We report new records of Triplophysa strauchii (Kessler, 1874) from the middle Zeravshan river drainage in Uzbekistan. Previously, within this drainage, the species was known only from the upper reaches of this river in Tajikistan. Morphological and molecular (COI) analyses of specimens collected in 2022 and 2024 confirm that these specimens are conspecific with populations from the Syr Darya drainage. These findings document a significant westward range expansion of T. strauchii in the Zeravshan River. Specifically, the record from Narpay District represents the westernmost known limit of this species’ distribution, highlighting its continued westward expansion in Central Asia.

Food scarcity is a major ecological challenge for cavefish; however, their coordinated physiological and molecular responses to prolonged starvation remain poorly understood. Here, we characterized the responses of Triplophysa rosa to 30, 60, and 90 days of food deprivation under controlled laboratory conditions by integrating growth measurements, histology, transcriptomics, quantitative reverse transcription PCR, and transmission electron microscopy. Starvation inhibited growth, reduced the condition factor and hepatosomatic index, and induced hepatocyte shrinkage, consistent with mobilization of hepatic energy reserves. Liver genes with declining temporal expression were enriched mainly in lipid biosynthesis, cholesterol metabolism, ribosomal function, and cell-cycle pathways, consistent with reduced biosynthetic activity. In the spleen, immune-related transcription increased during early starvation and declined at later stages, while the greater prominence of melano-macrophage centers was consistent with greater involvement of cellular clearance and tissue maintenance during prolonged starvation. Prolonged starvation also increased the expression of autophagy-related genes in the liver and spleen, and autophagy-related structures became more prominent in representative transmission electron microscopy images, consistent with increased involvement of intracellular recycling. Together, these findings reveal a coordinated temporal response involving metabolic adjustment, stage-dependent reorganization of splenic immune-related processes, and autophagy-associated cellular maintenance in T. rosa. This integrated approach improves our understanding of physiological maintenance during sustained nutrient limitation in cave-restricted fish.

A robust reassessment of extinction risk is crucial for developing evidence-based conservation strategies and preventing irreversible biodiversity loss. Sturgeons are among the most threatened freshwater fishes worldwide, yet extinction risk evaluations for the critically endangered Amu Darya false shovelnose sturgeons (Pseudoscaphirhynchus kaufmanni and P. hermanni) still largely depend on legacy information that does not reflect recent human disturbances. To re-evaluate the extinction risk of these sturgeons, we combined updated occurrence records, traditional morphometric data, mitochondrial genetic markers, and ethnobiological surveys from field expeditions, market inspections, and community interviews conducted during 2019-2024. Our results showed dramatic contraction in distribution range and an almost complete loss of population structure. The long-snouted form of P. hermanni is likely already extinct, and the short-snouted form now persists only in fragmented habitats in the middle and lower Amu Darya. Morphological comparisons revealed a marked decrease in body length and weight, indicating size-selective removal linked to illegal poaching. Genetic analyses also revealed declining diversity and signals of demographic bottlenecks, consistent with severely reduced adaptive potential. Taken together, our results indicate an urgent need for coordinated transboundary conservation to avert the imminent extinction of the two critically endangered species.

Local fish diversity in lakes has severely declined in the last century under the effects of climate change and human activities. Thus, examining the underlying factors and implementing appropriate measures are crucial for preventing further aquatic biodiversity losses. Environmental DNA (eDNA) metabarcoding represents a promising tool for improving fish population monitoring. While spatiotemporal variations of fish eDNA in lentic ecosystems have become a research focus, effective monitoring techniques remain limited. Therefore, this study used eDNA metabarcoding to monitor the diversity and spatiotemporal distribution of fish in Erhai Lake, China. Water samples from the shore, nearshore, and midline were collected from 2020 to 2021 during summer and autumn. Thirty-six taxa, including 5 native (one endangered species, Schizothorax taliensis) and 31 non-native taxa, were detected. Seasonal and spatial differences in fish community structure were observed. The seasonal distribution was primarily influenced by water temperature and nutrient status, while the spatial distribution was affected by water depth. Most fish species found in the lake were detected in shoreline samples, suggesting that shoreline sampling is a cost-effective strategy for monitoring fish diversity. These findings confirmed that fine-scale spatial sampling and eDNA metabarcoding represent effective tools for monitoring fish diversity and spatiotemporal distribution in lakes.

The South-Central China (SCC) region is a global biodiversity hotspot that harbors considerable aquatic endemism; however, the evolutionary history of its cave-adapted Triplophysa (Cypriniformes: Nemacheilidae) species remains unresolved to date because of limited genetic markers and sampling. Here, we employed low-coverage whole-genome sequencing (lcWGS) and a newly designed Nemacheilidae-specific ultraconserved element (UCE) probe set to generate multiple markers and investigated the phylogenomics of 89 individuals of genus Triplophysa, spanning both cave- and riverine-adapted lineages. (1) Our phylogenetic reconstruction revealed a well-supported backbone phylogeny for cave-adapted Triplophysa, subdividing them into four main clades. (2) Divergence dating suggested that cave-adapted Triplophysa originated in the early Miocene (∼21 MYA), sharing a common ancestor with Triplophysa wulongensis. (3) Genome-wide tests (QuIBL, f-branch) demonstrated extensive incomplete lineage sorting and ancient introgression among ancestral lineages, suggesting that reticulate evolution may have driven the radiation of these cave fishes by providing a reservoir of genetic variation. Based on our results, we propose a scenario in which the early colonization of cave-adapted Triplophysa species was catalyzed by tectonic activity along the Ailao Shan-Red River shear zone (ARSZ). Our findings provide the first genome-scale evidence linking Miocene tectonics to the origin and diversification of subterranean ichthyofauna in SCC.

Sperm storage within the female reproductive tract is widespread among animal species with internal fertilization, such as the fish family Poeciliidae, wherein the females possess a sperm storage micropocket (SSP) that can store sperm for up to a year. However, the underlying mechanism and morphogenesis of SSP remain unclear. Here, using histological analysis, we found that the SSP of the western mosquitofish (Gambusia affinis) was associated with protrusions arising from the previtellogenic oocyte (PO). Similar protrusions occur in the PO of Poecilia reticulata, P. latipinna, Xiphophorus helleri, and X. maculatus, suggesting that such PO-derived protrusions might be a universal feature in Poeciliidae. These protrusions exhibit significant differences in structural composition compared to the cytoplasm. Furthermore, the area of these protrusions positively correlates with the total area of the oocytes. After maturing, the protrusions split from the oocytes, leaving behind sac-like structures composed of germinal epithelium, which later develop into the SSP for storing sperm. The bottom of the SSP is composed of a single layer of germinal epithelium. We describe and depict the protrusion formation process in the fish family Poeciliidae during the previtellogenic stage, elucidating the SSP morphogenesis.

Sinibotia species, investigated for morphology and species divergence owing to comparable body patterns and frequent sympatric occurrences, show high morphological similarity and close phylogenetic relationships, which challenge their accurate distinguishing via conventional morphological methods. Hence, multivariate morphometric (MM) and geometric morphometric (GM) analyses were used to assess the morphological differences between Sinibotia species (S. superciliaris, S. reevesae, S. robusta, S. pulchra, and S. zebra) habiting the Tuo River (Zizhong County) and Li and Lipu Rivers (Pingle County) based on 40 morphological traits and 34 landmarks. The morphological traits of S. robusta contrasted with those of S. pulchra and S. zebra, whereas S. superciliaris and S. reevesae showed similar morphologies, consistent with the cluster results. MM analysis using discriminant function analysis along with GM methods such as canonical variate analysis and relative distortion analysis enabled the differentiation between the Sinibotia species. Morphological variations were primarily reflected in snout length, nasal snout distance, head depth, body depth, caudal fin length, and dorsal fin length. MM effectively quantified linear size differences, whereas GM better captured and visualized complex variations in overall shape. The combined morphological evidence presented in this study contributes significantly to the identification of species, phylogenetic relationships, and ecological adaptations of Sinibotia species, thereby strengthening the theoretical rationale for the conservation and sustainable utilization of this genus.

Sex chromosome (SC) evolution is a longstanding topic of focus in evolutionary biology. Teleosts often exhibit rapid turnover of SCs and sex-determining (SD) genes, alongside a diverse range of SC differentiation mechanisms. On the basis of new chromosome-scale assemblies of three Silurus species (S. microdorsalis, S. glanis, and S. lanzhouensis) and two outgroup species (Pterocryptis cochinchinensis and Kryptopterus bicirrhis), along with our previous assemblies of S. meridionalis and S. asotus, we traced the evolution of SC in the Silurus genus (Siluriformes), following the fate of the known SD gene amhr2y. Phylogenetic analysis showed that amhr2y occurred at least before the divergence of Pterocryptis, Kryptopterus, and Silurus and lost in P. cochinchinensis and K. bicirrhis. Chr24 has become the SC in the ancestor of five Silurus species due to the duplication-and-translocation of amhr2 mediated by LTR transposon. Then, a proto Y was formed and maintained with a shared 60 kb male-specific region of the Y chromosome (MSY) by transposable elements (TEs) expansion and gene gathering. Due to the continuous TEs accumulation, genes other than amhr2y in MSYs have degenerated or been lost, while non-recombinant regions continue to expend, forming MSYs of different sizes in different Silurus species (from 320 to 550 kb). Two turnover events, one homologous (from the left arm to the right arm of Chr24) and one nonhomologous (from Chr24 to Chr5), occurring among five Silurus species were possibly mediated by hAT and Helitron transposons. Our results on the dynamic evolutionary trajectory of SD gene amhr2y, MSYs, and SCs in Silurus catfish indicated the variability and diversity of fish SCs and confirmed that frequent turnover is an important way to maintain the homology and low differentiation of fish SCs.

We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs.Database URL: https://www.fishtedb.com/

The long-term impact of limited and species-specific antigen exposure on immune system evolution is not well understood. Herein, we conducted histological and comparative genomic analyses using the cavefish Triplophysa rosa in order to investigate how restricted antigen exposure influences the evolutionary path of the vertebrate immune system. The histology and cellular characteristics of mucosa-associated lymphoid tissues (gills, skin, and intestines) and the major immune organs (spleen, head kidney, and thymus) of T. rosa were systematically investigated. Histological studies showed that T. rosa had intact immune organs (tissues) and a well-developed adaptive immune system. Our findings suggested that the immune system might have evolved due to the non-degradation of the thymus, which may be an adaptation to the cave environment. A comparative genomic analysis of T. rosa and surface fish was carried out to explore the evolutionary adaptiveness of their immune systems and the potential genomic changes arising from thymus non-degeneration. The analysis revealed that T. rosa developed an efficient adaptive immune system due to the expansion of genes related to T-cell activation and differentiation, consistent with the histological results. Achievement of well-developed adaptive immunity through a limited number of fixed antigens in a cave environment could confer long-term protection against pathogens, highlighting it as a beneficial survival strategy for cavefish. Our findings could provide new ideas for further research on immunity in cavefish.

Extreme conditions in caves pose survival challenges for cave dwellers, who gradually develop adaptive survival features. Cavefishes are one of the most successful animals among cave dwellers. Triplophysa cavefishes are an important group of cavefishes, and they show remarkable adaptability to the extreme environments of caves. However, there is a limited understanding of their adaptation mechanisms. In this study, eight complete mitochondrial genomes of Triplophysa cavefishes were newly obtained, and their genomic characteristics, including the base composition, base bias, and codon usage, were analyzed. Phylogenetic analysis was carried out based on 13 mitochondrial protein-coding genes from 44 Nemacheilidae species. This showed that Triplophysa cavefishes and non-cavefishes separate into two reciprocally monophyletic clades, suggesting a single origin of the cave phenotype. Positive selection analysis strongly suggested that the selection pressure in cavefishes is higher than that in non-cavefishes. Furthermore, the ND5 gene in cavefishes showed evidence of positive selection, which suggests that the gene may play an important role in the adaptation of cavefishes to the cave environment. Protein structure analysis of the ND5 subunit implied that the sites of positive selection in cavefishes might allow them to acquire lower ND5 protein stability, compared to that in non-cavefishes, which might help the accumulation of nonsynonymous (mildly deleterious) mutations. Together, our study revealed the genetic signatures of cave adaptation in Triplophysa cavefishes from the perspective of energy metabolism.

Open AccessMoreSectionsView PDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmail Cite this article Zheng Shuqing, Tao Wenjing, Yang Haowen, Kocher Thomas D., Wang Zhijian, Peng Zuogang, Jin Li, Pu Deyong, Zhang Yaoguang and Wang Deshou 2023Correction to: 'Identification of sex chromosome and sex-determining gene of southern catfish based on XX, XY and YY genome sequencing' (2022) by Zheng et al.Proc. R. Soc. B.2902022238120222381http://doi.org/10.1098/rspb.2022.2381SectionOpen AccessCorrectionCorrection to: 'Identification of sex chromosome and sex-determining gene of southern catfish based on XX, XY and YY genome sequencing' (2022) by Zheng et al. Shuqing Zheng Shuqing Zheng http://orcid.org/0000-0003-1007-6116 Google Scholar Find this author on PubMed Search for more papers by this author , Wenjing Tao Wenjing Tao Google Scholar Find this author on PubMed Search for more papers by this author , Haowen Yang Haowen Yang Google Scholar Find this author on PubMed Search for more papers by this author , Thomas D. Kocher Thomas D. Kocher Google Scholar Find this author on PubMed Search for more papers by this author , Zhijian Wang Zhijian Wang Google Scholar Find this author on PubMed Search for more papers by this author , Zuogang Peng Zuogang Peng http://orcid.org/0000-0001-8810-2025 Google Scholar Find this author on PubMed Search for more papers by this author , Li Jin Li Jin Google Scholar Find this author on PubMed Search for more papers by this author , Deyong Pu Deyong Pu Google Scholar Find this author on PubMed Search for more papers by this author , Yaoguang Zhang Yaoguang Zhang Google Scholar Find this author on PubMed Search for more papers by this author and Deshou Wang Deshou Wang http://orcid.org/0000-0002-4967-524X Google Scholar Find this author on PubMed Search for more papers by this author Shuqing Zheng Shuqing Zheng http://orcid.org/0000-0003-1007-6116 Google Scholar Find this author on PubMed , Wenjing Tao Wenjing Tao Google Scholar Find this author on PubMed , Haowen Yang Haowen Yang Google Scholar Find this author on PubMed , Thomas D. Kocher Thomas D. Kocher Google Scholar Find this author on PubMed , Zhijian Wang Zhijian Wang Google Scholar Find this author on PubMed , Zuogang Peng Zuogang Peng http://orcid.org/0000-0001-8810-2025 Google Scholar Find this author on PubMed , Li Jin Li Jin Google Scholar Find this author on PubMed , Deyong Pu Deyong Pu Google Scholar Find this author on PubMed , Yaoguang Zhang Yaoguang Zhang Google Scholar Find this author on PubMed and Deshou Wang Deshou Wang http://orcid.org/0000-0002-4967-524X Google Scholar Find this author on PubMed Published:04 January 2023https://doi.org/10.1098/rspb.2022.2381This article corrects the followingResearch ArticleIdentification of sex chromosome and sex-determining gene of southern catfish (Silurus meridionalis) based on XX, XY and YY genome sequencinghttps://doi.org/10.1098/rspb.2021.2645 Shuqing Zheng, Wenjing Tao, Haowen Yang, Thomas D. Kocher, Zhijian Wang, Zuogang Peng, Li Jin, Deyong Pu, Yaoguang Zhang and Deshou Wang volume 289issue 1971Proceedings of the Royal Society B: Biological Sciences16 March 2022 Proc. R. Soc. B 289, 20212645. (Published online 16 March 2022). (https://doi.org/10.1098/rspb.2021.2645) In figure 3c of our recently published paper, 'Identification of sex chromosome and sex-determining gene of southern catfish (Silurus meridionalis) based on XX, XY and YY genome sequencing', the left part of image viii and the right part of image xvi show similar morphological structure. This may cause concerns about image duplication and alteration, and we wish to allay any concerns about the following explanation. First, the two images referred to above are original, uncropped and otherwise unaltered (see the electronic supplementary material of the original paper). We have also included a flow chart (figure 1) to describe the imaging methods. As shown in the flow chart, successive sections of the same gonad were used to analyse the expression and cellular localization of amhr2 and amhr2y in XX gonad at 120 dah by fluorescence in situ hybridization (FISH). The first section was hybridized with anti-sense probe of amhr2y and the second with anti-sense probe of amhr2. We used an Olympus FV3000 laser confocal microscope to take images with XY scan mode and 1 : 1 image size (aspect ratio). Therefore, the same area (circled by green dotted boxes) of the gonad would show similar, but not identical, morphological structure to neighbouring sections. We apologize for any confusion this may have caused. Figure 1. The flow chart showing the methods used for imaging. (Online version in colour.)Download figureOpen in new tabDownload PowerPoint Previous Article VIEW FULL TEXT DOWNLOAD PDF FiguresRelatedReferencesDetailsRelated articlesIdentification of sex chromosome and sex-determining gene of southern catfish (Silurus meridionalis) based on XX, XY and YY genome sequencing16 March 2022Proceedings of the Royal Society B: Biological Sciences This Issue 11 January 2023Volume 290Issue 1990 Article InformationDOI:https://doi.org/10.1098/rspb.2022.2381PubMed:36598021Published by:Royal SocietyOnline ISSN:1471-2954History: Manuscript received26/11/2022Manuscript accepted30/11/2022Published online04/01/2023Published in print11/01/2023 License:© 2023 The Authors.Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. Citations and impact Subjects bioinformatics genetics genomics Large datasets are available through Proceedings B's partnership with Dryad

Amur catfish (Silurus asotus) is an ecologically and economically important fish species in Asia. Here, we assembled the female and male Amur catfish genomes, with genome sizes of 757.15 and 755.44 Mb, respectively, at the chromosome level using nanopore and Hi-C technologies. Consistent with the known diploid chromosome count, both genomes contained 29 chromosome-size scaffolds covering 98.80 and 98.73 % of the complete haplotypic assembly with scaffold N50 of 28.87 and 27.29 Mb, respectively. The female (n = 40) and male (n = 40) pools were re-sequenced. Comparative analysis of sequencing and re-sequencing data from both sexes confirmed the presence of an XX/XY sex determination system in Amur catfish and revealed Chr5 as the sex chromosome containing an approximately 400 kb Y-specific region (MSY). Gene annotation revealed a malespecific duplicate of amhr2, namely amhr2y, in MSY, which is male-specific in different wild populations and expressed only in the testes. Amur catfish shared partially syntenic MSY and amhr2y genes with the southern catfish (S. meridionalis, Chr24), which were located on different chromosomes. High sequence divergence between amhr2y and amhr2 and high sequence similarity with amhr2y were observed in both species. These results indicate the common origin of the sex-determining (SD) gene and transition of amhr2y in the two Silurus species. Accumulation of repetitive elements in the MSY of both species may be the main driver of the transition of amhr2y. Overall, our study provides valuable catfish genomic resources. Moreover, determination of amhr2y as the candidate SD gene in Amur catfish provides another example of amhr2 as the SD gene in fish.

Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α2β2) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean dN/dS (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.

A market study on sturgeon products in the Lower Danube countries (Bulgaria, Romania, Serbia and Ukraine) resulted in a total of 149 samples of caviar and meat, which we subjected to genetic-isotope analyses. The samples comprised 31 samples (21%) of illegal wild-caught origin, 17 samples (11.4%) sold in violation of CITES and EU regulations, and 47 cases (32%) of consumer deception. Although poaching and illegal wildlife trade are often considered a problem in developing countries, these findings bear evidence that a high ratio of poached sturgeon products originates from EU and accession candidate states. Therefore, caviar and sturgeon trade urgently needs improvement to ensure that sturgeon populations will have a future.

Length–weight relations (LWR) were estimated for 14 endemic and indigenous fish species from the Aral Sea basin: Alburnoides holciki Coad et Bogutskaya, 2012; Capoetobrama kuschakewitschi (Kessler, 1872); Cottus spinulosus Kessler, 1872; Glyptosternon oschanini (Herzenstein, 1889); Gobio lepidolaemus Kessler, 1872; Gobio nigrescens (Keyserling, 1861); Iskandaria kuschakewitschi (Herzenstein, 1890); Iskandaria pardalis (Turdakov, 1941); Paracobitis longicauda (Kessler, 1872); Sabanejewia aralensis (Kessler, 1877); Schizothorax fedtschenkoi Kessler, 1872; Triplophysa daryoae Sheraliev, Kayumova et Peng, 2022; Triplophysa ferganaensis Sheraliev et Peng, 2021; and Triplophysa uranoscopus (Kessler, 1872). Measurements were taken for total length (0.1 cm precision) and total weight (0.1 g precision). The LWR parameters were determined using a linear logarithmic regression model of weight against length in which values for the slope of the regression, b, that are higher and lower than 3 indicate positive and negative allometric growth, respectively. The estimated values of parameter b ranged from 2.703 (Iskandaria kuschakewitschi) to 3.162 (Gobio nigrescens). The correlation coefficient (r2) values varied from 0.951 to 0.993, indicating a strong positive relation between length and weight. The maximum total lengths of four of the species (Glyptosternon oschanini, Iskandaria kuschakewitschi, Triplophysa daryoae, and Triplophysa uranoscopus) constitute new records, and the LWRs of twelve fish species have hitherto not been available in FishBase.

DATA REPORT article Front. Genet., 10 August 2022Sec. Livestock Genomics https://doi.org/10.3389/fgene.2022.962406