Galapagos Phyllodactylus species RAD-sequencing

Islands offer invaluable opportunities for studying evolutionary processes due to their isolation and distinct environmental conditions. The Galapagos Islands, renowned for their rich biodiversity, host several endemic gecko species of the genus Phyllodactylus. Despite their importance derived from their specialized adaptations and their crucial role in maintaining ecosystem balance, few studies have been conducted on these geckos. This highlights the need for comprehensive genomic research to understand their evolutionary patterns and population dynamics. This study elucidates the genetic diversity and population structure of six endemic Phyllodactylus species found on four human-inhabited islands in the Galapagos using a RAD-Seq approach. The analysis of over 30,000 loci from 93 individuals revealed five distinct genetic clusters, corresponding to P. baurii, P. galapagensis, P. darwini, P. leei, and a combined cluster of P. simpsoni and P. andysabini. Our results indicate that P. galapagensis clusters closely with the combined P. simpsoni - P. andysabini group, while P. baurii shows close genetic relationships with both clusters, aligning with their phylogenetic connectionsin accordance with the obtained phylogeny and the sequential emergence of the Galapagos Islands where each species is found. Substantial genetic differentiation was observed between species, with high FST and DXY values. Within-species population structure was associated with geographic barriers and gene flow restrictions. Surprisingly, human activity does not appear to be causing significant admixture among these populations; instead, population boundaries remain intact, indicating that geographic or behavioral barriers are stronger than human influences in limiting gene flow. Overall, we found low genetic diversity across species, probably due to their endemic nature and island isolation. This genomic study provides insights into the evolutionary dynamics shaping these unique geckos and highlights the importance of employing high-resolution genomic tools in insular ecosystems for their effective conservation and management.

岛屿因其隔离性与独特的环境条件，为进化过程研究提供了不可估量的契机。以丰富生物多样性闻名的加拉帕戈斯群岛，栖息着叶趾虎属（Phyllodactylus）的多种特有壁虎物种。尽管这些壁虎凭借其特化适应能力与维持生态系统平衡的关键作用而具备重要研究价值，但针对它们的相关研究仍较为匮乏。这凸显了开展全面基因组研究以解析其进化模式与种群动态的必要性。本研究采用限制性位点关联测序（RAD-Seq）技术，解析了加拉帕戈斯群岛四座人类定居岛屿上分布的6种特有叶趾虎属壁虎的遗传多样性与种群结构。对93个个体的3万余个基因位点进行分析后，共鉴定出5个独立的遗传簇，分别对应鲍尔叶趾虎（P. baurii）、加拉帕戈斯叶趾虎（P. galapagensis）、达尔文叶趾虎（P. darwini）、李氏叶趾虎（P. leei），以及由辛普森叶趾虎（P. simpsoni）和安迪萨宾叶趾虎（P. andysabini）组成的复合遗传簇。本研究结果显示，加拉帕戈斯叶趾虎与辛普森叶趾虎-安迪萨宾叶趾虎复合簇亲缘关系紧密，而鲍尔叶趾虎与两个遗传簇均存在较近亲缘关系，这与基于所构建系统发育树以及各物种分布的加拉帕戈斯群岛相继形成时序所得到的系统发育关联相符。物种间存在显著遗传分化，遗传分化系数（FST）与核苷酸差异均值（DXY）数值均较高。物种种内的种群结构与地理屏障及基因流限制密切相关。令人意外的是，人类活动似乎并未导致这些种群间出现显著的遗传混合；相反，种群边界仍保持完整，这表明在限制基因流方面，地理或行为屏障的作用强于人类活动的影响。总体而言，所有物种种群的遗传多样性均较低，这可能与其特有属性及岛屿隔离性有关。本基因组研究为解析塑造这些独特壁虎的进化动态提供了新视角，同时凸显了在岛屿生态系统中采用高分辨率基因组工具开展有效保护与管理的重要性。