Chen Yiqing, Dong Lina, Yi Huiqin, Kidner Catherine, Kang Ming
Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Plant Divers. 2024 Apr 15;46(5):575-584. doi: 10.1016/j.pld.2024.04.001. eCollection 2024 Sep.
Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the complex (, , and ) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between and occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.
了解小而孤立的种群中的全基因组多样性、近亲繁殖以及累积有害突变的负担，对于预测和增强种群的持久性和恢复力至关重要。然而，这些影响在石灰岩岩溶植物中很少得到研究。在此，我们对该复合体（、、和）的62个个体的核基因组进行了重测序，并研究了这四个物种的基因组差异和遗传负荷。我们的分析揭示了该复合体内对应于每个物种的四个不同聚类。值得注意的是，在重叠地理区域中，和之间仅存在有限的混合。所有物种在更新世期间都经历了历史瓶颈，这可能是由冰川气候波动引起的。我们在这个时间框架内检测到组对之间存在不对称的历史基因流，突出了一种归因于岩溶地理隔离的独特种间分化模式。我们发现，的孤立种群基因流有限，近期种群规模最小，近亲繁殖系数最高，隐性有害突变积累最多。这些发现强调了优先对这些孤立种群进行保护的紧迫性。本研究是首批在全基因组水平上解析岩溶植物的遗传分化和特定种群历史的研究之一，揭示了近亲繁殖几代人过程中有害突变积累所带来的潜在风险。此外，我们的发现可能有助于通过提供关键的基线遗传数据以及更好地理解塑造珍稀濒危岩溶植物当前种群结构的历史事件来进行保护规划。
