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Iranian Barbel taxonomy and evolutionary history (Cyprinidae: Barbinae and Torinae) remain contentious due to overlapping morphological traits and limited molecular data. This study applies an integrative taxonomic framework to elucidate species boundaries, phylogenetic relationships, and the environmental drivers of diversification within Barbels lineages across Iran. We analyzed mitochondrial DNA (Cytb and COI genes), seven meristic morphological characters, and five spatial environmental predictors from specimens collected across localities representing major Iranian basins. Phylogenetic reconstructions using Maximum Likelihood and Bayesian Inference revealed three main monophyletic groups: (1) Arabibarbus, Mesopotamichthys, and Carasobarbus (Torinae); (2) Luciobarbus; and (3) Barbus sensu stricto (Barbinae). Principal Component and Canonical Variate Analyses of meristic data corroborated molecular findings, supporting the delineation of this taxa. Ecological Niche Evolution analysis indicated several species occupy similar climatic niches, suggesting parallel evolutionary responses to environmental pressures. Divergence time estimates and lineage-through-time analyses linked major cladogenic events to regional orogeny and Quaternary climatic fluctuations. Species delimitation analyses suggested potential synonymy among specific taxa (e.g., L. capito with L. conocephalus; L. esosinus with L. xanthopetrus), highlighting the need for taxonomic revision. Our integrative approach demonstrates that geological history and climatic factors have shaped the diversity and distribution of Barbels in Iran. These findings provide a robust framework for future taxonomic, conservation, and biogeographic studies of Iranian freshwater fishes.

Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of paired appendage regeneration, regardless of the amputation level. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in polypterid fishes (Cladistia). Whether this ability evolved independently in sarcopterygians and actinopterygians or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-sequencing (RNA-seq) analysis of Polypterus and axolotl blastemas to provide support for a common origin of paired appendage regeneration in Osteichthyes (bony vertebrates). We show that, in addition to polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of 2 other nonteleost actinopterygians: the American paddlefish (Chondrostei) and the spotted gar (Holostei). Furthermore, we assessed regeneration in 4 teleost species and show that, with the exception of the blue gourami (Anabantidae), 3 species were capable of regenerating fins after endoskeleton amputation: the white convict and the oscar (Cichlidae), and the goldfish (Cyprinidae). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a shared genetic program of appendage regeneration. Comparison of RNA-seq data from early Polypterus blastema to single-cell RNA-seq data from axolotl limb bud and limb regeneration stages shows that Polypterus and axolotl share a regeneration-specific genetic program. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in Osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.

The family Cyprinidae is the largest freshwater fish group with 377 genera and over 3,000 described species. However, this group of fish has very limited cytogenetics and advanced molecular cytogenetics information. Therefore, in this study the karyotypes and other chromosomal characteristics of 15 species in the tribe Systomini (Cyprininae) were examined using Ag-NOR staining along with fluorescence in situ hybridization (5S and 18S rDNA). All species share a similar karyotype (2n = 50; NF = 88–100) in both sexes and no differentiated sex chromosome was observed. Chromosomes bearing NOR sites ranged from one to four pairs among the species, mostly mapped adjacent to telomeres in the short arms of distinct pairs in all analyzed species. This difference indicates an extensive rearrangement of chromosomes including genomic differences. The use of the 5S and 18S rDNA probe confirmed the Ag-NOR sites interstitially located in the telomeric regions of distinct chromosomes, characterizing an interspecies variation of these sites. In most of its analyzed species, the signals of 18S rDNA probe corresponded to the Ag-NOR regions, except in Barbonymus altus , B . gonionotus , B . schwanenfeldii and Puntius brevis having these signals on the same as Ag-NOR regions and other sites.

Background Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses. As an example of cryptic diversity and taxonomic controversy, the European Phoxinus phoxinus species complex was used. Results The results of the revision showed that of the fourteen primary species hypotheses, three were rejected, namely P. ketmaieri , P. likai , and P. apollonicus . For three species ( P. strandjae , P. strymonicus, P. morella ), further investigation with increased data sampling was suggested, while two primary hypotheses, P. bigerri and P. colchicus , were supported as secondary species hypotheses. Finally, six of the primary species hypotheses ( P. phoxinus , P. lumaireul , P. karsticus , P. septimanae , P. marsilii and P. csikii ) were well supported by mitochondrial but only limitedly corroborated by nuclear data analysis. Conclusion The approach has proven useful for revision of species complexes, and the study can serve as an overview of the Phoxinus genus in Europe, as well as a solid basis for further work.

Background Our previous study from 2024 indicated that Ptychobarbus leptosomus is a new species found only in the Yalong River (the largest tributary of the Jinsha River). P. leptosomus was historically classified as P. kaznakovi , which lives in the Jinsha River. To date, the evolutionary history and population dynamics of P. leptosomus and P. kaznakovi have not been reported. In our study, both species have similar morphologies, which may reflect gene flow between the two species. Genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single-nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Results Phylogenetic and population structural analyses based on SNPs indicated that P. leptosomus is an independent Picea species. Additionally, P. kaznakov is more closely related to P. chungtienensis , which is consistent with its geographic distribution. The obvious gene flow from P. kaznakovi and P. chungtienensis branches to P. dipogon was detected. Historical population dynamics analysis revealed that tectonic events in the Shaluli Mountains and the Quaternary climate oscillation had important impacts on the current distribution patterns of the two species, which experienced similar population contraction and expansion processes. Local adaptation promoted differentiation between P. leptosomus and P. kaznakov. Genotype and environment association analysis revealed that 35,654 SNPs were related to environmental factors, mainly related to adaptation to precipitation seasonality and temperature seasonality. Selective elimination analysis revealed that the selected genes were enriched mainly in glycan biosynthesis and metabolism and growth hormone synthesis, secretion, and action (genes such as glycine decarboxylase (gldc ), cyp51 , igf-1 , and tnf-α ), which can help P. leptosomus and P. kaznakov adapt better to the water environment of the high mountains and valleys in the Shaluli Mountains. Conclusions This study emphasizes the significant role of geological and environmental changes in shaping the population history and evolutionary processes of P. kaznakovi and P. leptosomus , and deepens our understanding of the species classification of Ptychobarbus and provides a basis for future species protection.

The genus Discogobio is distributed in the eastern three rivers on the Yunnan–Guizhou Plateau and its adjacent regions, located to the southeast of the Qinghai–Tibet Plateau. Its origin and evolution are likely influenced by the uplift of the Qinghai-Tibet Plateau. However, the historical impact of geological events on the divergence and distribution of this fish group has not been fully elucidated. In this study, we successfully assembled a chromosome-level genome for Discogobio brachyphysallidos, which is approximately 1.21 Gb in length with a contig N50 of 8.63 Mb. The completeness of the genome assembly was assessed with a BUSCO score of 94.78%. A total of 30,597 protein-coding genes were predicted, with 93.92% functionally annotated. Phylogenetic analysis indicated that D. brachyphysallidos was closely related to Labeo rohita, and the divergence of the subfamily Labeoninae coincided with the significant uplift events of the Qinghai–Tibet Plateau. Additionally, we analyzed 75 samples of D. brachyphysallidos and D. yunnanensis from five populations, yielding 1.82 Tb of clean data and identifying 891,303,336 high-quality SNP sites. Population structure analyses indicated that the populations were clustered into five distinct groups, demonstrating significant genetic differentiation among them and the presence of cryptic species within this genus. Analyses of linkage disequilibrium decay and selective sweep indicated that the Pearl River population exhibited relatively higher genetic diversity compared with the populations from other drainages, and none of the populations showed evidence of expansion. Notably, the two population declines coincided with the early Pleistocene and Quaternary glaciation. It can be assumed that the geological movements of the Qinghai–Tibet Plateau and the Quaternary glaciation contributed to the decline in Discogobio populations and shaped their current size. The population genomics results showed that the present distribution pattern of Discogobio was the outcome of a series of geological events following the uplift of the Qinghai–Tibet Plateau. This study reconstructed the geological evolutionary history of the region from the perspective of species evolution. Furthermore, our study presents the first genome-wide analysis of the genetic divergence of Discogobio.

Prior to this study, knowledge on the evolutionary lineage of remained inadequate, as previous phylogenetic investigations were primarily based on partial gene sequences. Although several mitogenomes of species have been reported, their structural organization and comprehensive genomic characteristics have not been thoroughly evaluated. In this study, , endemic to the Indo-Burma biodiversity hotspot, was identified based on its detailed morphology and meristic counts. The circular mitogenome of is 16,776 bp in length and contains the canonical set of 37 genes, along with duplicated control regions separated by tRNA-Proline. The comparative assessments across species indicate predominantly conserved GTG start codons, occasional alternative ATA initiation codons, and incomplete stop codons. The selection pressure examinations within Garrini taxa reveal a purifying selection across all protein-coding genes. The control region comprises four conserved sequence blocks and species-specific tandem repeats, reflecting a balance between functional constraint and lineage-dependent evolutionary dynamics. The phylogenetic inference supports the monophyly of and places in close affinity with , which is native to the western slope of Rakhine Yoma in Myanmar and Mizoram State in northeastern India. The genetic diversity analyses revealed haplotype differentiation, with shallow intraspecific genetic distances (0.000-0.011) observed samples between two distinct drainage systems in Manipur and Mizoram, northeastern India. The observed pattern of haplotype divergence in may reflect the historical or seasonal hydrological connectivity among the western-slope drainages of the Chin Hills, with the subsequent geographic isolation potentially contributing to the emergence of distinct genetic lineages. Nevertheless, the extent and evolutionary significance of this differentiation remain uncertain and warrant further investigation through expanded geographic sampling and the incorporation of additional molecular data. Collectively, these findings provide in-depth insights into the mitogenomic architecture, comparative gene arrangements, phylogenetic patterns, and matrilineal evolutionary history of and other congeners, thereby improving our understanding of the systematics and genetic diversity of this important cyprinid fish lineage.

The biodiversity of the Magdalena-Cauca Basin, Colombia's main fluvial system, is under severe threat from anthropogenic activities, imperiling endemic fish species such as Pimelodus yuma and Pimelodus grosskopfii. Using a population genomic approach based on single nucleotide polymorphisms (SNPs), we analyzed 64 individuals of P. grosskopfii and 57 individuals of P. yuma collected across ~1,600 km of the Magdalena-Cauca Basin. We identified two coexisting genetic stocks in both species, maintained by restricted gene flow that is associated with adaptive divergence rather than geographic distribution. Selection pressures, likely linked to the basin's bimodal hydrological regime, were detected as major drivers of genetic structure. Historical demographic reconstruction analyses indicate that stock 1 in both P. grosskopfii and P. yuma was established in the basin during the Late Miocene-Pliocene (~4.5-5.5 MYA), with P. grosskopfii exhibiting an early expansion followed by long-term stability up to the present, while P. yuma maintained a stable population size until a recent decline. Stock 2 in both species was established during the Early Pleistocene (~1.7-2.5 MYA), followed by expansion and stability in P. grosskopfii, and a stable population size followed by a contraction-recovery-expansion dynamic in P. yuma, suggesting long-term persistence of neutral/adaptive processes shaping these stocks. Each stock should be considered a Management and Adaptive Unit, highlighting the need for targeted conservation actions and broader strategies to ensure their persistence under ongoing environmental and anthropogenic pressures in the Magdalena-Cauca Basin.

Artificial transplantation of organisms and consequent invasive hybridization can lead to the extinction of native species. In Matsuyama, Japan, a native bitterling fish, Tanakia lanceolata, is known to form hybrids with another bitterling species, T. limbata, which was recently introduced from western Kyushu, Japan. These bitterlings spawn in the gills of two freshwater unionid species, Pronodularia japanensis and Nodularia douglasiae nipponensis, which have rapidly declined on the Matsuyama Plain in the past 30 years. To gauge the effect of invasive hybridization, we determined the genetic introgression between T. lanceolata and T. limbata and analyzed the morphology of these species and their hybrids to infer their niche overlap. We collected adult individuals of Tanakia spp. and genotyped them based on six microsatellite loci and mitochondrial cytochrome b sequences. We analyzed their meristic characters and body shapes by geometric morphometrics. We found that 10.9% of all individuals collected were hybrids. Whereas T. lanceolata were more densely distributed downstream and T. limbata were distributed upstream, their hybrids were widely distributed, covering the entire range of native T. lanceolata. The body height and anal fin length of T. limbata were greater than those of T. lanceolata, but their hybrids were highly morphologically variable, covering both parental morphs, and were widely distributed in the habitats of both parental species. Hybridization has occurred in both directions, but introduced T. limbata females and native T. lanceolata males are more likely to have crossed. This study shows that invasive hybridization with the introduced T. limbata is a potential threat to the native population of T. lanceolata via genetic introgression and replacement of its niche in streams.

Fishes from the genus Carasobarbus , widely distributed throughout the river systems of North Africa and West Asia, are commonly referred to as Himris. In the Persian Gulf basin, they are widespread and are also found in fast-flowing rivers or the deeper regions of lakes. In this region, representation of these fishes in scientific collections is scarce, and except for C. luteus , the other species are very poorly documented and frequently misidentified due to their similarities. In this study we analysed the relationships among Carasobarbus species using mitochondrial genes (Cyt b , COI) and present morphological characters based on examinations. Our results revealed three new species which we describe here. Carasobarbus doadrioi, new species, is distinguished by 40–44 scales on the lateral line and a prominent black blotch on end of caudal peduncle in specimens < 85 mm SL. Carasobarbus hajhosseini , new species is distinguished by 32–34 scales on the lateral line and long head length (20–24% SL). Carasobarbus saadatii , new species, is distinguished by 38–40 scales on the lateral line and short head length (19–20% HL). In the Persian Gulf basin, Carasobarbus species exhibit uncorrected genetic distances of 1.6 to 5.5% in the COI barcode region and 2.6% to 9.9% in the Cyt b gene. This study highlights the importance of investigating the unexplored diversity that exists within poorly sampled and understudied freshwater fish group. Such investigations are essential for developing a comprehensive understanding of the true extent of biodiversity, which is critical for informing effective conservation and protection strategies.