Fish Diversity Research Articles

Genetic diversity of salmonid fishes in the eastern part of the Onega Peninsula, Northern European Russia

The Onega Peninsula in the White Sea, north-western Russia, is a habitat for ecologically and economically significant salmonid species, i.e. Atlantic salmon Salmo salar Linnaeus, 1758 and brown trout S. trutta Linnaeus, 1758 (Salmoninae). However, these populations are currently understudied in terms of molecular approach. In this work, we assessed the genetic diversity and differentiation of S. salar and S. trutta from the eastern part of the Onega Peninsula based on mitochondrial (COI and cytb) and nuclear (RAG1) markers. We also traced a phylogeographic pattern of these species. Populations of brown trout in the studied watercourses mainly share low haplotype and nucleotide diversity, with the exception of the moderate values in the Gosdarea River. In turn, Atlantic salmon in the Ust’-Yaren’ga River has higher genetic diversity than brown trout. Our study reveals great importance of conservation measures and monitoring, as well as parasite pressure control, especially for brown trout, in the eastern part of the Onega Peninsula.

Taxonomic Diversity and Interannual Variation of Fish in the Lagoon of Meiji Reef (Mischief Reef), South China Sea.

Coral reef fish are important groups of coral reefs, which have great economic and ecological value. Meiji Reef is a representative tropical semi-enclosed atoll in the South China Sea, with rich fish resources. Based on the data from hand-fishing, line-fishing, and gillnet surveys of fish in Meiji Reef from 1998 to 2018, this study summarized the fish species list of Meiji Reef and analyzed the species composition, inclusion index at the taxonomic level (TINCL), genus-family diversity index (G-F index), average taxonomic distinctness index (Δ+), and variation in taxonomic distinctness (Λ+) and their changes. The results revealed that from 1998 to 2018, there were 166 reef-dwelling fish species on Meiji Reef, belonging to 69 genera, 33 families, and 11 orders, of which 128 species were from 20 families of Perciformes, accounting for 77.10% of the total cataloged species. Regarding the dependence of fish on coral reefs, there were 155 reef-dependent species or resident species (accounting for 93.37%) and 11 reef-independent species or wandering species (accounting for 6.63%). The TINCL of the order, families, and genus of fish in Meiji Reef were very high. The genus diversity index (G index), family diversity index (F index), and G-F index of fish in Meiji Reef were very high, and the G index of fish in Meiji Reef in 1998-1999 was higher than that in 2016-2018. The Δ+ and Λ+ values of fish in Meiji Reef from 1998 to 2018 were 56.1 and 148.5, respectively. Compared with 1998-1999, Δ+ and Λ+ of fish increased during 2016-2018, reflecting that the relatives of fish in Meiji Reef became further distant, and the uniformity of taxonomic relationships among species decreased. The research findings indicated that fish exhibited a high taxonomic diversity in Meiji Reef; however, it also revealed significant fluctuations in the fish diversity of Meiji Reef over an extended period, emphasizing the urgent need for timely protection measures. This investigation significantly contributes to our comprehension of the intricate dynamics governing fish species within Meiji Reef and holds broader implications for biodiversity conservation in tropical marine ecosystems.

Notes on the natural history and identity of the pelagic sea snake Hydrophis platurus (Serpentes: Elapidae) from Golfo Dulce, Puntarenas, Costa Rica

Introduction: The pelagic sea snake Hydrophis platurus has the broadest distributional range of all the snakes and is the only sea snake of tropical waters off the west coast of the Americas. Within the variation in the color pattern of this species, completely yellow specimens were considered very rare or occasional. However, a yellow pattern dominates a population established in the interior of the Golfo Dulce in the Southern Pacific of Costa Rica. Objective: We studied the abundance, activity patterns, morphometry, and feeding behavior of the yellow H. platurus within the Golfo Dulce. Methods: Between February 2009 and July 2018, we conducted surveys for sea snakes from a boat within the perimeter of the Golfo Dulce. Results: Adults from the gulf population are smaller than the bicolor oceanic population, with females having larger bodies. Sea snakes within the gulf float and move with surface currents without being linked to drift lines and debris. These snakes are mainly found in clean, calm waters with little turbulence. They feed on a wide diversity of small fish, which they capture using passive stalking predatory behaviors floating on the surface. Prey are quickly captured and swallowed alive. This species has an almost total absence of predation, a pattern that extends to this yellow population. Conclusions: The characteristics of the gulf and the direction and strength of the surface currents at its entrance might restrict the transit of this yellow population to the outside and the entry of the bicolored snakes of the oceanic population. We do not consider making taxonomic changes in this Golfo Dulce population prudent. This yellow population is relatively common within the basin. However, the high tourist traffic and other activities are risk factors for its conservation. Protection policies must be created to preserve and protect this small population of yellow sea snakes unique within this species' distribution range.

Environmental DNA metabarcoding in the Cape Fold aquatic ecoregion: Opportunities and challenges for eDNA uptake in an endemism hotspot

Abstract Environmental DNA (eDNA) metabarcoding has the potential to significantly improve surveys of biodiversity in freshwater systems. However, this methodology is still infrequently used in global hotspots of endemic species, in part because of two major barriers to the success of eDNA metabarcoding: (1) insufficient regional taxonomic representation in public reference sequence databases; and (2) inconsistent species incidence and abundance estimates when compared to conventional surveys. We sampled eDNA and conducted visual surveys in the headwaters of two rivers in the Cape Fold aquatic ecoregion, South Africa. A reference sequence database was generated for the regional diversity of fishes to improve taxonomic classification of endemic species. We also compared the consistency of incidence data and relative abundance estimates of fishes from eDNA metabarcoding sequencing results and visual surveys (snorkel and underwater cameras) at each site sampled. Only 1% of eDNA metabarcoding reads could be classified to fish species without the supplementation of reference sequence databases for local endemic species. Once regional reference sequences were added, a total of nine species were detected and >99% reads classified. A strong positive relationship (Φ = 0.75) was observed between the patterns of detections using eDNA and visual approaches. However, eDNA metabarcoding detected more species than visual methods. In addition, the relative read frequency and abundance observed in visual surveys was significantly correlated (R2 = 0.85–0.88, p < 0.001) in the majority of the small pools surveyed. Incomplete public reference sequence databases hinder the use of eDNA metabarcoding in regions of high endemicity. Local reference sequence libraries can overcome these challenges. When appropriately implemented, eDNA metabarcoding shows promise, producing results consistent or better than the more frequently used and labour‐intensive visual surveys. Efficient survey methods like eDNA metabarcoding are urgently needed to improve aquatic monitoring efforts globally. Understanding how eDNA metabarcoding sequencing results relate to conventional survey methods is a key step in its implementation in ecoregions with high endemicity.

L-Glutamate Regulates Npy via the mGluR4-Ca2+-ERK1/2 Signaling Pathway in Mandarin Fish (Siniperca chuatsi).

Metabotropic glutamate receptor 4 (mGluR4) is widely regarded as an umami receptor activated by L-glutamate to exert essential functions. Numerous studies have shown that umami receptors participate in food intake regulation. However, little is known about mGluR4's role in mediating food ingestion and its possible molecular mechanism. Mandarin fish, a typical carnivorous fish, is sensitive to umami substances and is a promising vertebrate model organism for studying the umami receptor. In this study, we identified the mGluR4 gene and conducted evolutionary analyses from diverse fish species with different feeding habits. mGluR4 of mandarin fish was cloned and functionally expressed to investigate the effects of L-glutamate on mGluR4. We further explored whether the signal pathway mGluR4-Ca2+-ERK1/2 participates in the process in mandarin fish brain cells. The results suggest that L-glutamate could regulate Neuropeptide Y (Npy) via the mGluR4-Ca2+-ERK1/2 signaling pathway in mandarin fish. Our findings unveil the role of mGluR4 in feeding decisions and its possible molecular mechanisms in carnivorous fishes.

Reef fish biodiversity and occurrence of endangered sharks within a small marine protected area off Sint Maarten, Dutch Caribbean

AbstractMarine protected areas (MPAs) are common conservation tools supporting the protection of threatened marine fishes, such as sharks. However, the creation of shark MPAs has been less common in the Greater Caribbean region despite a growing need and opportunity. In this study, we evaluated the occurrence of shark and reef fish biodiversity off Sint Maarten, Dutch Caribbean, with a particular emphasis on endangered shark presence within the Man of War Shoal Marine Protected Area (MPA). We utilized baited remote underwater video systems (BRUVs) to gather non-invasive data on the abundance and diversity of reef fish and shark species inside and outside the local MPA. Generalized linear models (GLMs) revealed no significant effect of protection status on the presence of the endangered Caribbean reef shark (Carcharhinus perezi). However, we found a significant influence of depth on shark occurrence, as well as an effect of habitat type on shark and reef fish biodiversity, with reef habitats showing the greatest significance. These results suggest that the effect of small coastal MPAs on bolstering local endangered species conservation in the Dutch Caribbean is likely to vary according to habitat features and how those species utilize those habitats across various life stages. These findings have implications for adaptive MPA management, which should be informed by the ecology and habitat preferences of target species to achieve maximum benefits for biodiversity conservation.

Mitochondrial markers revealed genetic panmixia in the data-deficient yellowfin snapper, Lutjanus xanthopinnis (Actinopterygii: Eupercaria: Lutjanidae), from a hotspot of the southern region of the South China Sea

Understanding the genetic structure and diversity of marine fish is crucial for a sustainable management program. We examined the genetic diversity and historical demographics of the yellowfin snapper, Lutjanus xanthopinnis Iwatsuki, Tanaka et Allen, 2015, in the coastal waters of east Peninsular Malaysia which is bordered by the southern part of the South China Sea using the mitochondrial genes (mtDNA) D-loop and Cytochrome b (Cyt-b). A total of 99 (D-loop) and 78 (Cyt-b) specimens of L. xanthopinnis were successfully sequenced from six locations within the range of species distribution along the Malaysian South China Sea. In the presently reported study, the lack of genetic differentiation among populations can be attributed to historical demographic events, eggs and planktonic larvae’ ability to disperse, spawning patterns, and the absence of physical barriers in the geographical landscape. Maximum likelihood gene trees demonstrated that the populations under study had limited structuring and formed a panmictic population that lacks support for internal clades. The AMOVA (Analysis of Molecular Variance) and population pairwise ФST values indicated high genetic exchange between the study areas. A high level of haplotype diversity (D-loop: 0.948–1.000; Cyt-b: 0.542–0.928), low nucleotide diversity (D-loop: 0.0095–0.0159; Cyt-b: 0.0022–0.0049) and starlike haplotype network indicates a recent expansion of L. xanthopinnis populations in Malaysian South China Sea. However, neutrality and goodness of fit tests revealed non-significant values. Furthermore, the BSP (Bayesian skyline plot) analysis estimated population expansion events during the late Pleistocene. During this epoch, the fluctuation in sea level may have led to an increase in the abundance of resources and favorable habitats for the yellowfin snapper. The presently reported findings could initiate efficient management strategies for L. xanthopinnis along the coastal areas of the Malaysian South China Sea and other nearby nations that share the same waterways.

High diversity and abundance of fish and coral in an artificial breakwater in Colombo, Sri Lanka

The diversity of reef fishes and the diversity and abundance of corals in artificial breakwaters were studied between June and August 2023 in Port City, Colombo in the Western Province of Sri Lanka. Four methods were used: visual census using video, photographs, stationary point count and environmental DNA (eDNA). A total of 137 fish species, 74 coral species and 175 other species were recorded using the four methods. There were similarities and differences between the methods for recording fish, corals and other species. Only three fish species: Moon wrasse (Thalassoma lunare); Yellowtail fusilier (Caesio cuning) and Diamond fish (Monodactylus argenteus) were recorded by all methods. The highest number of fish species was recorded by video, followed by photographs, eDNA and stationary point count in the sequence. Coral cover ranged from 9 to 50.8% and mean live coral varied from 24.4% to 34.5 ± 5.2%. The dominant coral species was Pocillopora damicornis. Rare observations of coral bleaching (n=1) and frequent observations of marine debris (n=20) and coral damage (n=25) were recorded. Species detection using eDNA is a biomonitoring tool that did not add significantly to the list of fish and corals, but included many microscopic groups such as bacteria, diatoms and ciliates that were not recorded using other methods, and provided new ecological insights into marine systems. This is the first use of multiple monitoring tools to identify and compare methods for the biodiversity of marine fish, coral and other species in Sri Lankan marine waters.

Scale effects of riparian forests on fish diversity in streams of the upper Paraná River basin

Scale effects of riparian forests on fish diversity in streams of the upper Paraná River basin

The role of DNA methylation in facilitating life history trait diversity in fishes

The role of DNA methylation in facilitating life history trait diversity in fishes

A whole-body micro-CT scan library that captures the skeletal diversity of Lake Malawi cichlid fishes

Here we describe a dataset of freely available, readily processed, whole-body μCT-scans of 56 species (116 specimens) of Lake Malawi cichlid fishes that captures a considerable majority of the morphological variation present in this remarkable adaptive radiation. We contextualise the scanned specimens within a discussion of their respective ecomorphological groupings and suggest possible macroevolutionary studies that could be conducted with these data. In addition, we describe a methodology to efficiently μCT-scan (on average) 23 specimens per hour, limiting scanning time and alleviating the financial cost whilst maintaining high resolution. We demonstrate the utility of this method by reconstructing 3D models of multiple bones from multiple specimens within the dataset. We hope this dataset will enable further morphological study of this fascinating system and permit wider-scale comparisons with other cichlid adaptive radiations.

Fish Genomics and Its Application in Disease‐Resistance Breeding

ABSTRACTGlobal aquaculture production has been rising for several decades, with up to 76% of the total production from fish. However, the problem of fish diseases is becoming more and more prominent in today's context of pursuing sustainable aquaculture. Since the first fish genome assembly reported in 2002, genomic approaches have been successfully implemented in fish breeding to enhance disease resistance and reduce economic losses caused by diverse fish diseases. Here, we present a review of the current progress in fish genomics and its application in disease‐resistance breeding. First, assembly data for all publicly available fish genomes were curated and statistical analysis of these data were performed. Subsequently, genomics‐assisted breeding approaches (including quantitative trait loci mapping, genome‐wide association study, marker‐assisted selection, genomic selection, gene transfer, and genome editing) that have been applied in practical disease–resistance breeding programs are outlined. In addition, candidate genetic markers that could possibly be utilized in breeding were summarized. Finally, remaining challenges and further directions were discussed. In summary, this review provides insight into fish genomics and genomics‐assisted breeding of disease‐resistant fish varieties.

Maiden study on fish diversity of the Diring River in Baksa District, Assam, India

The Northeast India has several natural water resources that support a variety of aquatic fauna. However, many parts of the region have remained unexplored for ichthyofauna. Research on the diversity of fishes in large water bodies has received significant attention from many researchers in the region. In contrast, studies on small stream rivers are very scant. Therefore, the present study aims to record the diversity of fish fauna in the small stream Diring River of Baksa District, Assam. In this survey, 27 species of fishes were recorded from five study sites. The dominant family was Cyprinidae, comprising 48% of the total fish species. The conservation status of the majority of species was Least Concern (88.8%) followed by Near Threatened (3.7%) and Vulnerable (3.7%). However, conservation status of 3.7% of the fish species was not evaluated by IUCN. The Shannon diversity index ranged from 1.5 to 2.6, the evenness index from 0.84 to 0.98, and the richness index from 1.1 to 2.6, indicating a good status of ichthyofaunal resources in the study sites. Since there were no existing records on the fish diversity of the Diring River, this maiden study might serve as baseline information for further research.

First record of metazoan parasites of hybrids between the genera Colossoma and Piaractus in natural environments.

The practice of hybridization is carried out globally in fish farms. Here, we present the first record of the parasitic fauna of hybrids among genus Colossoma and Piaractus in natural environments. We identified a total of 48 hybrids, nine F1 hybrids (nuclear DNA from both species present in the cross) and 38 advanced hybrids (nuclear DNA from one species), both from crosses between Piaractus brachypomus and Piaractus mesopotamicus, and one F1 "tambacu" corresponding to cross between Colossoma macropomum and Piaractus mesopotamicus. This is the first record of Anacanthorus penilabiatus, Anacanthorus toledoensis, Mymarothecium viatorum, Mymarothecium ianwhittington, Haementeria sp., Dadaytrema oxycephala, Rondonia rondoni, and Echinorhynchus gomesi parasitizing hybrids collected in a natural environment. With this, we expand knowledge about the diversity of fish and parasites in the upper Paraná River and warn about the risk that fish escapes can cause in the basin.

Habitat Inventory, Diversity and Structural Modification of Hill-Stream Fishes of Noa Dihing River, Eastern Himalayan Hotspot, Arunachal Pradesh, Northeast India

Habitat Inventory, Diversity and Structural Modification of Hill-Stream Fishes of Noa Dihing River, Eastern Himalayan Hotspot, Arunachal Pradesh, Northeast India

Species Diversity and Distribution of Freshwater Fish in The Mekong River, Northeast of Thailand

Species Diversity and Distribution of Freshwater Fish in The Mekong River, Northeast of Thailand

The possible inhibition mechanism of low salt dry-curing on volatile flavor deterioration in refrigerated grass carp (Ctenopharyngodon idella) blocks: Metabolomics and microorganisms

Complex microbial communities have an important impact on the flavor of low salt dry-curing (LSD)-pretreated grass carp blocks. Here, the flavors, metabolites, and bacterial diversity of LSD-pretreated fish during cold storage were analyzed using flavor analysis, metabolomics, and high-throughput sequencing to investigate their correlations in detail. LSD promoted the volatile flavor deterioration of grass carp blocks under 6 days of refrigeration but inhibited it under 15 days of refrigeration. Furthermore, 924 metabolites were identified in the refrigerated grass carp blocks, and LSD inhibited the growth of Psychrophilic dominant spoilage microorganisms (Proteobacteria) and promoted microbial abundance (Actinobacteriota, Firmicutes, Bacteroidota, and Cyanobacteria). Correlation analysis revealed that the degradation of phosphatidylcholine connected with the monomonas genus in LSD-pretreated fish blocks played a vital role in inhibiting the key volatile flavor (esters, aldehydes, and alcohols) deterioration. This information is useful for elucidating the inhibition mechanism of LSD on flavor deterioration in refrigerated fish blocks.

Evalvating the diversity and conservation status of fishes in Ujani Dam Solapur District, Maharashtra, India

Evalvating the diversity and conservation status of fishes in Ujani Dam Solapur District, Maharashtra, India

From source to lake: Multi‒taxon alpha and beta diversity patterns along a river above 4500 ​m AMSL on the Qinghai‒Tibetan Plateau

Understanding the distribution of species is highly important for optimizing future conservation priorities and strategies at the regional scale. Relatively little attention has been given to multi-taxon aquatic biota in extreme alpine environments. We examined the spatial and temporal patterns of alpha and beta diversity, site-specific contributions to beta diversity and assembly mechanisms of four taxonomic groups (fishes, macroinvertebrates, zooplankton and phytoplankton) from the source to the estuary of the Za'gya Zangbo River above 4500 ​m AMSL (above mean sea level) on the northern Qinghai-Tibetan (Q–T) Plateau. A total of 4 fish species, 45 macroinvertebrate taxa, 17 zooplankton taxa and 56 phytoplankton taxa were found in the study area. No consistent patterns in taxonomic richness were observed across taxa from upstream to estuary. The fish communities had the lowest dissimilarity between communities, the phytoplankton community had the highest dissimilarity in the dry season, and the macroinvertebrate community had the highest dissimilarity in the wet season. The relative importance of the turnover and nestedness components varied considerably across taxa and along spatial gradients. The diversity patterns of macroinvertebrate, zooplankton and phytoplankton communities were significantly correlated with several environmental factors, whereas only the beta diversity of fish was correlated with altitude. Stochastic processes dominated in shaping the macroinvertebrate communities whereas deterministic processes dominated the assembly of the phytoplankton communities. Weak congruence of diversity patterns across taxonomic groups suggested that biological groups cannot serve as reliable surrogates for one another and that multiple biological groups should be included in the biomonitoring of high-altitude rivers on the Q‒T Plateau. The relatively unique species in the upstream area and estuary of the Za'gya Zangbo River harbor should receive more attention in future conservation and management schemes.

Refining Sampling Efforts for Fish Diversity Assessment in Subtropical Urban Estuarine and Oceanic Waters Using Environmental DNA With Multiple Primers

ABSTRACTThe environmental DNA (eDNA) approach is an emerging tool for monitoring marine biodiversity. However, the sampling effort needs optimization according to the site characteristics and target taxonomic groups. In this study, we optimized the eDNA sampling effort in terms of sample volume and number of replicates to monitor the diversity of marine vertebrates (mainly fish) in Hong Kong's subtropical waters that show a gradient of estuarine to oceanic waters. To maximize detection, we used three pairs of metabarcoding primers (12S‐v5, MiFish‐U, and MiFish‐E). We compared vertebrate diversity in 78 water samples, ranging from 1 to 10 L, collected from oceanic and estuarine sites. Metabarcoding yielded a total of 140 vertebrate species, of which 18 were unique to the estuarine site, 66 unique to the oceanic site, and 56 shared between both sites. The detected species were predominantly ray‐finned fish (136 species), and the three primer pairs exhibited differential sensitivity toward different taxa, especially cartilaginous fish and cetaceans. Increasing sampling volume per replicate generally increased the total detected species, average species per replicate, and species coverage, and sampling 3 or 4 × 4 L represented the most efficient sampling effort for the estuarine and oceanic sites, respectively. The diversity analysis revealed that sampling >2 L per replicate reduced variability and improved diversity analysis. The results also showed that a larger sampling volume per replicate increased the probability of detecting endangered, indicator, invasive, and elusive species, with 4 L representing the most efficient volume. This study recommended sampling 4 L per replicate and 3 replicates for estuarine and 4 for oceanic sites, respectively for effectively monitoring marine fish in subtropical waters using the eDNA approach.