Exploring taxonomic diversity and biogeography of the family Nemacheilinae (Cypriniformes)

Abstract

Nemacheilidae, in the superfamily Cobitoidea, is comprised of many of morphologically similar fish species that occur in Eurasian water bodies. This large group shows inconsistencies between traditional morphological taxonomy and molecular phylogenetic data. We used mitochondrial genomes, recombinase‐activating gene proteins 1 (RAG1) and the mitochondrial cytochrome c oxidase I gene (COI) to study the phylogenetic relationships among Nemacheilidae species using Bayesian inference and maximum likelihood approaches. Phylogenetic analyses based on mitogenomes provided support for two clades (I and II). The mitogenomes, RAG1, and COI results indicated that several species and genera were not consistent with the traditional morphological subdivisions. The two clades inferred from mitogenomes showed clear geographical patterns. The Tibetan Plateau, Hengduan Mountains, and the Iran Plateau may act as a barrier dividing the clades. The estimated timing of clades separation (36.05 million years ago) coincides with the first uplift of the Tibetan Plateau. We conclude that the geological history of the Tibetan Plateau played a role in the diversification and distribution of the Nemacheilidae taxa. These results provided a phylogenetic framework for future studies of this complex group.

A review of the Cypriniform tribe Yunnanilini Prokofiev, 2010 from China, with an emphasis on five genera based on morphologies and complete mitochondrial genomes of some species

“…However, we find that this species is closer to the genus Schistura than Y. jiuchiensis, which represents true Yunnanilus and forms a clade with Paranemachilus and Troglonectes , indicating that Petruichthys is not a synonym of Yunnanilus . According to Sgouros et al (2019) , the genus Schistura is polyphyletic, and Chen et al (2019b) revealed that P. brevis is nested within the Schistura clade. Therefore, more morphological and molecular studies are needed to resolve the taxonomic problems of Petruichthys and Schistura as well as the complex relationships between these nemacheilid tribes.…”

Contrasting population differentiation in two sympatric Triplophysa loaches on the Qinghai–Tibet Plateau

“…The T. tibetana genome was retrieved from GenBank (accession number SOYY00000000; Yang X. et al, 2019) and used as the reference. The reference genome was first indexed using the "bwa index" in BWA Version 0.7.17-r1188 (Li, 2013), and then re-sequencing clean reads were aligned to the reference using "bwa mem."…”

“…Earlier studies in Triplophysa loaches mainly focused on taxonomy (Zhu, 1989;Wu and Wu, 1992;Prokofiev, 2010;Kottelat, 2012), systematics (Wang et al, 2016;Chen et al, 2019;Wang T. et al, 2020), and biogeography (Chen et al, 1992;Wang et al, 2012;Feng et al, 2019;Hu et al, 2020). Next-generation sequencing (NGS) data are now largely adopted to identify molecular signatures of adaptation to high altitude (Wang et al, 2015a;Wang et al, 2015b), cave (Zhao et al, 2020), and salt/alkali (Chen et al, 2020) in Triplophysa loaches with comparative genomic approach, and several Triplophysa genomes have been determined with NGS data (Yang L. et al, 2019;Yang X. et al, 2019;Yuan et al, 2020;Zhou et al, 2021). However, the population genetics and adaptive mechanisms to salinity changes using NGS data have been rarely investigated in Triplophysa loaches (but see Chen et al, 2020;Hu et al, 2020;Yuan et al, 2020;Huo et al, 2022).…”

“…For example, T. stewarti could be found in Lake Bam Co and Lake Sêrling Co with salinity exceeding the salinity tolerance reported in Triplophysa species (4.17 g L −1 in T. yarkandensis ( Yao et al, 2018 ) and 3.74 g L −1 in T. dalaica ( Wu et al, 2017 ). Earlier studies in Triplophysa loaches mainly focused on taxonomy ( Zhu, 1989 ; Wu and Wu, 1992 ; Prokofiev, 2010 ; Kottelat, 2012 ), systematics ( Wang et al, 2016 ; Chen et al, 2019 ; Wang T. et al, 2020 ), and biogeography ( Chen et al, 1992 ; Wang et al, 2012 ; Feng et al, 2019 ; Hu et al, 2020 ). Next-generation sequencing (NGS) data are now largely adopted to identify molecular signatures of adaptation to high altitude ( Wang et al, 2015a ; Wang et al, 2015b ), cave ( Zhao et al, 2020 ), and salt/alkali ( Chen et al, 2020 ) in Triplophysa loaches with comparative genomic approach, and several Triplophysa genomes have been determined with NGS data ( Yang L. et al, 2019 ; Yang X. et al, 2019 ; Yuan et al, 2020 ; Zhou et al, 2021 ).…”

The Complete Mitochondrial Genome of Schistura fasciolata: Phylogenetic and Evolutionary Implications within Tribe Nemacheilini

“…Proko ev performed a detailed comparative morphological analysis [3], which divided Nemacheilidae into ve tribes: Vaillantellini, Lefuini, Yunnanilini, Triplophysini, and Nemacheilini [4,[6][7][8][9][10]. However, the challenges of valid species identi cation exist due to morphological and genetic diversity, especially within the tribe Nemacheilini [9,11]. Besides, the distribution also has led to taxonomic issues, especially in Homatula, Nemacheilus and Schistura [9,11,12].…”