Black Amur bream (Megalobrama terminalis), a dominant species, resides in the Pearl River basin, known for its high plasticity in digestive ability. During spawning season, M. terminalis individuals with large body size and high fertility undergo a spawn migratory phase, while other smaller individuals prefer to settlement over migration. It is well known that gut microbial community often underpins the metabolic capability and regulates a wide variety of important functions in fish. However, little was known about how the gut microbiomes affect fish breeding migration. To investigate the variations in the gut microbiome of M. terminalis during the migration, we used high‐throughput 16S rRNA gene sequencing to reveal the distinct composition and diversity of the whole gut microbiome of migrated and nonmigrated population during period of peak reproduction, respectively. Our results indicated that nonmigrated population in estuary had a higher alpha diversity than that of migrated population in main stem. Additionally, an obvious abundant taxa shift between the gut microbiota community of nonmigrated and migrated M. terminalis was also observed. Change of dominant gut taxa from nonmigrated to migrated population was thought to be closely related to their degradation enzymes. Our results suggested that amino acid metabolism and lipid metabolism in migrated population were higher than that in nonmigrated population, providing a line of evidence for that M. terminalis change from partial herbivorous to partial carnivorous diet during breeding migration. We further concluded that, in order to digest foods of higher nutrition to supply energy to spawning migration, M. terminalis regulate activities of the gut microbiome and degradation enzymes, considered to be a key physiological strategy for reproduction.

Understanding genetic diversity patterns of endangered species is an important premise for biodiversity conservation. The critically endangered salamanderAndrias davidianus, endemic to central and southern mainland in China, has suffered from sharp range and population size declines over the past three decades. However, the levels and patterns of genetic diversity ofA. davidianuspopulations in wild remain poorly understood. Herein, we explore the levels and phylogeographic patterns of genetic diversity of wild‐caughtA. davidianususing larvae and adult collection with the aid of sequence variation in (a) the mitochondrial DNA (mtDNA) fragments (n = 320 individuals; 33 localities), (b) 19 whole mtDNA genomes, and (c) nuclear recombinase activating gene 2 (RAG2;n = 88 individuals; 19 localities). Phylogenetic analyses based on mtDNA datasets uncovered seven divergent mitochondrial clades (A–G), which likely originated in association with the uplifting of mountains during the Late Miocene, specific habitat requirements, barriers including mountains and drainages and lower dispersal ability. The distributions of clades were geographic partitioned and confined in neighboring regions. Furthermore, we discovered some mountains, rivers, and provinces harbored more than one clades.RAG2analyses revealed no obvious geographic patterns among the five alleles detected. Our study depicts a relatively intact distribution map ofA. davidianusclades in natural species range and provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this critically endangered organism.

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.

Geographical scale might be expected to impact significantly the efficiency of DNA barcoding as spatially comprehensive sampling provides opportunities to uncover intricate relationships among closely related species and to detect cryptic diversity for widespread taxa. Here, we present a DNA barcoding study on a Xencyprididae subfamily (Culterinae) involving the production of 998 newly generated DNA barcodes from East Asian drainages (80 localities). Together with 513 barcodes mined from BOLD and GenBank, a reference library consisting of 1511 DNA barcodes (116 localities) for 42 species was assembled, accounting for 66% of known Culterinae species. Intraspecific genetic distances are positively correlated to geographical scale, while a negative correlation is detected between interspecific genetic distances and geographical scale. The present study demonstrates that geographical scale influences the efficiency of DNA barcoding by narrowing the width of the barcoding gap. DNA‐based species delimitation analyses delimited 44 molecular operational taxonomic units (MOTUs). Rampant cryptic diversity is detected within eight species with multiple MOTUs, whereas 25 species present mismatch between morphological and molecular delimitations. A total of 18 species are lumped into nine MOTUs due to low interspecific divergence and/or mixed lineages. Several MOTU divergences are hypothesized to relate to known biogeographical barriers and geological events during the Pliocene and Pleistocene. This study provides new insights into the taxonomy and phylogeography of the subfamily Culterinae.

Delimiting ichthyoplankton is fundamental work for monitoring the recruitment process and identifying the spawning and nursing grounds of fishes. Nevertheless, it is extremely difficult to identify the fish during the early stages at the species level based on morphological characters because of the paucity of diagnostic features. In this study, we investigated the fish larval community through large-scale ecosystemic sampling in South China Sea (SCS) during 2013 and 2017 using DNA barcodes. To maintain the morphologies of fish larvae, we preserved the larvae in formalin and developed a technique to recover their DNA. Among the 3,500 chosen larvae, we successfully extracted DNA from 2,787 larval samples and obtained 1,006 high-quality sequences. Blast searches showed that 408 larvae (i.e., 40.5%) could be unambiguously identified to species, 413 larvae (i.e., 41.1%) were ambiguously species delimitation, and 185 larvae (i.e., 18.4%) showed a low match similarity with target sequences. A total of 101 species were identified, among which 38 and 33 species corresponded to demersal and reef-associated species, whereas the remaining 30 species corresponded to benthopelagic, pelagic-oceanic, bathypelagic, and pelagic-neritic species. High-quality larval photographs of the 101 diagnosed species showed intact morphological characters and thus provided a reference for identifying fish species during the early stages based on morphological characters. Our study highlighted the possibility of recovering and amplifying DNA from formalin-fixed samples and provided new insight into the fish larval community in the SCS.