DNA Barcoding Reveals Cryptic Diversity in the Underestimated Genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the Northeastern Qinghai-Tibet Plateau

Abstract

Background: The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs). Results: After careful identification and comparison of the morphology and DNA barcoding of 1,630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions.Conclusions: The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.

phylogatR: Phylogeographic data aggregation and repurposing

“…While single‐locus data has its limitations in making inferences about historical demography (Matumba et al, 2020), DNA barcoding, or the use of other single‐locus DNA markers, has provided tremendous insight into identifying evolutionary significant units and providing information on species in further need of exploration (Bousjein et al, 2021; León‐Tapia, 2021; Nneji et al, 2020; Sholihah et al, 2020; Wang et al, 2020). These data are particularly helpful when aiming to explore broad‐scale patterns such as those on a continental scale (Dincă et al, 2021) or across species (Doorenweerd et al, 2020), especially for a large number of taxonomic groups, as demonstrated here.…”

phylogatR: Phylogeographic data aggregation and repurposing

“…While single-locus data has its limitations in making inferences about historical demography (Matumba et al 2020), DNA barcoding, or the use of other single-locus DNA markers has provided tremendous insight into identifying evolutionary significant units and providing information on species in further need of exploration (Sholihah et al 2020;Wang et al 2020;Nneji et al 2020;Bousjein et al 2021;León-Tapia 2021). These data are particularly helpful when aiming to explore broad-scale patterns such as those on a continental scale (Dinça et al 2021) or across species (Doorenweerd et al 2020), especially for a large number of taxonomic groups, as demonstrated here.…”

Genetic Diversity and Cryptic Species Identification of Genus Triplophysa from River Swat in Malakand Division, Khyber Pakhtunkhwa, Pakistan

“…Te molecular approach is considered backbone for evaluating fsh species evolutionary variation and conservation process for biological resources [27]. Unfortunately, as far as Nucleotide composition and genetic pairwise distance recommend that the calculated species of subfamily Nemacheilinae are organically dissimilar [6]. Te fsh diversity study was conducted to evaluate the genetic diversity and cryptic species identifcation of the genus Triplophysa in the fresh waters of Malakand Division through a molecular and morphological approaches [28].…”

“…Triplophysa has a long confusing classifcation history therefore, the cryptic diversity of the genus Triplophysa will be examined in the study. It belongs to the subfamily Nemacheilinae [6]. Te diversity of fsh is so difcult on morphologically based therefore mitochondrial and nuclear gene sequences have been routinely used because the mitochondrial genomic part is mostly carrying heredity information [7] Te current investigation provides information on the genotype of a few Nemachilidae species from Iranian inland waters, including Paraschistura bampurensis, Oxynoemacheilus kiabii, Turcinemacheilus saadii, Leuciscine cyprinid, Alburnoides bipunctatus and Alburnus alburnus use mitochondrial gene COI [8].…”