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.