Molecular systematics of Xenocyprinae (teleostei: cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia

Genetic diversity, spatial connectivity, and population structure of Asian silurid catfish Wallago attu (Bloch and Schneider, 1801) in the Ganga River System: insights from mitochondrial DNA analysis

BACKGROUND

The Ganga River System (GRS) is a biodiversity hotspot, its ecological richness is shaped by a complex geological history. In this study, we examined the genetic diversity, spatial connectivity, and population structure of the Asian Silurid catfish, Wallago attu, across seven tributaries of the GRS.

METHODS AND RESULTS

We employed three mitochondrial DNA (mtDNA) regions: cytochrome c oxidase subunit I (COXI), cytochrome b (Cyt b), and control region (CR). Our comprehensive dataset encompassed 2420 bp of mtDNA, derived from 176 W. attu individuals across 19 sampling sites within the seven rivers of GRS. Our findings revealed high gene diversity (Hd:0.99) within W. attu populations. Analysis of Molecular Variance (AMOVA) highlighted that maximum genetic variations were attributed within the populations, and the observed genetic differentiation among the seven populations of W. attu ranged from low to moderate. Network analysis uncovered the presence of three distinct genetic clades, showing no specific association with seven studied rivers. Bayesian skyline plots provided insights into the demographic history of W. attu, suggesting a recent population expansion estimated to have occurred approximately 0.04 million years ago (mya) during the Pleistocene epoch.

CONCLUSIONS

These results significantly enhance our understanding of the genetic diversity and spatial connectivity of W. attu, serving as a vital foundation for developing informed conservation strategies and the sustainable management of this economically valuable resource within the Ganga River System.

Diversity and genetic structure of freshwater shark Wallago attu: an emerging species of commercial interest

Pakistan has natural freshwater resources acting as a hotspot for diverse fish fauna. However, this aquatic fauna is declining at an alarming rate due to over-exploitation, habitat degradation, water pollution, climate change, and certain anthropogenic activities. The freshwater shark, Wallago attu, is a popular edible catfish inhabiting these freshwater ecosystems. Habitat degradation, overfishing, and human activities are heavily impacting the natural population of this species. So, sound knowledge about its population structure is necessary for its proper management in natural waters. The current study involves utilizing two mtDNA markers (COI, Cytb) to assess the genetic structure and differentiation among W. attu populations of Pakistani Rivers. Genetic variability analysis indicated a high haplotype (0.343 ± 0.046-0.870 ± 0.023) and low nucleotide diversity (0.0024 ± 0.012-0.0038 ± 0.018) among single and combined gene sequences, respectively. Overall, River Indus was populated with more diverse fauna of Wallago attu as compared to River Chenab and River Ravi. Population pairwise, Fst values (0.40-0.61) were found to be significantly different (p < 0.01) among three Riverine populations based upon combined gene sequences. The gene flow for the combined gene (COI + Cytb) dataset among three populations was less than 1.0. The transition/transversion bias value R (0.58) was calculated for testing of neutral evolution, and it declared low genetic polymorphism among natural riverine populations of Wallago attu. The current study's findings would be meaningful in planning the management and conservation of this economically important catfish in future.

Descriptions of two new species of the botiid genus Leptobotia Bleeker, 1870 (Teleostei: Cypriniformes) from South China

Two new species of Leptobotia are here described as L. rotundilobus from the Xin'an-Jiang of the upper Qiantang-Jiang basin in both Anhui and Zhejiang Provinces and the Cao'e-Jiang in Zhejiang Province, and L. paucipinna from the Qing-Jiang of the middle Chang-Jiang basin in Hubei Province, South China. Both have a plain brown body as found in L. bellacauda Bohlen & Šlechtová, 2016, L. microphthalma Fu & Ye, 1983, L. posterodorsalis Chen & Lan, 1992 and L. tientainensis (Wu, 1930). The two new species are distinct from these species in vertebral counts, further from L. posterodorsalis in vent placement and further from the other three species in pectoral-fin length. Both differ in caudal-fin coloration and shape, and dorsal-fin location and coloration, and also in internal morphology. Their validity is confirmed by their own monophyly recovered in a phylogenetic analysis based on the mitochondrial cyt b and COI genes.

Age, growth, reproduction and mortality of Xenocypris argentea (Günther,1868) in the lower reaches of the Tangwang River, China

To investigate various population biological parameters of Xenocypris argentea in the lower reaches of the Tangwang River (China), a comprehensive study was conducted for the first time. A total of 1,003 samples were collected from April to November 2022. The collected samples revealed that female X. argentea had total lengths ranging from 12.4 cm to 25.7 cm (weighing 15.86 g to 159.55 g), and male X. argentea had total lengths ranging from 10.8 cm to 23.9 cm (weighing 9.27 g to 121.06 g). The age of the samples was determined using otolith analysis, indicating that the ages ranged from 1 to 5 years old in both females and males. The length-weight relationships were further analyzed, uncovering the allometric growth index (b) was 3.1296 for females, indicating a positive allometric growth pattern. Differently, males exhibited a b value of 3.0274, suggesting an isometric growth pattern. Furthermore, the von Bertalanffy growth formula provided insights into the growth characteristics of X. argentea, revealing an asymptotic total length (L∞) of 36.096 cm and a growth coefficient (K) of 0.121. The analysis of the gonadal somatic index (GSI) and ovarian development period indicated that the spawning period occurred from April to July, with peak spawning in June. The study also explored fecundity-related traits, finding that individual absolute fecundity (FA) ranged from 11,364 eggs to 56,377 eggs, while eviscerated body weight relative fecundity (FW) ranged from 209 eggs/g to 823 eggs/g. The exploitation rate (E) for X. argentea was calculated as 0.574, suggesting that the population of X. argentea has been overexploited. By revealing previously unknown data on the key life history traits of X. argentea, this study has provided valuable insights that are crucial for the development of conservation strategies and policies.

Formosaniaimmaculata, a new species of hillstream loach (Teleostei, Cypriniformes, Gastromyzontidae) from the Ou-Jiang River, Southeast China

Formosaniaimmaculata, a new species, is described from the Ou-Jiang basin in Zhejiang Province, Southeast China. It is distinguished from other species of the genus by having a combination of the following characteristics: body without obvious mottling; snout length longer than postorbital length; abdominal scaleless area extending to middle of pectoral-fin base; shorter rostral barbels, the outermost pair length 112.9%-140.0% of eye diameter; and shorter lower lip papillae, length 19.9%-24.4% of eye diameter. Its validity is also affirmed by its distinct Cytb gene sequence divergence from all congeners and its monophyly recovered in a Cytb gene-based phylogenetic analysis.

Oreonectesdamingshanensis (Cypriniformes, Nemacheilidae), a new species of stream fish from Guangxi, Southwest China

In this work, a new species of the genus Oreonectes is described, named Oreonectesdamingshanensis Yu, Luo, Lan, Xiao & Zhou, sp. nov., collected from the Damingshan Mountains of the Guangxi Zhuang Autonomous Region, China. Phylogenetic trees constructed based on the mitochondrial Cyt b showed that the new species represents an independent evolutionary lineage, with uncorrected genetic distances (p-distance) from congeners ranging from 6.1% to 8.9%. Morphologically, the new species can be distinguished from five other species of the genus by a combination of characters. The discovery of this new species raises the number of known species of Oreonectes from five to six. Our study suggests that O.platycephalus may be a complex containing multiple species and that previously recorded areas need to be further delimited and reevaluated.

Redescription of an endemic mahseer, Tor mahanadicus (David, 1953) from Mahanadi River basin, India based on integrated morphological and molecular techniques

Tor mahanadicus was originally described as Tor mosal mahanadicus with inadequate information on its morphological traits and no designated type specimen. Currently, T. mahanadicus is synonymized with Tor putitora, solely based on partial molecular data despite significant morphological differences. In this study, we performed an integrated morphological and molecular analysis to redescribe T. mahanadicus from the Mahanadi River. Tor mahanadicus is distinguished from all known Indian Tor species by the presence of 2 complete rows of scales between pelvic fin origin and lateral line, small eye (15.3-16.9% in head length), and a wide mouth gap (21.7-23.8% in head length). Moreover, it undoubtedly distinguished from the closely related species Tor putitora by having a wider body depth (26.8-28.2% in standard length vs. 14.5-19.9%), short snout length (23.3-26.4% in head length vs. 28.0-29.3%) and wide inter orbit space (30.5-37.3% in head length vs. 27.6-28.5%). Additionally, the molecular phylogenetic tree generated from a combination of three genes demonstrates a monophyletic clade separate from the Tor putitora clade. Based on the distinct morphological traits and mitochondrial gene sequences, we established Tor mahanadicus as separate species under the genus Tor.

LC-MS/MS based characterisation and differential expression of proteins in Himalayan snow trout, Schizothorax labiatus using LFQ technique

Molecular characterization of fish muscle proteins are nowadays considered as a key component to understand the role of specific proteins involved in various physiological and metabolic processes including their up and down regulation in the organisms. Coldwater fish specimens including snow trouts hold different types of proteins which help them to survive in highly diversified temperatures fluctuating from 0 to 20 °C. So, in current study, the liquid chromatography mass spectrometry using label free quantification technique has been used to investigate the muscle proteome profile of Schizothorax labiatus. For proteomic study, two weight groups of S. labiatus were taken from river Sindh. The proteomic analysis of group 1 revealed that a total of 235 proteins in male and 238 in female fish were recorded. However, when male and female S. labiatus were compared with each other on the basis of spectral count and abundance of peptides by ProteinLynx Global Server software, a total of 14 down-regulated and 22 up-regulated proteins were noted in this group. The highly down-regulated ones included homeodomain protein HoxA2b, retinol-binding protein 4, MHC class II beta chain and proopiomelanocortin while as the highly expressed up-regulated proteins comprised of gonadotropin I beta subunit, NADH dehydrogenase subunit 4, manganese superoxide dismutase, recombinase-activating protein 2, glycosyltransferase, chymotrypsin and cytochrome b. On the other hand, the proteomic characterisation of group 2 of S. labiatus revealed that a total of 227 proteins in male and 194 in female fish were recorded. When male and female S. labiatus were compared with each other by label free quantification, a total of 20 down-regulated and 18 up-regulated proteins were recorded. The down-regulated protein expression of group 2 comprised hepatic lipase, allograft inflammatory factor-1, NADH dehydrogenase subunit 4 and myostatin 1 while the highly expressed up-regulated proteins included glycogen synthase kinase-3 beta variant 2, glycogen synthase kinase-3 beta variant 5, cholecystokinin, glycogen synthase kinase-3 beta variant 3 and cytochrome b. Significant (P < 0.05) difference in the expression of down-regulated and up-regulated proteins was also noted between the two sexes of S. labiatus in each group. According to MS analysis, the proteins primarily concerned with the growth, skeletal muscle development and metabolism were down-regulated in river Sindh, which indicates that growth of fish during the season of collection i.e., winter was slow owing to less food availability, gonad development and low metabolic activity. While, the proteins related to immune response of fish were also noted to be down-regulated thereby signifying that the ecosystem has less pollution loads, microbial, pathogenic and anthropogenic activities. It was also found that the proteins involved in glycogen metabolism, reproductive and metabolic processes, particularly lipid metabolism were up-regulated in S. labiatus. The significant expression of these proteins may be connected to pre-spawning, gonad development and use of stored food as source of energy. The information generated in this study can be applied to future research aimed at enhancing food traceability, food safety, risk management and authenticity analysis.

Mitochondrial diversity and genetic structure of common carp (Cyprinus carpio) in Pearl River and Nandujiang River

Common carp (Cyprinus carpio) is an important valuable cyprinid in China and has been a popular cultured aquaculture species around the globe. Understanding the genetic diversity of wild native common carp not only provides basic data for the protection and utilisation of common carp resources but also assesses the effect of human activities on the genetic diversity of this species. In this study, genetic diversity and population structure of the common carp from 15 sampling populations in the Pearl River and Nandujiang River were determined using a coalescent mitochondrial locus (MLS), including mitochondrial cytochrome b gene (Cytb) and a control region (D-loop) segment. The haplotype diversity and nucleotide diversity were 0.962 and 0.00628 in the Pearl River and 0.808 and 0.00376 in the Nandujiang River, respectively. Phylogenetic and haplotype network analyses indicated that three sub-species (a) C. c. rubrofuscus, (b) C. c. haematopterus and (c) C. c. carpio all occur in both rivers. AMOVA revealed that the variation within populations (86.2%) was the main source of the total variation. Statistically significant genetic differentiation among different Pearl River populations of C. c. rubrofuscus (F_st  = 0.05-0.25) and relatively high genetic differentiation between the Nandujiang River population and the Pearl River populations (F_st  > 0.238) are apparent. Bayesian clustering analyses detected that global populations consisted of eight genetic clusters and examined that Nandujiang River population included relatively pure genetic clusters. Neutrality tests suggested that native populations experienced recent population expansion, and Extended Bayesian Skyline Plot indicated that the common carp populations likely experienced a historical expansion during 0.125-0.250 MYA. Artificial fish propagation and release, escape from fish farms and Fang Sheng may explain the invasion of non-native sub-species in many river sections, such as Laibin, Rongjiang, Huizhou, Heyuan and Zhaoqing. To conserve the native common carp populations, release station should be established to culture native common carp fry. Overall, the findings can be contributed to complementing scientific knowledge for conservation and management of the wild native common carp.

Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India)

Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.

Phylogeography of Aphyocypris normalis Nichols and Pope, 1927 at Hainan Island and adjacent areas based on mitochondrial DNA data

We investigated the genetic structure of the freshwater fish Aphyocypris normalis, in 33 populations around Hainan Island and southern mainland China. Sequencing of the mitochondrial DNA (mtDNA) cytochrome b from 127 specimens yielded 47 haplotypes, from which we inferred a Bayesian tree. This revealed three major divergences: a principal clade of specimens with widespread geographic distribution, plus two clades with limited distribution. We estimated that these diverged between 1.05-0.16 Ma. Additionally, based on molecular data and comparing with the climate patterns of Hainan Island, eight phylogeographic ranges (populations) of A. normalis were constructed: the eastern plain (E), northeastern hills and plain (NE), northwestern hills and lowlands (NW), central mountains (C), southeastern hills and plain (SE), southern mountains and hills (S), southwestern mountains and lowlands (SW), and western lowlands (W). The patterns of geographical divergence in this species do not reflect the isolation caused by the Qiongzhou (Hainan) Strait, which would generally be experienced by terrestrial animals on isolated islands. The present results indicate that the major clades within A. normalis have diverged before the temporary land bridge existed across the strait during the Last Glacial Maximum.

Three new species of Homatula (Teleostei: Nemacheilidae) from Yunnan, China, with comments on habitat conservation

Based on the morphological comparisons and molecular results, three new species of Homatula, i.e., H. geminusclathratus sp. nov., H. microcephala sp. nov., and H. longibarbatus sp. nov., have been described and named from the Lancang-jiang (the upper Mekong River) and the Chuan-he (the upper Black River, a tributary of the Red River) basins. The loaches of Homatula from the Lancang-jiang and the Chuan-he can be distinguished via morphology, genetics, and geographic distribution. All of the 10 recorded species distributed in the Nu-jiang (the upper Salween River), the Lancang-jiang, and the upper Black River share the following combination of character states: whole body, except head, densely scaled; lateral line complete; and a short adipose crest along the dorsal midline of the caudal peduncle, anteriorly not reaching vertically through the anal-fin origin. Species with these characters are called the densely-scaled group of Homatula. The three newly described species belong to the densely-scaled group of Homatula. Based on molecular phylogenetics, these Homatula species form a monophyletic group that can be divided into two clades, the densely-scaled group and the non-densely-scaled group. The densely-scaled group of Homatula includes 13 species occurring between the Nu-jiang and the upper Black River. The non-densely-scaled group is non-monophyletic and includes 14 species that are distributed in the Red, Pearl, Yangtze, and Yellow River basins. Species of the non-densely-scaled group are clustered into four sub-clades that are constrained to the four river basins. Homatula exclusively inhabits mountain streams with rapid or gentle currents, vauclusian springs, underground rivers connected to streams, and ditches near villages and farmland. No specimens of Homatula were collected from the main streams of Lixian-jiang, Lancang-jiang, and Nu-jiang as well as their large tributaries. Small environmental changes in the habitat of Homatula, such as water pollution or extensive human use, can lead to species/population extinction. Effective conservation of rare and endemic fishes, like loaches of Homatula, entails systematic observations and more targeted protection.

Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin

The ichthyofauna of continental islands is characterized by immigration through a land bridge due to fluctuating sea levels. Hainan Island is adjacent to the southern margin of mainland China and provides opportunities for understanding the origin and diversification of freshwater fishes. The aim of our study was to evaluate the level of genetic variation and phylogeographic structure of Opsariichthys hainanensis on Hainan Island and mainland China, using mtDNA cyt b gene (1140 bp) and D-loop (926 bp), nuclear RAG1 gene (1506 bp), and 12 microsatellite loci. Mitochondrial phylogenetic analysis identified five major lineages according to the geographical distribution from different populations. We suggested that two dispersal events occurred: the population in the Changhua River migrated to the Red River (Lineage B), and the populations in the South Hainan region moved northwards to the North Hainan region. However, populations in Northwest Hainan Island dispersed to the populations around the Gulf of Tonkin (Lineage A1) and populations in Northeast Hainan Island dispersed to the populations in mainland China (Lineage A2). Our results indicated that the populations of O. hainanensis suffered a bottleneck event followed by a recent population expansion supported by the ABC analysis. We suggest that O. hainanensis populations were found mostly in the lowlands and a lack of suitable freshwater habitat in southern mainland China and Hainan during the Last Interglacial period, and then expansion occurred during the Last Glacial Maximum.

Population genetic diversity and structure of Rhinogobius candidianus (Gobiidae) in Taiwan: Translocation and release

Rhinogobius candidianus is a freshwater goby distributed in north, northwest, west, and south Taiwan, but this species has been introduced to east Taiwan and became dominant. To investigate its native population genetic diversity and structure and evaluate the sources and diversity of translocated populations, the mitochondrial DNA control region and cytochrome b gene (1981 bp) from 220 specimens were analyzed. These results indicated that (1) the east populations originated from two sources in west Taiwan; (2) translocated populations exist in east Taiwan and south Taiwan; (3) many populations have likely been moved secondarily by human intervention; (4) the effective size of the populations had declined greatly; (5) within the native populations, the ancestral populations colonized Taiwan during the land bridge phase in the Pleistocene through north Taiwan; (6) the landform changes in Taiwan shaped the population structure; and (7) the landforms of the coastline during glaciation also shaped the native range. The low-level genetic diversity, high population differentiation, and population decline greatly suggest the need for resource management and conservation interventions. Four clades (α-δ) should be managed as four distinct evolutionarily significant units, while the translocated populations should be managed as separate management units. Moreover, the translocated populations in east Taiwan should be evaluated and monitored carefully.

Endangered Schizothoracin Fish in the Tarim River Basin Are Threatened by Introgressive Hybridization

Simple Summary

Interspecific hybridization and introgression may threaten the survival of endangered species. Big-head Schizothoracin (Aspiorhynchus laticeps) and Tarim Schizothoracin (Schizothorax biddulphi) are two recognized types of fish of Schizothoracinae which belong to the family Cyprinidae. Big-head Schizothoracin and Tarim Schizothoracin are sympatrically distributed in the Tarim River basin in Xinjiang, China, and have been listed as first-class and second-class national key protected animals, respectively. Based on morphological characteristics, Schizothorax esocinus (another Schizothoracin that occurs in the Tarim River basin) is speculated to be hybrid offspring of Big-head Schizothoracin and Tarim Schizothoracin, but there is no direct genetic evidence for this point. In this study, the hybridization status of Schizothorax esocinus was confirmed by comparing genetic constitutions of mitochondrial DNA (mtDNA) and inter transcribed spacer (ITS2) encoded by the nuclear genome. Extensive hybridization and introgression between Big-head Schizothoracin and Tarim Schizothoracin was detected. Since both Big-head Schizothoracin and Tarim Schizothoracin are critically endangered fishes, risk management due to hybridization is recommended to be considered as a part of current conservation programs.

Abstract

Big-head Schizothoracin (Aspiorhynchus laticeps) and Tarim Schizothoracin (Schizothorax biddulphi) are locally sympatric in the Tarim River Basin. Although another Schizothoracin (Schizothorax esocinus) in Tarim River basin has been speculated to be hybrid offspring of Big-head Schizothoracin and Tarim Schizothoracin, there was no genetic evidence. Previous studies on the genetics and evolution of Schizothoracins in Xinjiang Province were mostly based on mitochondrial DNA (mtDNA), whose characteristics of maternal inheritance made it hard to answer the question of whether there was hybridization and introgression between Big-head Schizothoracin and Tarim Schizothoracin. In this study, cytochrome b (cytb) gene of mtDNA and internal transcribed spacer 2 (ITS2) that is encoded by the nuclear genome were genotyped within the entire samples at the same time. Our results confirmed that Schizothorax esocinus was the hybrid offspring of Big-head Schizothoracin and Tarim Schizothoracin. The heterozygous ITS2 genotypes and/or Aspiorhynchus laticeps-like mtDNA were also detected in a subset of samples that should have been identified as pure Schizothorax biddulphi based on morphology. The ITS2 is characterized by multi-copy, concert evolution, and biparental inheritance. Thus, by comparing with mtDNA data, broad-scale bidirectional hybridization and introgression between Big-head Schizothoracin and Tarim Schizothoracin were revealed. Although interspecific hybridization may play a positive role in ecology and evolution, interspecific hybrids could threaten their parental species by the swamping of genetics and demography. As both parents of hybridization are critically endangered fishes, in this case, it is urgently necessary to strengthen the scientific assessment of the risks of the hybrids and the control of the hybridization and introgression between Aspiorhynchus laticeps and Schizothorax biddulphi in the Tarim River Basin.

Gobiobotia lii, a new species of gudgeon (Teleostei, Gobionidae) from the middle Chang-Jiang Basin, central China, with notes on the validity of G. nicholsi Bănărescu &amp; Nalbant, 1966

Gobiobotia lii is described from the Qi-Shui, a stream tributary on the northern bank of the middle Chang-Jiang mainstem in Hubei Province and Lake Dongting in Hunan Province, central China. The new species is distinguished from all other congeneric species by possessing a combination of the following characters: a naked region of the abdomen adjacent to the ventral mid-line extending to the vent and the vertebral count (4+31–32). The validity of G. lii is confirmed by its monophyletic nature recovered in a phylogenetic analysis, based on the cyt b gene and its significant sequence divergence with sampled congeneric species. Critical notes were given on the species recognition of historically documented eight-barbel gudgeons co-existing in Lake Dongting. Gobiobotia nicholsi Bănărescu &amp; Nalbant, 1966 should be a valid species distinct from G. filifer (Garman, 1912) and both G. pappenheimi Kreyenberg, 1911 and G. boulengeri (=Xenophysogobio boulengeri (Tchang, 1929)) have an erroneous record from the Lake.

Population Genetics Reveals Invasion Origin of Coilia brachygnathus in the Three Gorges Reservoir of the Yangtze River, China

Non-indigenous fish invasions have posed a serious threat to global fish diversity and aquatic ecosystem security. Studying the invasion sources, pathways, and genetic mechanisms by means of population genetics is helpful in the management and control of non-indigenous fishes. In this study, we used mitochondrial Cyt b gene, D-Loop region and microsatellite markers to analyze the genetic diversity and population structure of 12 Coilia brachygnathus populations from the native and invaded regions of the Yangtze River Basin in order to explore the invasion sources, pathways, and genetic mechanisms of C. brachygnathus in the Three Gorges Reservoir. The results showed that the main invasion sources of C. brachygnathus in the Three Gorges Reservoir were the Poyanghu Lake, Dongtinghu Lake, Changhu Lake, and other populations in the middle reaches of the Yangtze River. The invasion pathway may have involved moving upstream through the operation of ship locks. The genetic diversity of C. brachygnathus in the invasive populations was significantly smaller than in the native populations, indicating a founder effect. The low genetic diversity did not affect the successful invasion, confirming that genetic diversity and successful invasion do not always have a simple causal relationship. These results can provide basic data for the prevention and control of C. brachygnathus in the Three Gorges Reservoir and study case for understanding the mechanism of invasion genetics.

Otolith Microchemistry and Demographic History Provide New Insight into the Migratory Behavior and Heterogeneous Genetic Divergence of Coilia grayii in the Pearl River

Coilia grayii is the anadromous form of anchovy that is distributed in the East and South China Seas. It is a common fish species in the estuarine area of the Pearl River. Nevertheless, freshwater populations appear upstream in the Pearl River, but the migratory pathway has been mostly impeded by dam construction. Behavioral differences and constrained habitat within tributaries are suspected of promoting genetic divergence in these populations. In this study, we investigated the migratory behavior and genetic divergence of six populations of C. grayii fragmented by dams based on the otolith strontium/calcium (Sr/Ca) ratio, mitochondrial DNA, and microsatellite genotyping. All populations were in freshwater with low Sr/Ca ratios, except the estuarine population (Humen population) hatched in brackish water. Reduced nucleotide diversity corresponding to distance was observed. Populations from distant hydrological regions exhibited a decline in genetic diversity and a significant difference with the remaining populations after fitting the isolation by distance model. Pairwise fixation indices confirmed these results and moderate and significant differentiation was found between Hengxian site and downstream sites. Furthermore, STRUCTURE analyses revealed that all separated populations exhibited an admixed phylogenetic pattern except for individuals from the Hengxian locality. The upstream sites showed significantly increased resistance to gene flow from the estuarine population because of isolation by the dam. The results of the neutrality test and Bayesian skyline plots demonstrated complex demography—individuals’ experienced historical expansion and partial upper-dam populations had recently undergone a colonization, forming a new genetic structure. Accordingly, this study demonstrates differences in the migration pattern and genetic differentiation of C. grayii as a consequence of demographic history and current processes (habitat fragmentation and colonization).

Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China

There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.

Mitochondrial sequence diversity reveals the hybrid origin of invasive gibel carp (Carassius gibelio) populations in Hungary

BACKGROUND

Invasive gibel carp, Carassius gibelio (Bloch, 1782) has become well-established in the Hungarian waters and now are spreading in the European waters. On major concern now is the potential hybridization between gibel carp and the other invasive species in the Carassius auratus complex (CAC), which may further accelerate the spread of the whole invasive species complex. The identification of gibel carp and their hybrids is difficult because of its morphological similarity to the other species in CAC. Here we carry out a genomic assessment to understand the history of gibel carp invasion and its phylogenetic relationship with the other species in CAC. Three loci of the mitochondrial genome (D-loop, CoI, Cytb) were used to determine the phylogenetic origin of individuals and relarionship among six gibel carp populations and the other species in the CAC.

METHODOLGY

A total of 132 gibel carp samples from six locations in Southern Transdanubia (Hungary) were collected after phenotypic identification to measure the genetic diversity within and among gibel carp populations of Southern Transdanubia (Hungary). The genetic background was examined by the sequences of the mitochondrial genome: D-loop, Cytochrome c oxidase I (CoI) and Cytochrome b (Cytb). Mitochondrial genetic markers are excellent tools for phylogenetic studies because they are maternally inherited. Successfully identified haplotypes were aligned and with reference sequences in nucleotide databases (i.e., NCBI-BLAST: National Centre for Biotechnology Information and BOLD: Barcode of Life Data System). The phylogenetic relationships among gibel carp populations were then analyzed together with the reference sequences to understand the relationship and the level of hybridization with the species in CAC.

RESULTS

Among the 132 aligned D-loop sequences 22 haplotypes were identified. Further examination of representative individuals of the 22 haplotypes, six Cytb and four CoI sequences were detected. The largest number of haplotypes of all three loci were found in Lake Balaton, the largest shallow lake in Central Europe. Based on the NCBI-BLAST alignment of the D-loop, haplotypes of Carassius auratus auratus and Carassius a. buergeri in CAC were identified in the C. gibelio samples. Further analysis of haplotypes with the other two mitochondrial markers confirmed the occurrence of intragenus hybridization of C. gibelio in the Hungarian waters.

CONCLUSION

By using three mitochondrial markers (D-loop, Cytb, CoI), we genomically characterized a gibel carp-complex in Hungarian waters and assessed the C. gibelio phylogenetic status between them. Hybrid origin of locally invasive Carassius taxon was detected in Hungary. It points out that invasive species are not only present in Hungary but reproduce with each other in the waters, further accelerating their spread.

Vanmaneniamarmorata, a new species of loach (Teleostei: Gastromyzontidae) from the middle Chang-Jiang Basin in Guizhou Province, south China

Background

The gastromyzontid genus Vanmanenia was established by Hora in 1932, based on the type species Vanmaneniastenosoma. The genus is a loach group adapted to running waters of streams from southern China, northern Vietnam and Laos. Currently, 19 valid species of the genus have been recognised. The northernmost distribution of the genus is the Yangtze River (= Chang-Jiang in Chinese) Basin and five species (V.maculata, V.intermedia, V.stenosoma, V.pseudostriata and V.gymnetrus) have been reported from the Basin.

New information

Vanmaneniamarmorata, a new hillstream species of loach, is here described from the middle Chang-Jiang Basin in Guizhou Province, south China. It is distinguished from its congeners by having a combination of the following characters: three triangular-shaped rostral lobules; postdorsal saddles wider than interspaces; a more backwards-placed anus (the vent to anal distance 30.5–36.9% of the pelvic to anal distance); a larger gill opening with its upper extremity reaching the level of the middle of the orbit; anal-fin base length 5.6–6.4% of SL; caudal-peduncle length 11.6–12.9% of SL; prepelvic length 51.1–53.4% of SL. Its validity is also affirmed by its distinct cyt b gene sequence divergence with all sampled congeners and its monophyly recovered in a cyt b gene-based phylogenetic analysis.

Relationships Among Trophic Niche Width, Morphological Variation, and Genetic Diversity of Hemiculter leucisculus in China

According to the niche variation hypothesis (NVH), the populations with wider niches are phenotypically more variable than those with narrow niches. Giller expanded the NVH, suggesting that the niche width, morphological variation, and genetic diversity are all positively correlated. However, the hypothesis has been a subject of debate and discussion. In the present study, the NVH was tested by analyzing the relationships among trophic niche width, morphological variation, and genetic diversity of Hemiculter leucisculus, a widespread cyprinid fish. The fish samples were collected from six sites across Haihe, the Yellow, and the Yangtze River basins in China. The relationships among trophic niche width, morphological variation, and genetic diversity were analyzed using Pearson correlation at the inter-population level. Our analysis indicated that trophic niche width is significantly positively correlated with morphological variation, which corroborates the NVH. Morphological variation was significantly correlated to genetic diversity. However, no relationship was observed between trophic niche width and genetic diversity. We inferred that the dietary niche of H. leucisculus might change due to the plastic response toward environmental changes rather than due to the genetic variation. We also suggest that the effects of environment and heredity on the niche of the freshwater fish should be quantified separately in further studies.

Phylogeographic structure of the dwarf snakehead (Channa gachua) around Gulf of Tonkin: Historical biogeography and pronounced effects of sea-level changes

Geological events, landscape features, and climate fluctuations have shaped the distribution of genetic diversity and evolutionary history in freshwater fish, but little attention has been paid to that around the Gulf of Tonkin; therefore, we investigated the phylogeographic structure of the dwarf snakehead (Channa gachua) on Hainan Island and mainland China, as well as two populations in Vietnam. We attempted to elucidate the origins of freshwater fish in South Hainan by incorporating genetic data from DNA markers on both the mitochondrial cytochrome b gene (cyt b) and the nuclear recombination-activating gene 1 (RAG-1). Mitochondrial phylogenetic analysis identified two major lineages (lineages A and B), which may represent separate species. Divergence data suggested that C. gachua populations diverged between 0.516 and 2.376 myr. The divergence of the two cryptic species is congruent with sea-level rise, which subsequently isolated Hainan from the mainland. During the Pleistocene glaciations, the entire region of the Gulf of Tonkin and the Qiongzhou Strait became part of the coastal plain of the Asian continent, which might have resulted in the current distribution patterns and dispersal routes of C. gachua populations. The formation of three sublineages in lineage A indicated that the Gulf of Tonkin was a geographical barrier between Hainan Island and mainland China but not between Vietnam and Hainan Island. The results of this study may help to elucidate the origins of freshwater fish in South Hainan and the phylogeographic structure of C. gachua.

Population genetic structure of sharpbelly Hemiculter leucisculus (Basilesky, 1855) and morphological diversification along climate gradients in China

Sharpbelly Hemiculter leucisculus (Basilewski, 1855) is a small, widespread, and native cyprinid fish with prominent habitat suitability and high invasive potential and is becoming the dominant species in freshwater ecosystems under intensified environmental disturbances. But how H. leucisculus acclimates to extremely heterogeneous environments remains unclear. In current study, the genetic structure of H. leucisculus was analyzed using Bayesian phylogenetic inference, haplotype network, and STRUCTURE base on cytb gene across 18 populations spanning 20 degrees of latitude and 18 degrees of longitude in China. The morphological diversification of body size and shape for H. leucisculus along the climate gradient was studied. The results showed that the 18 H. leucisculus populations were divided into 3 clusters: one cluster mainly from Huanghe River Basin, another cluster mainly from Yangzi River Basin, and H cluster containing Hainan and Beihai populations. The fish from southern populations were deeper bodied while individuals from northern populations were more slender. Inland individuals were more streamlined while coastal individuals were of deeper body. The partial Mantel test predicts that the potential mechanism underlining the intraspecies morphological diversification along climate gradients is primarily the divergent selection pressures among different environments, while genetic variation had less contribution to morphological differentiation. The formation of the Nanling Mountain Range could drive genetic differentiation between Beihai population and those from Yangzi River Basin. The present results highlight strong selective pressures of climate on widespread species and enrich morphological differentiation basis of acclimation for species with high habitat suitability and invasive potential.

Triplophysa wulongensis, a new species of cave-dwelling loach (Teleostei, Nemacheilidae) from Chongqing, Southwest China

We describe a new species of cave-dwelling loach, Triplophysawulongensissp. nov., based on specimens collected in a subterranean pool in a cave in Wulong County, Chongqing, Southwest China. The pool is connected to the Wujiang River drainage. Triplophysawulongensis differs from its congeners by the following combination of characters: eyes present, caudal fin with 18 branched rays; posterior chamber of the air bladder degenerate; stomach U-shaped; intestine without bends or loops immediately posterior to stomach; body smooth and scaleless, and lateral line complete. The mitochondrial cytochrome b sequence differs from those of other published sequences of species of Triplophysa by 14.9–24.9% in K2P distance. Phylogenetic analysis based on cytochrome b gene sequences recovered T.wulongensis as sister taxon to all other cave-dwelling species of Triplophysa.

Re-description of the loach species Leptobotia citrauratea (Teleostei, Botiidae), with the description of L. brachycephala from southern Zhejiang Province, China

Leptobotiacitrauratea (Nichols, 1925), a loach species, originally described from Dongting Lake, was recently rehabilitated, based on the examination of the holotype and non-topotypical specimens. Several field surveys conducted from 2016 to 2019 in Zhejiang, Jiangxi and Hunan Provinces, P.R. China, yielded many specimens of Leptobotia which were initially identified as L.citrauratea. Molecular and morphological analyses of these specimens demonstrated that two distinct species are involved. One was identified as L.citrauratea, represented by specimens from both the Poyang and Dongting Lake (type locality) systems in Jiangxi and Hunan Provinces, and the other species is described as L.brachycephala, represented by specimens from the Ou-Jiang and Qu-Jiang, two coastal rivers of Zhejiang Province, China. Leptobotiabrachycephala resembles L.citrauratea and L.micra in having a row of orange dots or an orange stripe along the dorsal mid-line of the body, extending from the nape to the caudal-fin base – a unique character in Leptobotia. Leptobotiabrachycephala differs from L.citrauratea and L.micra Bohlen & Šlechtová, 2017, in caudal-fin shape and pelvic-fin insertion and proportional measurements including caudal-fin length, head length, predorsal length and anal-fin length. Its species status was further corroborated by position in a molecular phylogenetic analysis, based on the mitochondrial cyt b gene and its minimum uncorrected p-distance (2.9%) from congeneric species.

Genetic and morphological assessment of a vulnerable large catfish, Silonia silondia (Hamilton, 1822), in natural populations from India

Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.

Temporal species-level composition of larvae resources in the lower Pearl River drainage and implications for species' reproductive cycles

Resolving the temporal community composition of a larvae population can not only further our understanding of the regional species composition but also help us to infer the reproductive times of regional fish taxa, which can have implications on the development of effective monitoring and conservation policies for the regional fish stock. Nevertheless, correctly diagnosing the fish larvae is extremely challenging due to the paucity of diagnostic morphological characters at the species level. Based on daily larval samplings during March and October in 2018, this study combined morphological features with a DNA barcode technique to determine the species composition of fish larvae in the lower Pearl River drainage (LPR) and evaluate the spawning periods of identified species. Due to an absence of reference barcodes for LPR fishes, a DNA barcode library of adult fishes in the LPR was built for 384 individuals representing 78 morphological species. Analyses demonstrated the usability of the barcode library and uncovered many undetected mitochondrial lineages in 12 species. Morphological analyses performed on 81 temporal larval samples revealed 25 morphotypes and assigned 9 morphotypes into the species level. A total of 1624 larvae from 96 temporal larval samples were selected for molecular identification, and high quality barcoding sequences were obtained from 1391 larvae. We accurately assigned 1078 larvae to 37 species using our barcode library and published database. Among the identified species, a critically endangered species, namely, Ochetobius elongatus, and several invasive species were examined, providing a new perspective to assess the stock of regional endangered and invasive species. Furthermore, this study found high species diversity occurred primarily between May and September, and clarified the spawning periods of identified species inferred from the temporal occurrences of larvae. Above all, our study highlights the applicability to fish larval ecology to assist conservation and fishery management efforts.

Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration

The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.

Genetic diversity of Rhinogobius delicatus (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan

Mitochondrial DNA cytochrome b and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby Rhinogobius delicatus from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation (F _ST=0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of R. delicatus were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, Onychostoma alticorpus, Aphyocypris kikuckii and Hemimyzon taitungensis, our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.

Mitochondrial DNA markers reveal genetic connectivity among populations of Osteoglossiform fish Chitala chitala

Genetic diversity and population structure in Indian featherback fish, Chitala chitala (Hamilton, 1822) was investigated by combined analyses of two full mitochondrial genes, ATPase 6/8 and Cytochrome b. A total of 403 individuals, collected from 14 rivers yielded 61 haplotypes. Hierarchical partitioning analysis identified 19.01% variance 'among' and 80.99% variance 'within groups and populations'. The mean coefficient of genetic differentiation (F_ST) was observed to be significant 0.26 (p < 0.05). Mantel tests rejected the hypothesis that genetic and geographic distances were correlated. The patterns of genetic differentiation, AMOVA and principal coordinate analyses indicated that natural populations were sub-structured and comprised of four genetic stocks of C. chitala in Indian rivers. The results also supported the higher resolution potential of concatenated gene sequences. The knowledge of genetic variation and divergence, from this study, can be utilized for its scientific conservation and management in the wild.

Coexistence of Three Divergent mtDNA Lineages in Northeast Asia Provides New Insights into Phylogeography of Goldfish (Carssius auratus)

Simple Summary

Goldfish (Carassius auratus) is a well-known fish as food and as a pet, which is also frequently used as experimental animal. A unique mtDNA sequence was detected in a sample from our experimental station, which motivated us to study genetic constitution of goldfish in Northeast Asia. Three divergent mtDNA lineages were confirmed to coexist in this region. Two of which corresponded to the known lineages (C2 and C6), which was consistent with the zoogeographical records that there were two sympatric subspecies in Amur river basin. However, the third one (lineage C7) was largely neglected in the previous studies. Our results suggested lineage C7 had a wide distribution from Central Asia to Northeast Asia.

Abstract

Goldfish (Carassius aurautus), which is a middle size cyprinid, widely distribute throughout Eurasia. Phylogeographic studies using mtDNA markers have revealed several divergent lineages within goldfish. In this study, mtDNA variations were determined to elucidate the phylogeographical pattern and genetic structure of goldfish in Northeast Asia. A total of 1054 individuals from Amur river basin were analyzed, which including five newly collected populations and four previously reported populations. Three distinct mtDNA lineages were identified in those samples, two of which corresponded to two known lineages C2 and C6, respectively. The third lineage referred to as C7, following six known lineages of goldfish in mainland Eurasia. AMOVA results suggested that most of the genetic variations were among lineages, rather than among populations or twice samplings. We noted that the control region (CR) and cytochrome b (cytb) sequences of lineage C7 have been reported in previous studies, respectively. However, the evolutionary position and distribution pattern of this lineage was not discussed in the context of the species. Our results showed that “odd” CR and “hidden” cytb sequences from Central Asia represent the same mtDNA lineage of goldfish. The known samples of C7 lineage were collected from Central Asia (Eastern Kazakhstan and Western Mongolia) to East Asia (Northeast China and Far East Russia), which suggested that it had a wider distribution, rather than limit in Central Asia.

Genetic diversity and structure of the Chinese lake gudgeon (Sarcocheilichthys sinensis)

Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (θ _π = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (T_MRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, S. sinensis dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.

Evaluation of the effect of longitudinal connectivity in population genetic structure of endangered golden mahseer, Tor putitora (Cyprinidae), in Himalayan rivers: Implications for its conservation

In many aquatic species, alteration of habitats and human-induced barriers shape the population's genetic structure in rivers with longitudinal connectivity. The golden mahseer, Tor putitora (GM) is an endangered and sensitive cyprinid species. It is considered an indicator of a healthy freshwater ecosystem and is found in cold-water habitats. Therefore, it is crucial to understand how longitudinal connectivity and anthropogenic factors affect the diversity and population genetic structure of GM. The population genetic structure, gene flow and demography of the GM in four Himalayan rivers were investigated by mitochondrial cytochrome b gene (cyt b) as well as microsatellite genotyping. The results showed overall high mtDNA diversity (hd: 0.795) couple with low nucleotide diversity (π: 0.0012) in all GM populations. We also found significant levels of observed heterozygosity (ranging from 0.618 to 0.676), with three genetic clusters. The mtDNA and microsatellite analysis suggested that there are close genetic relationships between the Bhagirathi and Ganga populations; whereas, significant level of genetic differentiation was observed with that of Alaknanda and Yamuna populations. Haplotype distribution, unimodal distribution graph and results of the neutrality test indicated a sign of recent population growth in the GM population. Analysis of molecular variance (AMOVA) and spatial molecular variance (SAMOVA) revealed existence of genetic structures in GM populations. In addition, spatial genetic analysis detected a significant correlation between the pairwise genetic and geographical distances for the entire study area (Mantel test, rM = 0.126; P = 0.010). Considering the significant level of heterozygosity, high rate of unidirectional migration and the intra-population structuring in Alaknanda and Yamuna, it is crucial to propose an effective conservation plan for the GM populations. In general, dams obstruct continuous water flow and create isolated microhabitats. Therefore, we recommend the establishment of microscale protected areas near GM breeding sites and construction of fish pass to maintain the genetic connectivity of fish species that enhance viable populations.

Molecular phylogeny and biogeography of Triplophysa stone loaches in the Central Chinese Mountains

The geological structure and history of mountains often cause highly complex patterns of evolution. The origin and diversity of the genus Triplophysa is considered to be closely associated with the rapid and persistent rise of the Qinghai-Tibet Plateau (QTP). Species of the genus are widely distributed in the QTP and adjacent regions, and are strongly adapted to its extreme environments. However, the Central Chinese Mountains (CCM), which are far apart from the QTP, also have many Triplophysa populations and yet their taxonomy, phylogeny and origin are unknown. We used three mitochondrial genes of 266 individuals from 29 sites in the CCM to shed light on the evolution of these Triplophysa populations. Phylogenetic analyses and species delimitation revealed seven distinct molecular operational taxonomic units (mOTUs) in the CCM, each with low genetic diversity. Molecular clock and biogeographic analyses suggested that vicariance events resulting from the rapid uplifting of the Qinling and Taihang Mountains initialized diversification in the Pliocene. During the early Pleistocene, dispersal events in the central parts of the Yellow River drainage altered genetic diversity and led to the currently observed biogeographic patterns. Our results suggest the presence of at least six species of Triplophysa in the CCM and more are likely to be discovered in the future.

Spatial genetic structure of Opsariichthys hainanensis in South China

South China presents an excellent opportunity to build a phylogeographic paradigm for complex geological history, including mountain lifting, climate change, and river capture/reversal events. The phylogeography of cyprinids, particularly Opsariichthys hainanensis, an endemic species restricted to South China, was examined to explore the relationship between the populations in Red River, Hainan Island and its adjacent mainland China. A total of 37 haplotypes were genotyped for the mitochondrial cytochrome b (Cyt b) gene in 115 specimens from 11 river systems. Relatively high levels of haplotype diversity (h = 0.946) and low levels of nucleotide diversity (π = 0.014) were detected in O. hainanensis. Four major phylogenetic haplotype groups revealed a relationship between phylogeny and geography. Our results found that (i) the ancestral populations of O. hainanensis were distributed south of the Wuzhishan and Yinggeling mountains, including the Changhua River on Hainan Island, and then spread to the surrounding areas, (ii) the admixtures within lineages occurred between the Red River in North Vietnam and the Changhua River in western Hainan Island and (iii) indicated that the exposure of straits and shelves under water retreat, provides opportunities for population dispersion during glaciations.

Better Resolution for Cytochrome b than Cytochrome c Oxidase Subunit I to Identify Schizothorax Species (Teleostei: Cyprinidae) from the Tibetan Plateau and Its Adjacent Area

The genus Schizothorax is one of the most diverse groups of schizothoracine fish. Many species within this genus possess highly similar morphological characters and are very difficult to be identified accurately only based on morphology. The present study aims to test the effectiveness of mitochondrial cytochrome c oxidase subunit I (COI) gene and cytochrome b (Cytb) gene for discriminating the Schizothorax fish. A total of 185 individuals of 11 species for COI gene and 264 individuals of 23 species for Cytb gene were used for analyzing, respectively. According to the genetic distances, only one species based on COI gene and five species based on Cytb gene had "barcoding gaps," respectively. The tree-based analysis displayed that four species based on COI gene and six species based on Cytb gene clustered monophyletic group with strong support, respectively. The optimal threshold value of Schizothorax is 0.005 based on COI gene and 0.008 based on Cytb gene. The results of genetic similarity tests performed through online BLAST showed that 108 of 185 similarity searches succeeded in identifying conspecific sequences based on COI gene and 199 of 264 succeeded in identifying conspecific sequences based on Cytb gene. Considering greater interspecific genetic distance in Kimura 2-parameter (K2P) analysis and many clades with higher supporting values in tree-based analysis, we suggest that Cytb gene has better resolution in discrimination of Schizothorax species than COI gene. However, there are still many confused clustering relationships based on molecular data currently available. Incomplete lineage sorting, the existence of possible cryptic species and problematic morphological identification, etc. might have greatly weakened the resolution of Cytb gene in discrimination of Schizothorax species.

Phylogeographic analyses of a migratory freshwater fish (Megalobrama terminalis) reveal a shallow genetic structure and pronounced effects of sea-level changes

Different types of fish taxa generally seem to present diverse phylogeographic structures and show different responses to environmental changes. In southern China, however, a large number of phylogeographic studies have been employed for small and/or benthic fish species, while phylogeographic patterns of larger and migratory species are not well understood. In this study, we chose Megalobrama terminalis, an endemic cyprinid from Southern China with a median size and relatively high migratory potential as a candidate to explore the phylogeographic structure and to seek the relevant driving forces using a multilocus approach (two mitochondrial markers and three nuclear markers). Our results show that M. terminalis exhibits three mtDNA genetic groups, each presenting genetic structure to the local geography, but the differentiation level was much weaker than that of small and/or benthic fish species reported in earlier studies. Nuclear loci did not observe pronounced genetic group subdivision, but did examine noteworthy genetic differentiation between the Hainan Island population and the mainland populations. Divergence time estimation and demographic analyses suggest that sea-level changes associated with the Late Pleistocene glacial cycles have exerted pronounced effects on the divergence of the three groups and the expansion of M. terminalis populations. Above all, our study provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this endemic organism.

Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA

The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.

Genetic diversity and temporal changes of an endemic cyprinid fish species, Ancherythroculter nigrocauda, from the upper reaches of Yangtze River

Small populations with low genetic diversity are prone to extinction. Knowledge on the genetic diversity and structure of small populations and their genetic response to anthropogenic effects are of critical importance for conservation management. In this study, samples of Ancherythroculter nigrocauda, an endemic cyprinid fish from the upper reaches of Yangtze River, were collected from five sites to analyze their genetic diversity and population structure using mitochondrial cytochrome b gene and 14 microsatellite loci. Haplotype diversity, nucleotide diversity, and expected heterozygosity indicated that the A. nigrocauda populations had low genetic diversity, and decreased heavily from 2001 to 2016. Significant genetic differentiation was found among different populations in the cyt b gene and SSR markers based on the genetic differentiation index (F ST), whereas no differentiation was found in 2001. Haplotype genealogy showed that eight out of 15 haplotypes were private to one population. The SSR STRUCTURE analysis showed that there were four genetic clusters in the A. nigrocauda samples, with each population forming a single cluster, except for the Chishui River (CSR) and Mudong River (MDR) populations, which formed a common cluster. Therefore, loss of genetic diversity and increased genetic differentiation were found in the A. nigrocauda populations, which could be attributed to dam construction, overfishing, and water pollution in the upper Yangtze River. It is therefore recommended that the government should ban fishing, control water pollution, increase river connectivity, and establish artificial breeding and stocking.

Population structure of Aphyocypris normalis: phylogeography and systematics

Aphyocyprisnormalis (Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of A.normalis using sequences of the mitochondrial DNA control region and cytochrome b gene (2,086 bp). In total, 107 specimens were collected from nine populations. All 105 mtDNA haplotypes were identified as belonging to two allopatric phylogroups. The results of a statistical dispersal-vicariance analysis (S-DIVA) suggested that the ancestral populations of A.normalis were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices N_ST (0.532) and G_ST (0.004) revealed that the phylogeny and geography had a significant relationship. Our study found that (1) the Wuzhishan and Yinggeling Mountain Range was an important barrier limiting gene exchange between populations on both sides; (2) cyclic climate changes may have shaped migrations and population differentiations; and (3) different colonization times caused different population diversities between codistributed species. In addition, the inter- and intraspecific diversities of the genus Aphyocypris were estimated.

Genetic structure of two sympatric gudgeon fishes (Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin

Background

Xenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions.

Methods

In the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa. Microsatellite DNA data, jointly with traditional summary statistics including F _ST and F _is, were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history.

Results

Xenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa.

Discussion

The genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity.

Molecular identification and phylogenetic analysis of mitogenome of the Xenocypris davidi from Cao’e River

In this study, the complete mitochondrial genome sequence of a Xenocypris davidi from Cao’e River was sequenced. The complete mitogenome of X. davidi was 16,630 bp in length, it contains the structure of 22 transfer RNA genes, 13 protein coding genes, 2 ribosomal RNA genes, and 1 non-coding region. The gene arrangement and organization in the mitogenome of X. davidi were in accordance with other Cyprinidae fishes. The results of phylogenetic analysis revealed that the mitochondrial genome sequence could provide useful information for the conservation genetics and evolution study of X. davidi.