Freshwater fish scale database.

Scales of the ray finned fishes can be used for multiple purposes. Beside others by their specific structure and elemental composition they are usable for age determination and food-web researches. Additionally, just their presence, absence, shape, location, or numbers could provide a reliable taxonomic information. The fish scales show remarkable size variation also, which characteristics provide reliable information about the environmental needs of freshwater fish. But till now this information was not interpretable and comparable in the absence of a sufficiently large and detailed database. In this study we provide a database which can facilitate the further complex comparative studies. Our dataset consists of 2954 scale photos characterising 193 freshwater fish species. All photos have a uniquely identification code showing exactly which species the scale belongs to. In addition to the photos, our database includes a table showing the exact taxonomic classification of the studied species, the average body profile-index, and the relative scale size, as well as the ecological (flow and feeding habitat preferences) and life strategic characteristics (feeding and breeding guild memberships) of each species. The sampled species have diverse origin, covering five biogeographical regions. An average of five adults from each species were selected for sampling. Three-to-four scales were collected from the anterior part of the body between the dorsal fin and the lateral line. The removed scales were cleaned and prepared to microscope slides, and after this process they were photographed or scanned. Our database can be used for both research and educational purposes. A large number of scale photos assigned of species can be an opportunity to create an automatic species identification system. Moreover, the subjectivity in morphometric measurements can be eliminated by analysing the database with artificial intelligence.

Speciation and repeated origins of hypertrophied lips in parallel adaptive radiations of cyprinid fish from East Africa.

The evolution of convergent phenotypes is one of the most interesting phenomena of repeated adaptive radiations. Here, we examined the repeated patterns of thick-lipped or "rubberlip" phenotype of cyprinid fish of the genus Labeobarbus discovered in riverine environments of the Ethiopian Highlands, East Africa. To test the adaptive value of thickened lips, identify the ecological niche of the thick-lipped ecomorphs, and test whether these ecomorphs are the products of adaptive divergence, we studied six sympatric pairs of ecomorphs with hypertrophied lips and the normal lip structure from different riverine basins. Trophic morphology, diet, stable isotope (δ15N and δ13C) signatures, as well as mtDNA markers and genome-wide SNP variation, were analyzed. Our results show that thick-lipped ecomorphs partition trophic resources with generalized ecomorphs in only one-half of the examined sympatric pairs despite the pronounced divergence in lip structure. In these thick-lipped ecomorphs that were trophically diverged, the data on their diet along with the elevated 15N values suggest an invertivorous specialization different from the basal omnivorous-detritivouros feeding mode of the generalized ecomorphs. Genetic data confirmed an independent and parallel origin of all six lipped ecomorphs. Yet, only one of those six thick-lipped ecomorphs had a notable genetic divergence with sympatric non-lipped ecomorphs based on nuclear SNPs data (F ST = 0.21). Sympatric pairs can be sorted by combinations of phenotypic, ecological, and genetic divergence from an ecologically non-functional mouth polymorphism via ecologically functional polymorphism to a matured speciation stage via divergent evolution.

Caucasian treasure: Genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock.

Five ecologically and phenotypically divergent ecomorphs of the genus Salmo are known from a landlocked alpine lake in the Caucasus, Lake Sevan. It is an example of sympatric diversification within a species-rich lineage with predominate mode of speciation being allopatric. The diversification of Sevan trouts was accompanied by spawning resource partitioning. Four lacustrine ecomorphs with different temporal-spatial spawning strategies and divergent morphology and coloration evolved along with a fifth ecomorph, brook trout, inhabiting the tributaries. Unfortunately, the Sevan trout diversity was almost destroyed by human activity, with two ecomorphs becoming extinct in the 1980s. We performed reconstruction of the evolutionary history of Sevan trouts based on high-throughput sequencing of both contemporary and historical DNA (∼ 50 y.o.) of all Sevan trout ecomorphs. Our study of complete mitogenomes along with genome-wide SNP data revealed the monophyly of four lacustrine ecomorphs and local brook trout, all derived from the anadromous form Caspian salmon, S. caspius. The species tree suggests a scenario of stepwise evolution from riverine to lacustrine spawning. Three genomic clusters were revealed, of which two refer to the riverine and lacustrine spawners within the flock of Sevan trouts (with FST value = 0.069). A few SNP outliers under selection were discovered that could be responsible for assortative mating based on visual recognition. The Holocene climatic oscillations and the desiccation of tributaries could have played an important role in the origin of lacustrine spawning. The relationships between lacustrine ecomorphs were not yet fully resolved. This radiation warrants further investigation.

Fish occurrence in the Kama River Basin (Russia).

Background: Dataset contains information on fish occurrences in the Kama River Basin (Russian Federation). The Kama River is the largest tributary (1805 km) of the Volga River and is geographically often considered the main river due to the larger volume of water at their confluence. New information: Dataset is based on our own field studies conducted during 2008-2021. It includes 6,447 occurrences relating to 48 taxa, 46 of which were identified at species level and two at the genus level. All occurrences have coordinates and belong to 13 families of Actinopterygii. All presented data are published for the first time.

Fish occurrence in the Kuban River Basin (Russia).

BACKGROUND: This publication describes a dataset containing information on 1328 occurrences of fishes in the Kuban River Basin, the longest river of Northern Caucasus and representing its own freshwater ecoregion (428 Kuban Ecoregion). All observations have precise geo-referencing with the names of water bodies (rivers, lakes etc.). The dataset is based on both literature data (509 occurrences) and our own sampling (814 occurrences). Observations were carried out between 1889 and 2020. NEW INFORMATION: The majority (> 61%) of occurrences in the presented data are published for the first time. This extended dataset contributes significantly to fish fauna survey in the Kuban River ecoregion.

Rapid adaptive radiation in a hillstream cyprinid fish in the East African White Nile River basin.

Adaptive radiation of freshwater fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that riverine and stream environments also provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeast Asia to West Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have probably been found among these ecomorphs in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra ("thick-lipped" and "predatory") that had not been discovered before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intrabasin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide single nucleotide polymorphism data, mitochondrial DNA was unable to identify any genetic structure suggesting recent and rapid speciation events. Some data suggest a hybrid origin of the novel "thick-lipped" ecomorph. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly radiated in a riverine environment promoted by the evolution of novel feeding strategies.

A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)?

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, have led to morphological description of 47 extant nominal species. However, many of these species have not been supported by previous phylogenetic studies, which could be partly due to lack of significant genetic differences among them, the limited resolution offered by molecular methods previously used, as well as the often local scale of these studies. The development of next-generation sequencing (NGS) and related analytical tools have enhanced our ability to address such challenging questions. In this study, Genotyping-by-Sequencing (GBS) of 15,169 filtered SNPs and mitochondrial DNA (mtDNA) D-loop sequences were combined to assess the phylogenetic relationships among 166 brown trouts representing 21 described species and three undescribed groups collected from 84 localities throughout their natural distribution in Europe, west Asia, and North Africa. The data were analysed using different clustering algorithms (admixture analysis and discriminant analysis of principal components-DAPC), a Bayes Factor Delimitation (BFD) test, species tree reconstruction, gene flow tests (three- and four-population tests), and Rogue taxa identification tests. Genomic contributions of the Atlantic lineage brown trout were found in all major sea basins excluding the North African and Aral Sea basins, suggesting introgressive hybridization of native brown trouts driven by stocking using strains of the Atlantic lineage. After removing the phylogenetic noise caused by the Atlantic brown trout, admixture clusters and DAPC clustering based on GBS data, respectively, resolved 11 and 13 clusters among the previously described brown trout species, which were also supported by BFD test results. Our results suggest that natural hybridization between different brown trout lineages has probably played an important role in the origin of several of the putative species, including S. marmoratus, S. carpio, S. farioides, S. pellegrini, S. caspius (in the Kura River drainage) and Salmo sp. in the Danube River basin. Overall, our results support a multi-species taxonomy for brown trouts. They also resolve some species in the Adriatic-Mediterranean and Black Sea drainages as members of very closely related genomic clusters that may need taxonomic revision. However, any final conclusions pertaining to the taxonomy of the brown trout complex should be based on an integrative approach combining genomic, morphological, and ecological data. To avoid challenges in taxonomy and conservation of species complexes like brown trouts, it is suggested to describe species based on genomic clusters of populations instead of describing species based only on morphologically differentiated single type populations.

Monsters with a shortened vertebral column: A population phenomenon in radiating fish Labeobarbus (Cyprinidae).

The phenomenon of a massive vertebral deformity was recorded in the radiating Labeobarbus assemblage from the middle reaches of the Genale River (south-eastern Ethiopia, East Africa). Within this sympatric assemblage, five trophic morphs-generalized, lipped, piscivorous and two scraping feeders-were reported between 1993 and 2019. In 2009, a new morph with prevalence of ~10% was discovered. The new morph, termed 'short', had an abnormally shortened vertebral column and a significantly deeper body. This type of deformity is common in farmed Atlantic salmon and other artificially reared fish, but is rare in nature. In the Genale Labeobarbus assemblage, the deformity was present exclusively within the generalized and lipped morphs. The short morph had between seven and 36 deformed (compressed and/or fused) vertebrae. Their body depth was positively correlated with number of deformed vertebrae. In another collection in 2019, the short morph was still present at a frequency of 11%. Various environmental and genetic factors could contribute to the development of this deformity in the Genale Labeobarbus, but based on the available data, it is impossible to confidently identify the key factor(s). Whether the result of genetics, the environment, or both, this deep-bodied phenotype is assumed to be an anti-predator adaptation, as there is evidence of its selective advantage in the generalized morph. The Genale monstrosity is the first reported case of a massive deformity of the vertebral column in a natural population of African fishes.

In the rivers: Multiple adaptive radiations of cyprinid fishes (Labeobarbus) in Ethiopian Highlands.

Multiple repeated patterns of adaptive radiation were revealed in cyprinid fish inhabiting the compact geographic region of the Ethiopian Highlands. We found four independently evolved radiations in the evolutionary hexaploid (2n = 150) Labeobarbus lineage based on matrilineal relationships of >800 individuals. Each radiation displayed similar patterns of mouth phenotype diversification, and included ecomorphs/species of the generalized, lipped, scraping (one or two), and large-mouthed (one to three) types. All radiations were detected in geographically isolated rivers, and originated from different ancestral populations. This is the first documented case in which numerous parallel radiations of fishes occurred-via different ways-in a riverine environment. Some radiations are very recent and monophyletic, while others are older and include ecomorphs that originated in separate mini flocks and later combined into one. The diversification bursts among Ethiopian Labeobarbus were detected in the mid-upper reaches of rivers (1050-1550 m above sea level), which likely offer ecological opportunities that include diverse habitats yet poor fauna (i.e. lower competition and relaxed selection). This promising example of parallel evolution of adaptive radiation warrants further investigation.

Morphological and mtDNA data reveal broader distribution of Alburnoides holciki (Teleostei: Leuciscidae) in inland waters of Central Asia.

Alburnoides holciki was described from the Hari River basin, which was the only basin it was known from. Populations from the Amu Darya basin were previously recognized as A. eichwaldii or Alburnoides sp. Our study recognized specimens of Alburnoides from the Amu Darya basin as A. holciki based on morphological data and the COI barcode gene. The population from the Zeravshan basin showed some morphological differences compared to others but were similar in the COI gene and needs further investigation. New results extend the range of A. holciki for almost 1000 km -from the Hari River to the upper Amu Darya tributaries in Tajikistan. The intraspecific genetic similarity in the COI gene between populations in the Hari and Amu Darya rivers supports the geographical hypothesis of a recent connection of these rivers.

Phylogeny, phylogeography and hybridization of Caucasian barbels of the genus Barbus (Actinopterygii, Cyprinidae).

Phylogenetic relationships and phylogeography of six species of Caucasian barbels, the genus Barbus s. str., were studied based on extended geographic coverage and using mtDNA and nDNA markers. Based on 27 species studied, matrilineal phylogeny of the genus Barbus is composed of two clades - (a) West European clade, (b) Central and East European clade. The latter comprises two subclades: (b1) Balkanian subclade, and (b2) Ponto-Caspian one that includes 11 lineages mainly from Black and Caspian Sea drainages. Caucasian barbels are not monophyletic and subdivided for two groups. The Black Sea group encompasses species from tributaries of Black Sea including re-erected B. rionicus and excluding B. kubanicus. The Caspian group includes B. ciscaucasicus, B. cyri (with B. goktschaicus that might be synonymized with B. cyri), B. lacerta from the Tigris-Euphrates basin and B. kubanicus from the Kuban basin. Genetic structure of Black Sea barbels was influenced by glaciation-deglaciation periods accompanying by freshwater phases, periods of migration and colonization of Black Sea tributaries. Intra- and intergeneric hybridization among Caucasian barbines was revealed. In the present study, we report about finding of B. tauricus in the Kuban basin, where only B. kubanicus was thought to inhabit. Hybrids between these species were detected based on both mtDNA and nDNA markers. Remarkably, Kuban population of B. tauricus is distant to closely located conspecific populations and we consider it as relic. We highlight revealing the intergeneric hybridization between evolutionary tetraploid (2n = 100) B. goktschaicus and evolutionary hexaploid (2n = 150) Capoeta sevangi in Lake Sevan.

Heterochronic development of lateral plates in the three-spined stickleback induced by thyroid hormone level alterations.

The three-spined stickleback Gasterosteus aculeatus is an important model for studying microevolution and parallel adaptation to freshwater environments. Marine and freshwater forms differ markedly in their phenotype, especially in the number of lateral plates, which are serially repeated elements of the exoskeleton. In fishes, thyroid hormones are involved in adaptation to salinity, as well as the developmental regulation of serially repeated elements. To study how thyroid hormones influence lateral plate development, we manipulated levels of triiodothyronine and thiourea during early ontogeny in a marine and freshwater population with complete and low plate phenotypes, respectively. The development of lateral plates along the body and keel was heterochronic among experimental groups. Fish with a low dosage of exogenous triiodothyronine and those treated with thiourea exhibited retarded development of bony plates compared to both control fish and those treated with higher a triiodothyronine dosage. Several triiodothyronine-treated individuals of the marine form expressed the partial lateral plate phenotype. Some individuals with delayed development of lateral plates manifested 1-2 extra bony plates located above the main row of lateral plates.

DNA barcoding of the fishes of the genus Alburnoides (Actinopterygii, Cyprinidae) from Caucasus.

Spirlins of the genus Alburnoides are widespread fishes, which taxonomy has been rapidly developing in recent years. Mitochondrial cytochrome c oxidase subunit I (COI) was used as DNA barcode marker to create a reference dataset of Caucasian Alburnoides and to test its barcoding efficiency. All four previously known Caucasian species of Alburnoides were confirmed as valid species with high genetic distances to sister species as well confirmed as Caucasian endemics. Alburnoides samiii, previously known from Sefidroud basin (Iran), was discovered in Transcaucasia. The accuracy of species identification of Ponto-Caspian Alburnoides by DNA barcodes was 100%. In addition, one potentially new species within A. gmelini was revealed. Despite the limited ability of COI to infer phylogenetic relationships, study provided evidence that Ponto-Caspian lineage of Alburnoides includes significantly larger number of species from Caspian Sea basin and inland basins of Central Asia.

Sequencing of two mitochondrial genomes of endangered form of the Sevan trout Salmo ischchan aestivalis.

The two complete mitochondrial genomes of endangered form of the Sevan trout Salmo ischchan aestivalis are published in this paper. The mitochondrial DNA (mtDNA) is 16,677 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The overall base composition of the genome in descending order was 29.4% - C, 27.9% - A, 26.0% - T, 16.7% - G, without a significant AT bias of 53.9%.

A century in synonymy: molecular and morphological evidence for the revalidation of Glyptosternon osсhanini (Herzenstein, 1889) (Actinopterygii: Sisoridae).

Exostoma oschanini, presently treated as a junior synonym of Glyptosternon reticulatum, is revalidated within Glyptosternon based on a phylogenetic analysis of the CO1 gene and morphological characters. Glyptosternon oschanini is known to occur in tributaries of the Syr Darya River in Uzbekistan and Kyrgyzstan and may also occur in the Amu Darya River drainage. A morphological diagnosis and description are provided for G. oschanini. Exostoma gracile is a junior synonym of G. oschanini rather than of G. reticulatum.

Two complete mitochondrial genomes of extinct form of the Sevan trout Salmo ischchan danilewskii.

The mitochondrial genomes from two individuals of the extinct subspecies of the Sevan trout Salmo ischchan danilewskii are published in this paper. The mitochondrial DNA (mtDNA) is 16,665 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The overall base composition of the genome in descending order was 27.9% of A, 29.4% of C, 16.7% of G, and 26.0% of T without a significant AT bias of 53.9%.

Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes).

The cyprinid tribe Labeonini (sensuRainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and sequenced for four nuclear genes and five mitochondrial genes (totaling 9465bp). Phylogenetic relationships and subdivision of this tribe were investigated and the placement and status of most genera are discussed. Partitioned maximum likelihood analyses were performed based on the nuclear dataset, mitochondrial dataset, combined dataset, and the dataset for each nuclear gene. Inclusion of the genera Paracrossochilus, Barbichthys, Thynnichthys, and Linichthys in the Labeonini was either confirmed or proposed for the first time. None of the genera Labeo, Garra, Bangana, Cirrhinus, and Crossocheilus are monophyletic. Taxonomic revisions of some genera were made: the generic names Gymnostomus Heckel, 1843, Ageneiogarra Garman, 1912 and Gonorhynchus McClelland, 1839 were revalidated; Akrokolioplax Zhang and Kottelat, 2006 becomes a junior synonym of Gonorhynchus; the species Osteochilus nashii was found to be a member of the barbin genus Osteochilichthys. Five historical hypotheses on the classification of the Labeonini were tested and rejected. We proposed to subdivide the tribe, which is strongly supported as monophyletic, into four subtribes: Labeoina, Garraina, Osteochilina, and Semilabeoina. The taxa included in each subtribe were listed and those taxa that need taxonomic revision were discussed.

Phylogenetic relationships of the algae scraping cyprinid genus Capoeta (Teleostei: Cyprinidae).

We reconstructed the matrilineal phylogeny of Asian algae-eating fishes of the genus Capoeta based on complete mitochondrial gene for cytochrome b sequences obtained from 20 species sampled from the majority of the range and 44 species of closely related barbs of the genera Barbus s. str. and Luciobarbus. The results of this study show that Capoeta forms a strongly supported monophyletic subclade nested within the Luciobarbus clade, suggesting that specialized scraping morphology appeared once in the evolutionary history of the genus. We detected three main groups of Capoeta: the Mesopotamian group, which includes three species from the Tigris-Euphrates system and adjacent water bodies, the Anatolian-Iranian group, which has the most diversified structure and encompasses many species distributed throughout Anatolian and Iranian inland waters, and the Aralo-Caspian group, which consists of species distributed in basins of the Caspian and Aral Seas, including many dead-end rivers in Central Asia and Northern Iran. The most probable origination pathway of the genus Capoeta is hypothesized to occur as a result of allopolyploidization. The origin of Capoeta was found around the Langhian-Serravallian boundary according to our molecular clock. The diversification within the genus occurred along Middle Miocene-Late Pliocene periods.

Nonlinear oscillating structures in the earthquake and seaquake dynamics.

The article deals with the problem of parametric excitation of oscillating structures during an earthquake and a seaquake associated with external forces. Tidal forces and their linear and nonlinear components are considered as possible causes of earthquakes. A seaquake is regarded as a typical large-scale structural disturbance of the water surface resulting from the ocean bottom earthquake. There are given results of original laboratory seaquake modeling where wave structures with hexagonal and square cells appeared. The received wave lattices were similar to Faraday ripples, but with the size of cells from 15 to 120 mm. These experiments provided parameters on transition from a wave structure to chaos. Comparison of laboratory experimental data with descriptions of full-scale seaquakes and parametric wave theory has confirmed the submitted interpretation of the phenomenon. (c) 1996 American Institute of Physics.