.
2. We assessed the contributions of historical and contemporary population demographic processes to genetic diversity and structure, by using two mitochondrial DNA genes (cytochrome b and d‐loop), one nuclear gene (GAPD), and 12 nuclear microsatellite loci. We comprehensively analysed these data to address historical patterns of demography, migration, genetic diversity, and times of divergence across the valley for T. coahuila. We also evaluated recent patterns of genetic variation and structure, inbreeding, bottleneck signals, and effective population size.
3. Our results dated the time to the most recent common ancestor for T. coahuila in the CCB at c. 10.1 million years ago, with highest diversification during the Holocene. Structure consistently comprised two genetic clusters, Cuatrociénegas East and Cuatrociénegas West on either side of the main historical barrier, the Sierra San Marcos. Demographic results supported a divergence between western and eastern populations from 47,500 to 110,950 years ago, and colonisation of the southernmost Cuatrociénegas West distribution (Churince) 28,500–66,500 years ago, which experienced a recent bottleneck. All populations showed low values of haplotype and nuclear genetic diversity, migration, effective population size, and relatedness; significant inbreeding and bottleneck signals were also identified within genetic clusters.
4. In accordance with the biogeographic history of the basin, our results show that T. coahuila’s diversification across the Cuatrociénegas valley continued throughout the Pleistocene, peaking during the Holocene, when the valley started to gradually dry. As predicted, T. coahuila exhibited an overall, long‐term, and probably continuing decrement in genetic variation, increased genetic differentiation, and low population sizes, as a consequence of contemporary habitat loss and fragmentation across the CCB.
5. Changes in species demography and population connectivity have the potential to permanently alter the genetic patterns of freshwater species. Hence, given its restricted distribution, high habitat specificity and habitat loss, Terrapene coahuila is at utmost risk of extinction. Captive breeding programmes of the Coahuilan box turtle should consider our results, to prevent further loss of genetic diversity and truly expect reintroduction success. Also, it is crucial to restore connectivity among wetlands, for the conservation of species and the Cuatrociénegas valley altogether.

中文翻译：

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惊人地减少栖息地，减少遗传多样性，并危及水生赤耳天然种群的保护

1. 长期的进化史和人口统计过程决定了自然种群中遗传变异的当前模式。遗传多样性对于物种的长期生存至关重要，特别是受到威胁或濒危的物种，这些物种可能会在几代后消失，可能需要数百年才能恢复。值得注意的是，海龟是世界上最濒危的脊椎动物类群之一。Coahuilan箱龟Terrapene coahuila是该属中唯一的水生物种，对Cuatrociénegas盆地（CCB）的沙漠春天生态系统是微特有的。近几十年来，CCB的生境发生了重大变化，使原本相互联系的湿地系统变得支离破碎。我们旨在对T. coahuila的进化和遗传模式进行详细的评估，无论是历史的还是当代的，都与CCB的生物地理环境和控制物种分布的过程相关联。
2. 我们通过使用两个线粒体DNA基因（细胞色素b和d环），一个核基因（GAPD）和12个核微卫星基因座，评估了历史和当代人口人口统计过程对遗传多样性和结构的贡献。我们对这些数据进行了全面分析，以解决人口分布，迁徙，遗传多样性和跨谷类T. coahuila的扩散时间的历史模式。我们还评估了遗传变异和结构，近交，瓶颈信号和有效种群规模的最新模式。
3. 我们的研究结果日的时间为最近的共同祖先T.科阿韦拉州在建行Ç。1010万年前，是全新世以来多样化程度最高的时期。结构始终由两个基因簇组成，即东库阿特罗西涅加斯（Cuatrociénegas）和西库阿特罗西涅加斯（CuatrociénegasWest），位于主要历史屏障塞拉圣马科斯山脉的两侧。人口统计结果表明，东西方人口从47,500到110,950年前有所不同，最南端的CuatrociénegasWest分布（Churince）在28,500-66,500年前就开始殖民化，最近经历了瓶颈。所有种群的单倍型和核遗传多样性，迁徙，有效种群规模及相关性均显示出较低的价值；在遗传簇中也发现了重要的近交和瓶颈信号。
4. 根据该盆地的生物地理历史，我们的研究结果表明，T。coahuila在整个Cuatrociénegas谷地的多样化在整个更新世持续进行，并在新世时期达到顶峰，当时该谷地开始逐渐干燥。如预期的那样，由于当代栖息地的丧失和整个CCB的破碎，T。coahuila表现出总体的，长期的，可能持续的遗传变异，增加的遗传分化和较小的种群规模。
5. 物种人口学和种群连通性的变化有可能永久改变淡水物种的遗传模式。因此，由于其分布受限，高栖息地特异性和栖息地丧失，Terrapene coahuila面临灭绝的最大风险。Coahuilan箱龟的圈养繁殖计划应考虑我们的结果，以防止遗传多样性的进一步丧失，并真正期望重新引入成功。同样，恢复湿地之间的连通性对于保护物种和Cuatrociénegas谷地也至关重要。