Taxonomy Of Fishes Research Articles (Page 1)

The 2000s are the revolutionary decade for the taxonomy of freshwater fishes of Türkiye in terms of the most significant ever rate of increase in species descriptions. Among the approximately 390 freshwater fish species reported from Türkiye, a remarkable 136 have been described since 2000, reflecting an accelerated pace of taxonomic and morphological activity. This surge has been prompted by the influx of new researchers and the widespread adoption of molecular sequencing techniques, currently at the center of taxonomic work since the 2010s. This synthesis gives a complete view of these 136 new species named, examining predominant parameters such as genera, descriptors, contributing countries, and the chronological order of discoveries. The results are presented through visual data, which help illustrate the progress in taxonomic research and the contributions of international collaboration. The study also highlights the rapid development of freshwater biodiversity research in Türkiye and emphasizes the value of using integrated methods and global partnerships to better understand less-studied aquatic species. The bibliometric analysis indicates that a substantial proportion of new species descriptions is ascribed to a limited cohort of prolific researchers, with the majority of contributions made by a core group of the top 10 authors. These discoveries not only augment our comprehension of Türkiye’s freshwater fish fauna but also illuminate broader trends influencing taxonomic study in the 21st century.

We provide a detailed taxonomic redescription of Lutjanus rufolineatus, based on six specimens collected from the Andaman Islands, India. The species' taxonomic status and distribution have historically been misinterpreted within Indian waters due to close similarities with congeners, leading to frequent misidentification. To address this, we performed comprehensive morphological and molecular analyses, including DNA barcoding and phylogenetic reconstruction, to confirm the identity of L. rufolineatus and clarify its relationships with related species. Our findings emphasize the value of thorough taxonomic assessment in delineating species boundaries, particularly for understudied marine fauna. Additionally, this research fills critical gaps in the taxonomy of Indian marine fishes, addressing past ambiguities and enhancing regional biodiversity records. By integrating morphological and molecular data, this study underscores the importance of precise species identification for improved biodiversity conservation and management efforts in the Indo-Pacific.

DNA barcoding is a technique in which identification of species using DNA barcodes. We generated a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 226 barcodes belonging to 83 fish species from 67 genera, 39 families and 21 orders of fishes with the average divergence within a species is 010%, 13.57% within a genus, and 17.33% within a family with 97-100% identity with comparison to the Genbank database and BOLD of the Chilika lagoon, India. Data analysis done by barcode gap analysis, barcode index number and automatic barcode gap discovery to discriminate the species up to 97.53%, 93.90% and 95.06% respectively. The Barcode Index Number (BIN) discordance analysis reflected 226 specimens belongs to 83 BINs, of which 73.49%were taxonomically concordant and 26.50% were singletons and absence of discordant BIN in our dataset. Finally, the identification success rate of DNA barcoding was evaluated based on the sequencing success rate and species discrimination rate.

The identification and taxonomy of fishes is a prerequisite to studying them from a biological perspective for their conservation and management. The basic source of taxonomy and evolutionary studies in the case of fishes are morphological attributes. The present study was undertaken to study in detail some of the specific morphological attributes of five Schizothorax species (S. plagiostomus, S. labiatus, S. esocinus, S. curvifrons and S. niger) native to Kashmir Himalayas. During the present study, the analysis of morphometric and meristic attributes and pictorial representation of the five Schizothorax species revealed that some of the typical features of the Schizothorax species viz., the shape of body and head, structure of mouthparts especially the shape of the lower lips and the arrangement and number of gill rakers are quite significant to vary among the five native Schizothorax species, thus could be considered important attributes for their identification process. The present study could serve as a handy note for quick on-spot identification of the five Schizothorax species in the field without consulting whole literature for their identification that otherwise would be a laborious and time-consuming process.

The article presents some information on two new families of Ptychodictyidae fam. nov. and Nostolepidae fam. nov. that were established on the basis of the author’s personal research and the available literature data. Their main diagnostic features, generic composition, number of species, comparison, stratigraphic and geographical distribution are given. The obtained data supplement the taxonomy of the Palaeozoic acanthodian fishes.

Abstract It has long been recognized that presence–absence, localisation, size, number and shape of fish scales can be important taxonomic features. Although there are some notes on the relationship between scale morphology and ecological needs, in the absence of a sufficiently large and detailed database, the morphological variability of fish scales and the factors responsible for this variability have not yet been explored in detail. For this reason, a database—which contains the shape and relative size data of 193 freshwater fish taxa of 14 orders, originated from five biogeographic realms—has been built. Database analyses showed that both the scale shape and relative size are proper taxonomic indicators. They can be used to separate higher taxonomic categories (e.g., orders), and by the simultaneous analysis of shape and size scale morphology, we showed increased sensitivity for species‐level detachments. Our results suggest that while both the shape and the size of the fish scales are genetically determined, they are also useful descriptors of the niche segregation (habitat use, flow preference) of close relative species. Scale morphology is a promising additional tool to specify the environmental preferences of lesser known or close relative recent and extinct fish species. And also can be of great help in such cases when only the scales are available for taxonomic identification, for example, in the research field of archaeology and palaeontology.

Abstract Despite supporting a disproportionately large fraction of the global biodiversity, freshwater ecosystems are ranked as the most highly threatened habitats ahead of both terrestrial and marine ecosystems. Furthermore, many regions are still characterized by limited knowledge on taxonomy and ecology of freshwater fishes. The need for ecological information in understudied regions is important particularly where there are recent discoveries of new species and unique lineages and for threatened and endangered taxa that require conservation management. This study evaluated the trophic ecology of two freshwater fish species Sandelia bainsii and Amatolacypris trevelyani that are both classified as endangered in the International Union for Conservation of Nature (IUCN) Red List. These two species, which are narrow‐range endemics in the Eastern Cape, South Africa, comprise allopatric lineages whose ecology is poorly known. This study used stable isotope analysis to evaluate the food web patterns, explore the trophic niche dynamics and estimate the prey source contributions for the two species in different headwater habitats. The fishes isotopic niche sizes were spatially variable, suggesting the likely importance of stochastic variation in resource availability and probable interspecific interactions. The three lineages within S. bainsii exhibited low isotopic niche overlap onto those of sympatric fishes in most habitats. Isotopic mixing model revealed that these lineages' diets were mostly dominated by gatherers/collectors. In comparison, the two lineages within A. trevelyani exhibited high niche overlap with other species and generally had variable diets. Despite the low and high niche overlap patterns of S. bainsii and A. trevelyani, respectively, the isotopic niche overlap patterns of co‐occurring species onto those of the former suggest the likely lack of competitive hierarchies. The trophic niche patterns of these two endangered species helped to shed some light on the potential invasion risks by non‐piscivorous fishes with opportunistic feeding habits, which could exert competitive interspecific interactions.

The taxonomy of the order Tetraodontiformes is not well studied from the Indian coast, hence an integrated approach was attempted in this paper. Forty-two species of tetraodontiform fishes classified under 8 families in 25 genera were identified using morpho-molecular approach from southern west coast of India. Tetraodontidae is the most speciose family with fourteen species, followed by Balistidae and Monacanthidae with seven species each; Ostraciidae, Diodontidae, Triacanthodidae and Tricanthidae harbour three species each and Molidae is represented by two species. Eight species collected during the present study are new records to the Kerala coast. DNA barcoding using mitochondrial CO1 gene confirmed 12 species of tetraodontiform fishes. The molecular data of the present study were compared with sequences from GenBank, and the selected published sequences by expert taxonomists were matched for their maximum identity. The heat map shows low pairwise distances between the nearest species, and the phenetic tree shows that the studied species are nested in clades with closely related species.

Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: “sand burrower”), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (Hyperoplus lanceolatus). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. It is highly contiguous with a scaffold and contig N50 of 33.7 and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as this family is of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.

Because adult and juvenile eel gobies usually hide within the burrows of muddy substrates, their diversity and life history have not yet been fully elucidated. We investigated larval specimens of the eel gobies collected on Okinawa Island in southern Japan. The genus Trypauchenopsis was previously thought to consist of only one species, but our larval collection identified two species, Trypauchenopsis limicola and Trypauchenopsis intermedia, distinguished by their species-specific melanophore arrangements and differences in their fin-ray counts. Taenioides kentalleni were previously known from only two specimens worldwide. A third specimen of this species has now been added from the larval collection. In addition to the three species above, Taenioides gracilis and Caragobius urolepis were identified and the larval morphologies of the five species were described for the first time. All the larvae collected in the present study were at late postflexion stage. T. limicola, T. intermedia and T. gracilis were presumably collected in the estuaries and beaches when approaching their adult habitats at the end of pelagic life. They were 8.5-10.3 mm in standard length, and otolith analysis suggests that their pelagic larval durations are a little longer than 1month (average 34-37 days). The larval occurrence suggested that the spawning season of T. limicola is May-December, when the water temperature is warmer than approximately 20°C. Our work reveals that studying the larval stage can provide new information on the taxonomy and life history of the elusive cryptobenthic fish.

The Southern Ocean is experiencing complex climate change, and the Amundsen Sea is one of the regions that has responded most rapidly to climate change. Due to their role in ecosystems, environmental sensitivity and high endemism, Antarctic demersal fish are a favorable group that can act as an indicator of the response of Antarctic organisms to climate change. However, our knowledge of Antarctic fish fauna is insufficient, with knowledge gaps even in their taxonomy. This situation is greatly influenced by the limitations of traditional taxonomy and thus calls for alternative solutions such as DNA barcoding. In this study, DNA barcoding analyses of 69 fish samples obtained from the Amundsen Sea were conducted using the mitochondrial COI gene. Based on the molecular species delimitation results, 13 fish species were found to belong to two orders, six families, and 12 genera. Both the maximum likelihood and Bayesian inference methods showed that the phylogenetic relationships of Bathydraconidae were paraphyletic, which was consistent with previous phylogenetic research. Our research showed that the COI gene, as a DNA barcode, is not only suitable for the identification of Antarctic fish species but also reflects some phylogenetic characteristics that might provide important evidence and support for studies of Antarctic fish phylogenetic relationships. In summary, our study provides an important reference for fish diversity and taxonomy in the Amundsen Sea, which may further enhance our understanding of the biodiversity, taxonomy and biogeography of fish in this area.

Molecular assessment of demersal fish diversity in Prydz Bay using DNA taxonomy

To date, information related the skeletal morphology of fish in Indonesia is still limited. Therefore, we firstly described the morphology of the cranium of African catfish (Clarias gariepinus) collected from aquaculture pond in Aceh Province, Indonesia. In the present study, research methodology included the preparation of cranium, photographing, editing images and identifying the terminology of cranium. The cranium was prepared physically and chemically. Each part of the cranium was documented using a Canon EOS 700D camera and edited using Adobe Photoshop CS6. The cranium nomenclature was determined by comparing the similarity of the shape and location of each part of the fish cranium that has been studied previously. The cranium of African catfish was divided into two major parts, namely neurocranium (ossa neurocranii) and splanchnocranium (ossa splanchnocranii). Neurocranium had four regions belonging to etmoidal, orbital, otic and occipital, while splanchnocranium had five regions belonging to maxillaris, mandibularis, arcus mandibularis, arcus hyoideus, and apparatus operculare. The African catfish had a strong and thick neurocranium structure. However, orbital, arcus hyoideus and apparatus operculare regions were not well developed. The results of this study could be used as a basic for further research, especially in the field of taxonomy and phylogeny of fish.

The richly fossiliferous deposits of the Brazilian Pedra de Fogo Formation originated in an extensive aquatic system in tropical Pangaea, and grade from marginal lacustrine into marine deposits at the depocenter in the western part of the Parnaíba Basin. In addition to the well-known tetrapod and macrofloral records from these deposits, the Pedra de Fogo Formation yields extensive fish fossils indicating a diverse and abundant ichthyofauna. Among the actinopterygians, deep-bodied morphotypes are represented by whole fish as well as disarticulated dermal scales found at various localities in the states of Maranhão and Piauí. The gross morphology, ornamentation, and histology of some of these scales is highly distinctive, indicating the presence of a novel taxon (Piratata rogersmithii gen. et sp. nov.). The external surface of a Piratata scale is covered in multiple round-to-slightly elongated tubercles. The scale lacks a ganoin cover and is made up of cellular bone and odontocomplexes of orthodentine composing the tuberculated scale surface. The scale morphology and ornamentation most closely resemble that of Cleithrolepis granulatus from the Triassic of Australia and Cleithrolepis extoni from the Triassic Stormberg Beds of South Africa, but the new taxon differs from previously described species in several diagnostic morphological features. The use of scale characters in the taxonomy of ray-finned fishes and the palaeogeographic, palaeoenvironmental, and geochronological implications of the new taxon are discussed.

In this study we report the first complete and annotated mitochondrial genome of the Mexican blind brotula, Typhlias pearsei, a troglobitic cavefish endemic to the Yucatán peninsula karst aquifer in southeastern Mexico. Genomic sequencing was accomplished via next generation sequencing (NGS). The resulting mitogenome is 16,813 bp long and, as in most vertebrates, consists of a total of 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs) and two non-coding regions (control region and origin of the light strand replication). Other than a rearrangement in the position of two tRNAs (shuffling between tRNA-Ile and tRNA-Gln), the mitogenome of T. pearsei exhibits a genomic composition and organization similar to that of most teleost mitogenomes. Besides offering this valuable genomic resource for future studies, the resulting mitogenome was used in a comparative context to test the current higher-level taxonomy of ophidiiform fishes and to examine the phylogenetic position of T. pearsei among viviparous brotulas. Our phylogenetic results confirm those from the most comprehensive molecular phylogenetic study of the group.

Taxonomy and Phylogenetic Relationships of Cyprinid Fish of Genus Hemiculter (Cyprinidae, Xenocypridinae): Sharpbellies of the Species Group Hemiculter lucidus

Oman, a country in Southwest Asia, situated on the southeastern quarter of the Arabian Peninsula presents a high level of biological diversity especially marine elements. Although arid habitats cover most parts of Oman (82%), the region has several freshwater systems that are vital for the survival of people as well as for different groups of animals and plants. Research works on Oman biodiversity including terrestrial and marine, have been steadily increasing over the last few decades, but freshwater ecosystems have not been well investigated. Oman comprises parts of three freshwater ecoregions including the Oman Mountains, Southwestern Arabian Coast, and Arabian Interior having xeric freshwaters and endorheic (closed) basins which support a variety of inland fishes. The current checklist provides for each species of inland waters of Oman all recognized and named taxa, documenting recent changes and controversies in nomenclature, its records, taxonomic status, synonyms, etymology, common English name, short description, range expansion, and detailed distribution map based on several field surveys throughout the country. We also provide native, endemic, and introduced species. The diversity of inland fishes of Oman included in this annotated checklist consists of 23 recognized species in 15 genera, 10 families, seven orders, and a class. Also, for the first time, we report and confirm the presence of four species in the inland waters of Oman. The most diverse order is Cypriniformes (nine species, 39.13%), followed by Gobiiformes (six species, 26.09%), Cyprinodontiformes (three species, 13.04%), Cichliformes (two species, 8.69%), and Centrarchiformes, Gonorynchiformes and Mugiliformes (one species, 4.35% each). 21 native species (91.3%) in nine families and two exotic species (8.7%) in two families are listed here. Out of 21 native species, eight species (16.8%) in two families are endemic elements that are restricted to the Oman territory only. Identification of all recognized species was confirmed by DNA barcoding (mitochondrial COI). Oman Mountains Ecoregion (OME), Southwestern Arabian Coast Ecoregion (SACE), and Arabian Interior Ecoregion (AIE) harbor 15, 12, and one species, respectively. The provided data will be necessary for increasing the fish knowledge, the development of competent and pragmatic management plans and effective conservation policies.

Taxonomic studies on freshwater fishes of Iraq were reviewed. Considerable differences in number of species that have been recorded in Iraqi freshwater were noticed, the number ranged from 44 to 70 species. The difference might be due to recording of synonyms or incorrect records. The continuous record of new species on various periods may have contributed to such variation. Thirty eight species, mainly cyprinids, fell into the disagreement category. A final list of the species which have received majority agreement was proposed with a total of 53 species and 12 families.

Phylogenetic Relationships and Taxonomy of the Carp Fish of Genus Hemiculter (Cyprinidae, Xenocypridinae): Species of the Group H. leucisculus

Trematomus species (suborder Notothenioidei; family Nototheniidae) are widely distributed in the southern oceans near Antarctica. There are 11 recognized species in the genus Trematomus, and notothenioids are known to have high chromosomal diversity (2n = 24–58) because of relatively recent and rapid adaptive radiation. Herein, we report the chromosomal-level genome assembly of T. loennbergii, the first characterized genome representative of the genus Trematomus. The final genome assembly of T. loennbergii was obtained using a Pacific Biosciences long-read sequencing platform and high-throughput chromosome conformation capture technology. Twenty-three chromosomal-level scaffolds were assembled to 940 Mb in total size, with a longest contig size of 48.5 Mb and contig N50 length of 24.7 Mb. The genome contained 42.03% repeat sequences, and a total of 24,525 protein-coding genes were annotated. We produced a high-quality genome assembly of T. loennbergii. Our results provide a first reference genome for the genus Trematomus and will serve as a basis for studying the molecular taxonomy and evolution of Antarctic fish.