Genetic Diversity and Fine-Scale Population Structure Analysis of the Placocheilus cryptonemus in the Nujiang River from mtDNA and Microsatellite Markers

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Abstract
The Nujiang River is rich in aquatic biodiversity, especially endemic fish. However, long-term human interference, such as cascade hydropower construction, has significantly changed aquatic habitats and threatened populations’ number and genetic diversity. This study used two mitochondrial gene markers, cyt b, and COI, combined with microsatellite molecular markers developed based on transcriptome data, which were used to study the genetic structure and genetic diversity of Placocheilus cryptonemus in Nu River. The cyt b gene showed that the haplotype mismatch distribution map of the P. cryptonemus population showed a unimodal distribution, indicating that the population expansion may occur during the evolutionary process. Microsatellite analysis showed high information content with high genetic diversity, the whole population was moderately genetically differentiated. There are certain differences in various molecular markers, and the results obtained are not completely consistent, but the overall results show that the level of genetic diversity among the populations of P. cryptonemus is moderate, and the genetic differentiation was not obviously, but the genetic differentiation of the mainstream population in different river basins was obviously. It may be related to different geographical and climatic differences, as well as the species’ own habitat habits.

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