1 | INTRODUCTION
In comparison with freshwater fish in lakes in plain regions, fish communities in plateau lakes are characterized by small populations as well as high endemicity, species richness, and interspecific variation (Chu & Chen, 1989). Such fishes are also more vulnerable to threats such as environmental pollution, alien species invasions, overfishing and other impacts stemming from human activities around lakes.
The Yunnan-Guizhou Plateau, located in the center of Yunnan Province, contains six of the province’s nine plateau lakes. Situated along the Xiao-Jiang fault zone, these lakes were formed between the late Pliocene and early Pleistocene, with most being formed during the middle to late stages of the Pleistocene (Li et al., 1963; Yang, 1984). During the Qingzang (3.6~1.7 Ma) and Kunhuang (1.1~0.6 Ma) periods, the Yunnan-Guizhou Plateau was uplifted from an average elevation of < 1,000 m to 4,000 m. Subsequently, the region was subjected to an intensification of the Asian monsoonal climate and increased precipitation (Li & Fang, 1999) and saw the formation of numerous glaciers (Shi et al., 1999). The freshwater fish genus Sinocyclocheilus originated around 10.16 Ma, with most speciation events occurring in the last two million years. Such speciation was likely favored by the uplifting of the Qinghai-Tibetan Plateau and the aridification of the regional climate, which led to the isolation of Sinocyclocheilus populations in cave systems (Mao et al., 2021). Similar geological processes have been proposed to shape the divergence and evolution of other faunal species of the central Yunnan Plateau (Che et al., 2010; Zhao & Li, 2017; Guo et al., 2019; Deng et al., 2020; Xiang et al., 2021), including fish species in plateau lakes (Yang et al., 2016; Wen et al., 2022). Nonetheless, the relative importance of key geological events in shaping the distributions and genetic structures of faunal communities of the central Yunnan lake basin remains poorly understood.
Fishes in the genus Sinocyclocheilus are morphologically distinct. Their populations are distributed across karst landforms of the Yunnan-Guizhou Plateau, where they reside in vauclusian springs, karst caves or underground river outlets. As such,Sinocyclocheilus fishes live in extremely challenging environmental conditions where little photosynthesis occurs and food resources are low (Camacho, 1992; Bitchuette & Trajano, 2010). Due to environmental pollution and human impacts, the habitats ofSinocyclocheilus include some of the most threatened ecosystems in the world, and Sinocyclocheilus populations have decreased sharply (Shu et al., 2013). In China, the genus is listed under Class II of the nationally protected animals classification. Intraspecific phylogeographic patterns are useful for elucidating the spatio-temporal dynamics of a species’ population size, dispersal history and extent of geographical isolation (Baker & Marshall, 1997; Merila et al., 1997; Zink, 1997; Kvist et al., 1999; Leonard et al., 2000; Zhang et al., 2005). Such patterns can thus provide a theoretical basis for species conservation. Despite the steep decline of Sinocyclocheiluspopulations, there has been limited understanding of the genetic population structures of these fishes as well as the phylogenetic relationships between Sinocyclocheilus species (Zhao & Zhang, 2009; Jiang et al., 2019; Mao et al., 2021). These gaps need to be addressed because they can result in the application of inappropriate conservation and management actions to Sinocyclocheiluspopulations (Gutierrez & Helgen, 2013; Zachos, 2013). Hence, it is necessary to clarify the phylogenetic relationships between and within different Sinocyclocheilus species in Yunnan.
In the present study, we measured the SNP (Single Nucleotide Polymorphisms) of 108 Sinocyclocheilus individuals from 24 different populations and used RAD-seq as a genetic method to analyze their population structure, with the aim of addressing the following questions: (i) What is the population structure ofSinocyclocheilus in central Yunnan? (ii) Have historic geological events in central Yunnan affected the genetic structures and distributional patterns of Sinocyclocheilus populations? (iii) What factors influence the genetic structure and differentiation patterns of the Sinocyclocheilus population in the central Yunnan Basin? (iv) What is the role of river capture events in shaping the distribution of genetic lineages of fishes in the central Yunnan Basin? Finally, we discussed the implications of our findings for the protection and management of Sinocyclocheilus and other cave fish.