AUTHOR=Wanghe Kunyuan , Feng Chenguang , Tang Yongtao , Qi Delin , Ahmad Shahid , Nabi Ghulam , Li Xiaohui , Wang Guojie , Jian Longsheng , Liu Sijia , Zhao Kai , Tian Fei 

TITLE=Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing

JOURNAL=Frontiers in Ecology and Evolution

VOLUME=10

YEAR=2022

URL=https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2022.933632

DOI=10.3389/fevo.2022.933632

ISSN=2296-701X

ABSTRACT=<p>Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in <italic>Gymnocypris eckloni</italic>, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of <italic>G. eckloni</italic> between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes.</p>