Spatially explicit estimation of freshwater fish stock biomass with limited data: A case study of an endangered endemic fish on the Tibetan Plateau, China

Accurate evaluation of fish stock biomass is essential for effective conservation management and targeted species enhancement efforts. However, this remains challenging owing to limited data availability. Therefore, we present an integrated modeling framework combining catch per unit effort with ensemble species distribution modeling called CPUESDM, which explicitly assesses and validates the spatial distribution of stock biomass for freshwater fish species with limited data, applied to Herzensteinia microcephalus. The core algorithm incorporates the Leslie regression model, ensemble species distribution modeling, and exploratory spatial interpolation techniques. We found that H. microcephalus biomass in the Yangtze River source area yielded an initial estimate of 113.52 tons. Our validation results demonstrate high accuracy with a Cohen's kappa coefficient of 0.78 and root mean square error of 0.05. Furthermore, our spatially-explicit, global, absolute biomass density map effectively identified areas with high and low concentrations of biomass distribution centers. Additionally, this study offers access to the source code, example raw data, and a step-by-step instruction manual for other researchers using field data to explore the application of this model. Our findings can help inform for future conservation efforts around fish stock biomass estimation, especially for endangered species.

Monsoon boosted radiation of the endemic East Asian carps

Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.

Phylogenetic relationship and taxonomic status of Gymnocypris eckloni (Schizothoracinae) based on specific locus amplified fragments sequencing

Accurately delimiting phylogenetic relationships and taxonomic status is important for understanding species diversity and distributions and devising effective strategies for biodiversity conservation. However, species delimitation is controversial in Gymnocypris eckloni, a schizothoracine fish endemic to the Qinghai–Tibetan Plateau. The aim of this study is robustly identifying the phylogeny of G. eckloni in the Yellow River (YR) population and Qaidam basin (QB) population. The specific-locus amplified fragments sequencing (SLAF-seq) is employed with comprehensively sampling of schizothoracine fishes. In total, 350,181,802 clean reads and 5,114,096 SNPs are identified from SLAF-seq. Phylogenetic analysis recovers a non-monophyletic population of G. eckloni between YR and QB populations, representing an independent phylogenetic relationship between the two populations. Species delimitation analyses by SNAPPER and GMYC methods using the genome-wide SNP data confirm that their taxonomic statuses are separated. This study highlights the importance of further reconsidering clearer taxonomy, which would improve the genetic diversity conservation of Tibetan highland fishes.

A review of the endocrine disrupting effects of micro and nano plastic and their associated chemicals in mammals

Over the years, the vaste expansion of plastic manufacturing has dramatically increased the environmental impact of microplastics [MPs] and nanoplastics [NPs], making them a threat to marine and terrestrial biota because they contain endocrine disrupting chemicals [EDCs] and other harmful compounds. MPs and NPs have deleteriouse impacts on mammalian endocrine components such as hypothalamus, pituitary, thyroid, adrenal, testes, and ovaries. MPs and NPs absorb and act as a transport medium for harmful chemicals such as bisphenols, phthalates, polybrominated diphenyl ether, polychlorinated biphenyl ether, organotin, perfluorinated compounds, dioxins, polycyclic aromatic hydrocarbons, organic contaminants, and heavy metals, which are commonly used as additives in plastic production. As the EDCs are not covalently bonded to plastics, they can easily leach into milk, water, and other liquids affecting the endocrine system of mammals upon exposure. The toxicity induced by MPs and NPs is size-dependent, as smaller particles have better absorption capacity and larger surface area, releasing more EDC and toxic chemicals. Various EDCs contained or carried by MPs and NPs share structural similarities with specific hormone receptors; hence they interfere with normal hormone receptors, altering the hormonal action of the endocrine glands. This review demonstrates size-dependent MPs' bioaccumulation, distribution, and translocation with potential hazards to the endocrine gland. We reviewed that MPs and NPs disrupt hypothalamic-pituitary axes, including the hypothalamic-pituitary-thyroid/adrenal/testicular/ovarian axis leading to oxidative stress, reproductive toxicity, neurotoxicity, cytotoxicity, developmental abnormalities, decreased sperm quality, and immunotoxicity. The direct consequences of MPs and NPs on the thyroid, testis, and ovaries are documented. Still, studies need to be carried out to identify the direct effects of MPs and NPs on the hypothalamus, pituitary, and adrenal glands.

Heavy metals bioaccumulation and subsequent multiple biomarkers based appraisal of toxicity in the critically endangered Tor putitora

The construction of hydropower projects discharges effluents to aquatic bodies. The effluents consist of different chemicals including heavy metals. The current study assessed the effects of effluents discharged from an under-construction hydropower project on the bioaccumulation of heavy metals in the tissues of critically endangered Tor putitora (Hamilton, 1822) in the river Panjkora. The subsequent toxic impacts of higher bioaccumulation of heavy metals on different biochemical, hematological, and serum biochemical profiles were also studied. Different biochemical changes were observed in the tissues of T. putitora including stress biomarkers such as reactive oxygen species, lipid peroxidation, total protein contents, antioxidant enzymes (peroxidase, superoxide dismutase, catalase, reduced glutathione, glutathione reductase, and glutathione-s-transferase), acetylcholinesterase, and whole-body cortisol. The hematotoxic effects were also observed as the count of red blood cells, hematocrit, and hemoglobin decreased whereas the count of white blood cells increased. Serum biochemical analysis revealed that cholesterol, urea, total bilirubin, and glucose concentration increased, whereas total proteins and albumin decreased with an increase in the concentration of heavy metals across the sampling sites. The fish from the river was found to be under severe stress as compared to the fish from the reference site. To mitigate the current scenario, stocking fish in an appropriate amount is suggested. The fish diversity and water quality should be assessed at regular intervals to avoid further deterioration and diversity loss. The safety and conservation of wild fisheries should be ensured by implementing strict environmental protection and fishing laws.

Rhinogobius houheensis, a new species of freshwater goby (Teleostei: Gobiidae) from the Houhe National Nature Reserve, Hubei province, China

A new freshwater goby, Rhinogobius houheensis, is described based on 40 specimens in a freshwater stream from the Houhe National Nature Reserve, Hubei Province, China. The new species can be distinguished from all its congeneric species by the following combination of characters: thee first dorsal fin rays VI, the second dorsal fin rays I/9-I/10; anal fin rays I/7-I/8; pectoral-fin rays 16-17; longitudinal scale series 37-40; transverse scales 12-14; predorsal scale series 0; and vertebrae counts 12+18=30. The first three spinous rays in the first dorsal fin are colored with two dark-blue stripes and one black spot in alive.

Molecular systematics of the Triplophysa robusta (Cobitoidea) complex: Extensive gene flow in a depauperate lineage

Gene flow between populations assumed to be isolated frequently leads to incorrect inferences of evolutionary history. Understanding gene flow and its causes has long been a key topic in evolutionary biology. In this study, we explored the evolutionary history of the Triplophysa robusta complex, using a combination of multilocus analyses and coalescent simulation. Our multilocus approach detected conspicuous mitonuclear discordances in the T. robusta complex. Mitochondrial results showed reticular clades, whereas the nuclear results corresponded with the morphological data. Coalescent simulation indicated that gene flow was the source of these discordances. Molecular clock analysis combined with geological processes suggest that intense geological upheavals have shaped a complicated evolutionary history for the T. robusta complex since the late Miocene, causing extensive gene flow which has distorted the molecular systematics of the T. robusta complex. We suggest that frequent gene flow may restrict speciation in the T. robusta complex, leading to such a depauperate lineage. Based on this comprehensive understanding, we provide our proposals for taxonomic revision of the T. robusta complex.

Transcriptomic profiling of Tibetan highland fish (Gymnocypris przewalskii) in response to the infection of parasite ciliate Ichthyophthirius multifiliis

Gymnocypris przewalskii is a native cyprinid in the Lake Qinghai of the Qinghai-Tibetan Plateau. G. przewalskii is highly susceptible to the infection of a parasite, Ichthyophthirius multifiliis, in the artificial propagation and breeding. To better understand the host immune reaction to I. multifiliis infection, we characterize the gene expression profiles in the spleen of healthy and I. multifiliis infected G. przewalskii by RNA-seq. Totally, the transcriptomic analysis produces 463,031,110 high quality reads, which are assembled to 213,538 genes with N50 of 1918 bp and the average length of 1205 bp. Of assembled genes, 90.52% are annotated by public databases. The expression analysis shows 744 genes are significantly changed by the infection of I. multifiliis, which are validated by qRT-PCR with the correlation coefficient of 0.896. The differentially expressed genes are classified into 689 GO terms and 230 KEGG pathways, highlighting the promoted innate immunity in I. multifiliis infected G. przewalskii at 2 days post infection. Our results pinpoint that the up-regulated genes are enriched in TLR signaling pathway, inflammatory response and activation of immune cell migration. On the contrary, complement genes are down-regulated, indicating the evasion of host complement cascades by I. multifiliis. The repressed genes are also enriched in the pathways related to metabolism and endocrine, suggesting the metabolic disturbance in I. multifiliis treated G. przewalskii. In summary, the present study profiles the gene expression signature of G. przewalskii in the responses to I. multifiliis infection, and improves our understanding on molecular mechanisms of host-parasite interaction in G. przewalskii, which focuses the crucial function of TLRs, cytokines and complement components in the host defense against I. multifiliis.

Phylogeography of Schizopygopsis stoliczkai (Cyprinidae) in Northwest Tibetan Plateau area

Schizopygopsis stoliczkai (Cyprinidae, subfamily Schizothoracinae) is one of the major freshwater fishes endemic to the northwestern margin of the Tibetan Plateau. In the current study, we used mitochondrial DNA markers cytochrome b (Cyt b) and 16S rRNA (16S), as well as the nuclear marker, the second intron of the nuclear beta-actin gene (Act2), to uncover the phylogeography of S. stoliczkai. In total, we obtained 74 haplotypes from 403 mitochondrial concatenated sequences. The mtDNA markers depict the phylogenetic structures of S. stoliczkai, which consist of clade North and clade South. The split time of the two clades is dated back to 4.27 Mya (95% HPD = 1.96-8.20 Mya). The estimated split time is earlier than the beginning of the ice age of Pleistocene (2.60 Mya), suggesting that the northwestern area of the Tibetan Plateau probably contain at least two glacial refugia for S. stoliczkai. SAMOVA supports the formation of four groups: (i) the Karakash River group; (ii) The Lake Pangong group; (iii) the Shiquan River group; (iv) the Southern Basin group. Clade North included Karakash River, Lake Pangong, and Shiquan River groups, while seven populations of clade South share the haplotypes. Genetic diversity, star-like network, BSP analysis, as well as negative neutrality tests indicate recent expansions events of S. stoliczkai. Conclusively, our results illustrate the phylogeography of S. stoliczkai, implying the Shiquan River is presumably the main refuge for S. stoliczkai.