Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly.

This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8-2387) and contractions (16-2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii.

Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes.

BACKGROUND: Mitochondrial DNA (mtDNA) has become a significant tool for exploring genetic diversity and delineating evolutionary links across diverse taxa. Within the group of cold-water fish species that are native to the Indian Himalayan region, Schizothorax esocinus holds particular importance due to its ecological significance and is potentially vulnerable to environmental changes. This research aims to clarify the phylogenetic relationships within the Schizothorax genus by utilizing mitochondrial protein-coding genes. METHODS: Standard protocols were followed for the isolation of DNA from S. esocinus. For the amplification of mtDNA, overlapping primers were used, and then subsequent sequencing was performed. The genetic features were investigated by the application of bioinformatic approaches. These approaches covered the evaluation of nucleotide composition, codon usage, selective pressure using nonsynonymous substitution /synonymous substitution (Ka/Ks) ratios, and phylogenetic analysis. RESULTS: The study specifically examined the 13 protein-coding genes of Schizothorax species which belongs to the Schizothoracinae subfamily. Nucleotide composition analysis showed a bias towards A + T content, consistent with other cyprinid fish species, suggesting evolutionary conservation. Relative Synonymous Codon Usage highlighted leucine as the most frequent (5.18%) and cysteine as the least frequent (0.78%) codon. The positive AT-skew and the predominantly negative GC-skew indicated the abundance of A and C. Comparative analysis revealed significant conservation of amino acids in multiple genes. The majority of amino acids were hydrophobic rather than polar. The purifying selection was revealed by the genetic distance and Ka/Ks ratios. Phylogenetic study revealed a significant genetic divergence between S. esocinus and other Schizothorax species with interspecific K2P distances ranging from 0.00 to 8.87%, with an average of 5.76%. CONCLUSION: The present study provides significant contributions to the understanding of mitochondrial genome diversity and genetic evolution mechanisms in Schizothoracinae, hence offering vital insights for the development of conservation initiatives aimed at protecting freshwater fish species.

Redescription of Cyprinion muscatense (Teleostei: Cyprinidae) with the first phylogenetic analysis of the genus.

Members of the genus Cyprinion (Cypriniformes: Cyprinidae) are found in the Indus River basin west to the Arabian Peninsula and the Tigris-Euphrates River drainages (Persian Gulf basin). The taxonomic status of Cyprinion including Cyprinion muscatense is poorly understood when compared to other cyprinid genera. C. muscatense has been considered as a member of the Cyprinion watsoni-microphthalmum group and a valid species endemic to the Arabian Peninsula. Here, we redescribe C. muscatense based on an integrative morphological and molecular approach and freshly sampled material from several localities in the Oman Mountains ecoregion. The results showed that C. muscatense is distinguished from the other Cyprinion species in the Arabian Peninsula by having a short, thin, and slightly serrated last unbranched dorsal fin ray; the lower number of circumpeduncular scales; lateral line scales; and also scales between the lateral line and the dorsal-fin origin. Subterminal mouth, presence of one pair of small barbels at the mouth corner, 3-4 unbranched and 9½-10½ dorsal-fin branched rays, 12-14 pectoral-fin rays, 7-8 pelvic-fin rays, 2-3 unbranched and 6½-7½ branched anal-fin rays, and 37-40 lateral line scales are other morphological characteristics of C. muscatense. C. muscatense is also well distinguished by molecular characters among its congeners. The first molecular phylogenetic analysis of the genus, covering all currently recognized Cyprinion species except for C. watsoni, is also presented. C. muscatense is resolved as the sister species to another endemic fish of the Arabian Peninsula Cyprinion mhalense, with a Kimura-2-Parameter model distance of 5.3%.

An overview of the taxonomic instability of endangered Golden and Zhobi mahseer in Pakistan / Uma visão geral da instabilidade taxonômica do golden em perigo e do Zhobi mahseer no Paquistão

In South and South East Asia three genera of fish species i.e. Tor, Neolissochilus and Naziritor are commonly known as Mahseer with at least 47 species. Among these 23 belongs to genus Tor, 22 to Neolissochilus and one to Naziritor i.e. Naziritor zhobensis. Recently another species added to genus Naziritor is Naziritor chelynoides in India. Among Tor species Tor putitora (Hamilton) is the most widely distributed Mahseer in Pakistan and other countries of the Indian subcontinent. However, based alone on morphological characters some authors identify the Pakistani counterparts as Tor macrolepis (Heckel), (a species presumed to be found exclusively in the Indus River system) distinct from Tor putitora (a species found in Ganga Brahmaputra River system). In order to resolve this taxonomic ambiguity, present study carried out meristic and morphometric measurements of Mahseer collected from a total of 11 water bodies of Pakistan. Ratios between the morphometric characters were calculated and statistically analyzed using t-test and correlation coefficient. Two species identified as Tor putitora and Naziritor zhobensis were the sole Mahseer inhabitants of Indus system in Pakistan. Tor putitora occurred at all surveyed sites while Nazirtor zhobensis had a distribution range from river Zhob to tributaries of river Gomal the right bank tributaries of River Indus. The study corroborates that there are no unequivocal morphological synapomorphies in any existing populations of both species. The study further demonstrates that head length, a character frequently used in Mahseer taxonomy, is not a good measure for species identification. Finally the present study establishes that Naziritor zhobensis still exists in the water bodies of Pakistan and that golden Mahseer occurring in Indus riverine system of Pakistan is Tor putitora.

No sul e sudeste da Ásia, três gêneros de espécies de peixes, ou seja, Tor, Neolissochilus e Naziritor, são comumente conhecidos como Mahseer com pelo menos 47 espécies. Entre estas, 23 pertencem ao gênero Tor, 22 a Neolissochilus e um a Naziritor, ou seja, Naziritor zhobensis. Recentemente, outra espécie adicionada ao gênero Naziritor é Naziritor chelynoides na Índia. Entre as espécies de Tor, Tor putitora (Hamilton) é o Mahseer mais amplamente distribuído no Paquistão e em outros países do subcontinente indiano. No entanto, com base apenas em caracteres morfológicos, alguns autores identificam as contrapartes paquistanesas como Tor macrolepis (Heckel) (uma espécie que se presume ser encontrada exclusivamente no sistema do rio Indo), distinta de Tor putitora (uma espécie encontrada no sistema do rio Ganga Brahmaputra). A fim de resolver essas ambiguidades taxonômicas, o presente estudo realizou medidas merísticas e morfométricas de Mahseer coletadas em um total de 11 corpos d’água do Paquistão. As razões entre os caracteres morfométricos foram calculadas e analisadas estatisticamente usando o teste t e o coeficiente de correlação. Duas espécies identificadas como Tor putitora e Naziritor zhobensis foram os únicos habitantes Mahseer do sistema fluvial Indo no Paquistão. Tor putitora ocorreu em todos os locais pesquisados, enquanto Nazirtor zhobensis tinha uma faixa de distribuição do rio Zhob aos afluentes do rio Gomal, afluentes da margem direita do rio Indo. O estudo corrobora que não há sinapomorfias morfológicas inequívocas em nenhuma das populações existentes de ambas as espécies. O estudo demonstra ainda que o comprimento da cabeça, um caractere frequentemente usado na taxonomia de Mahseer, não é boa medida para identificação das espécies. Finalmente, o presente estudo estabelece que Naziritor zhobensis ainda existe nos corpos d'água do Paquistão e que o Mahseer dourado ocorrendo no sistema fluvial Indo do Paquistão é Tor putitora.

Evolving in the darkness: Phylogenomics of Sinocyclocheilus cavefishes highlights recent diversification and cryptic diversity.

Troglomorphism-any morphological adaptation enabling life to the constant darkness of caves, such as loss of pigment, reduced eyesight or blindness, over-developed tactile and olfactory organs-has long intrigued biologists. However, inferring the proximate and ultimate mechanisms driving the evolution of troglomorphism (stygomorphism) in freshwater fish requires a sound understanding of the evolutionary relationships between surface and stygomorphic lineages. We use Restriction Site Associated DNA Sequencing (RADseq) to better understand the evolution of the Sinocyclocheilus fishes of China. With a remarkable array of derived stygomorphic traits, they comprise the largest cavefish diversification in the world, emerging as a multi-species model system to study evolutionary novelty. We sequenced a total of 120 individuals throughout the Sinocyclocheilus distribution. The data comprised a total of 646,497 bp per individual, including 4378 loci and 67,983 SNPs shared across a minimum of 114 individuals at a given locus. Phylogenetic analyses using either the concatenated RAD loci (RAxML) or the SNPs under a coalescent model (SVDquartets, SNAPP) showed a high degree of congruence with similar topologies and high node support (>95 for most nodes in the phylogeny). The major clades recovered conform to a pattern previously established using Sanger-based mt-DNA sequences, with a few notable exceptions. We now recognize six major clades in this group, elevating the blind cavefish S. tianlinensis and the micro-eyed S. microphthalmus as two new distinct clades due to their deep divergence from other clades. PCA plots of the SNP data also support the recognition of six major clusters of species congruent with the identified clades in ordination space. A Bayes factor delimitation (BFD) analysis showed support for 21 species, recognizing 19 previously described species and two putative new cryptic ones. Two species whose identities were previously disputed, S. furcodorsalis and S. tianeensis, are supported here as distinct species. In addition, our multi-species calibrated tree in SNAPP suggests that the genus Sinocyclocheilus originated around 10.16 Mya, with most speciation events occurring in the last 2 Mya, likely favored by the uplift of the Qinghai-Tibetan Plateau and cave occupation induced by climate-driven aridification during this period. These results provide a firm basis for future comparative studies on the evolution of Sinocyclocheilus and its adaptations to cave life.

Genetic diversity and genetic differentiation of Megalobrama populations inferred by mitochondrial markers.

BACKGROUND: Megalobrama is economically one of the most important freshwater fish genera in China. However, phylogenetic relationships among M. amblycephala, M. skolkovii, M. hoffmanni and M. pellegrini remain unresolved. OBJECTIVE: To explore the genetic diversity and phylogenetic relationship of Megalobrama populations belonging to all four species. METHODS: The concatenated sequences of mitochondrial cytochrome b (Cytb) and control region (CR) were used to analyze the genetic variation, genetic differentiation and population expansion of 15 Megalobrama populations. RESULTS: The study showed that haplotype diversity and nucleotide diversity of M. hoffmanni and M. skolkovii were high, and that M. hoffmanni was the most genetically divergent of the four species. Haplotype network analysis revealed that M. hoffmanni and M. amblycephala formed a monophyletic group each, while M. skolkovii and M. pellegrini clustered together. There was a high genetic differentiation among the four Megalobrama species, and genetic distance among populations was not affected by geographical distance. Additionally, the results indicated that there was gene flow between the Liangzi Lake (LZL) population and Jinsha River Reservoir (JS) population. Also, Zhaoqing (ZQ) population of M. hoffmanni might have experienced a population expansion. CONCLUSION: Our study verifies genetic diversity and differentiation of Megalobrama populations, and these findings will represent a significant contribution to the conservation and utilization of germplasm resources of Megalobrama.

Cassia fistula ameliorates chronic toxicity of cypermethrin in Catla catla.

Protective effects of Cassia fistula, in Catla catla exposed to synthetic pyrethroid cypermethrin were evaluated. Fish, after chronic exposure to environmentally relevant sub-lethal concentration 0.41 µg/l of the pesticide were assessed for antioxidant activity, histopathological and ultrastructural alterations. Significant (p < 0.05) decrease in the activities of antioxidants such as CAT, SOD, GST, GSH was registered, whereas LPO level got elevated. Histological damage depicted necrosis, epithelial hypertrophy, hyperplasia and fusion of secondary lamellae and changes in gill vasculature. Histopathological alteration index was employed for the semi quantitative evaluation of the degree of tissue change (DTC). Transmission electron microscopy displayed swollen and distorted mitochondria, damaged chloride cells and necrosis. Dietary supplementation of Cassia fistula bark extract significantly (p < 0.05) improved the antioxidant activity, reduced lipid peroxidation and prevented histopathological alterations. The findings suggest that sub-lethal concentration of cypermethrin is toxic to fish. The study also draws attention towards potential of plant derived antioxidants in mitigating pesticide induced toxic effects.

Osteology of Hemigrammocypris neglecta (Teleostei: Cypriniformes) with comments on its systematic position.

Hemigrammocypris neglecta is a small-sized cyprinid fish that is endemic to Japan and the sole member of the genus Hemigrammocypris. We examined the osteological features of the species, and its relationships with related genera are discussed. The present data suggest that H. neglecta is most likely the sister taxon of Metzia lineata. This relationship is supported by one possible synapomorphy: the presence of a postepiphysial fontanelle, which is absent in all other Xenocypridinae.

Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers.

The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.

emGarra/em emorontesi/em, a new species from the Orontes River drainage (Teleostei: Cyprinidae).

Garra orontesi, new species, is described from the Orontes River drainage in the eastern Mediterranean Sea basin in Turkey and Syria. It is distinguished from its congeners in the Mediterranean Sea basin and adjacent Mesopotamia by possessing 17-21 gill rakers on the lower part of the first gill arch, the pelvic-fin origin usually below the second branched dorsal-fin ray, 8½ branched dorsal-fin rays, usually 2-3 scales between the tip of the pectoral and pelvic-fin origins, and no tubercles behind the upper posterior eye margin. It is also distinguished by a minimum K2P distance of 2.7% in its COI barcode region against G. rufa, and 3.9% against the geographically adjacent G. turcica.

Genomic Signature of Shifts in Selection and Alkaline Adaptation in Highland Fish.

Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed primarily related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species, and four alkaline intolerant species. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of shared genes associated with ion transport, apoptosis, immune response, and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.

Cryptic diversity within endemic Italian barbels: revalidation and description of new Barbus species (Teleostei: Cyprinidae).

Two fluviolacustrine lineages (SI1 Barbus and SI2 Barbus) of the Barbus genus have been recently detected in the Apulia-Campania ichthyogeographic district (southern Italy). The aim of this study was to determine the taxonomic status of these lineages by comparing them with the two already-established Italian fluviolacustrine species Barbus plebejus and Barbus tyberinus through a more in-depth molecular and morphological investigation. Genetic analyses were performed on both mitochondrial (cytochrome b) and nuclear (growth hormone paralog 2) DNA markers, and morphological analyses were carried out on specific age classes and purebred populations. Molecular analyses detected four evolutionary lineages at the mitochondrial level, whereas the nuclear data set highlighted the strict evolutionary relation between B. plebejus sensu stricto and the new lineages, converged in the B. plebejus complex clade. The morphological analyses allowed us to discriminate SI1 Barbus and SI2 Barbus from both B. plebejus and B. tyberinus. The new taxa could be discriminated by the greatest maximum body height and the longest pre-orbital distance, respectively. Both the new lineages have longer ventral and pectoral fins than B. plebejus and B. tyberinus, a larger caudal fin than B. tyberinus and a lower number of scales along the lateral line than B. plebejus. Both molecular and morphological results suggested the two southern Italian lineages could be considered as distinct endemic species: the formal description of the new species Barbus samniticus sp. nov. (i.e., SI1 Barbus) and the revalidation of Barbus fucini Costa, 1853 (i.e., SI2 Barbus) were thus proposed, and, for both species, molecular and morphological diagnosis were provided.

The evolutionary analysis of complement component C5 and the gene co-expression network and putative interaction between C5a and C5a anaphylatoxin receptor (C5AR/CD88) in human and two Cyprinid fish.

The complement system is a complex network of soluble and membrane-associated serum proteins that regulate immune response. Activation of the complement C5 generates C5a and C5b which generate chemoattractive effect on myeloid cells and initiate the membrane attack complex (MAC) assembly. However, the study of evolutionary process and systematic function of C5 are still limited. In this study, we performed an evolutionary analysis of C5. Phylogeny analysis indicated that C5 sequences underwent complete divergence in fish and non-fish vertebrate. It was found that codon usage bias improved and provided evolution evidence of C5 in species. Notably, the codon usage bias of grass carp was evolutionarily closer to the zebrafish genome compared with humans and stickleback. This suggested that the zebrafish cell line may provide an alternative environment for heterologous protein expression of grass carp. Sequence comparison showed a higher similarity between human and mouse, grass carp, and zebrafish. Moreover, selective pressure analysis revealed that the C5 genes in fish and non-fish vertebrates exhibited different evolutionary patterns. To study the function of C5, gene co-expression networks of human and zebrafish were built which revealed the complexity of C5 function networks in different species. The protein structure simulation of C5 indicated that grass carp and zebrafish are more similar than to human, however, differences between species in C5a proteins are extremely smaller. Spatial conformations of C5a-C5AR (CD88) protein complex were constructed, which showed that possible interaction may exist between C5a and CD88 proteins. Furthermore, the protein docking sites/residues were measured and calculated according to the minimum distance for all atoms from C5a and CD88 proteins. In summary, this study provides insights into the evolutionary history, function and potential regulatory mechanism of C5 in fish immune responses.

Phylogenetic analysis and expression differences of eye-related genes in cavefish genus Sinocyclocheilus.

The adaptive evolution of visual systems has been observed in many cavefish. However, little is known about the molecular mechanisms underlying these adaptations, which include regressive changes such as eye degeneration. Here, we analyzed phylogenetic and expression patterns of 6 eye-related genes (crx, foxg1b, opn1sw2, otx2, rho and sox2) in 12 Sinocyclocheilus species from China, including 8 stygobionts and 4 stygophiles, and examined photoreceptor cell morphology of these species. Those eye-degenerated species of Sinocyclocheilus were polyphyletic and showed different degrees of photoreceptor defects in responses to cave environments. The eye loss and degeneration are the result of convergent evolution. Although S. anophthalmus grouped with the eye-normal species, it displayed not only a high degree of eye degeneration but also significant expression differences in eye-related genes compared with the eye-normal species. The gene foxg1b, which was determined to be under positive selection, might play an important role in the process of eye degeneration in S. anophthalmus based on differential expression. Eye-related gene expression and selection may have contributed to the polyphyly of the cave species. We examined gene expression and duplication in 6 eye-related genes and revealed that these genes displayed considerable diversity in relative expression in Sinocyclocheilus fishes. Otx2 and sox2 were significantly up-regulated in individual cave species, while the other 4 genes (crx, foxg1b, opn1sw2 and rho) were significantly down-regulated. These findings provide a valuable resource for elucidating molecular mechanisms associated with visual system evolution in cavefish.

Ecomorphological diversification of some barbs and carps (Cyprininae, Cyprinidae) in the Lower Mekong Basin of Thailand.

Morphological variation is fundamentally related to various aspects of fish ecology, including foraging, locomotion, and habitat utilisation. Twenty-six species of closely related cyprinid fish (n = 502) were analysed for patterns of morphological variations by using geometric morphometric methods. Ecological data of feeding and habitat preferences were determined by the observations in fields and laboratory together with the gathering of bibliographic information. The findings of major variation displayed in all parts of the fish body and correlated with ecological parameters. Variations of head shape especially form and position of mouthpart involved with feeding behaviours, whereas the variations of body depth and length which affected swimming patterns reflected responsiveness of water currents and habitat uses. Adaptation of head shape and body elongation was remarkably related to the feeding regime, swimming manoeuvrability and habitat utilisation of the species. Some convergent variation was observed between the tribes Smiliogastrini and Poropuntiini. Therefore, we propose that the morphological diversity of cyprinine fish is mainly affected by ecological gradients, while phylogenetic effects on morphology are minor.

Cryptic species in White Cloud Mountain minnow, Tanichthys albonubes: Taxonomic and conservation implications.

Cryptic species describe two or more species that had mistakenly been considered to be a single species, a phenomenon that has been found throughout the tree of life. Recognizing cryptic species is key to estimating the real biodiversity of the world and understanding evolutionary processes. Molecular methods present an unprecedented opportunity for biologists to question whether morphologically similar populations are actually cryptic species. The minnow Tanichthys albonubes is a critically endangered freshwater fish and was classified as a second-class state-protected animal in China. Previous studies have revealed highly divergent lineages with similar morphological characters in this species. Herein, we tested for cryptic species across the ranges of all known wild populations of this minnow. Using multilocus molecular (one mitochondrial gene, two nuclear genes and 13 microsatellite loci) and morphological data for 230 individuals from eight populations, we found deep genetic divergence among these populations with subtle morphological disparity. Morphological examination found variance among these populations in the number of branched anal-fin rays. Based on genetic data, we inferred eight monophyletic groups that were well supported by haplotype network and population clustering analyses. Species delimitation methods suggested eight putative species in the T. albonubes complex. Molecular dating suggested that these cryptic species diverged in the period from the Pliocene to the Pleistocene. Based on these findings, we propose the existence of seven cryptic species in the T. albonubes complex. Our results highlight the need for a taxonomic revision of Tanichthys. What is more, the conservation status of and conservation strategies for the T. albonubes complex should be reassessed as soon as possible.

Genetic diversity and structure of the Chinese lake gudgeon (Sarcocheilichthys sinensis).

Mitochondrial DNA cytochrome b and d-loop sequences (2,137 bp) in 65 specimens of Sarcocheilichthys sinensis from five populations were identified as two lineages (I and II). The pairwise genetic distance between lineages I and II was 1.94%. SAMOVA analyses suggested that the best grouping occurred at three groups, Yangtze, Qiantang and Minjiang Rivers. High haplotype diversity (0.949) and low nucleotide diversity (θπ = 1.067%) were detected. The results of the neutrality tests, mismatch distribution and approximate Bayesian computation (ABC) did not support demographic expansions. The results of phylogenetic analysis, statistical dispersal-vicariance analysis (S-DIVA), ABC, MIGRATE-N and the time to the most recent common ancestor (TMRCA) indicated two colonization routes. First, before the Wuyi Mountains lifted, S. sinensis dispersed from the Yangtze River to the Minjiang River. Second, during glaciation, the continental shelf was exposed, which contributed to the dispersion of populations from the Yangtze River.

Molecular systematics and phylogeography of the genus Alburnus Rafinesque, 1820 (Teleostei, Leuciscidae) in Turkey.

In this study, the phylogeny of Alburnus genus distributed in Turkish freshwaters was performed by analyzing mitochondrial cyt b gene (1141 bp) and COI gene (1551 bp) sequences from 1172 samples representing 112 populations of 24 species through their geographical distribution. According to our findings, 20 valid species are distributed in Turkey of which 18 have already been known. While six Alburnus species (A. battalgilae, A. istanbulensis, A. carinatus, A. schischkovi, A. nasreddini ve A. adanensis) have been synonomized, two new species (Alburnus sp.1 and Alburnus sp.2) from Dicle River and Çapraz Stream/Susurluk River have been identified. Extinct species such as A. akili and A. nicaeensis have not been observed in situ. Phylogenetic tree topologies and haplotype network of the 119 cyt b and 80 COI haplotypes detected in Alburnus species have indicated a consensus tree topology containing twenty lineages, each of corresponding to one species, and three Alburnus haplogroups corresponding to the geographical origins: Eastern Anatolia (I), Mediterranean (2) and Western & Northern Anatolia (3). The results indicate that the divergence between those haplogroups may have occurred during the Middle Miocene-Middle Pleistocene periods (from 14.9 to 5.29 million years).

Comparative phylogenetic analysis of Schizothorax plagiostomus and Schizothorax esocinus with other members of subfamilies of cyprinidae on the basis of complete mitochondrial genome and 12S, 16S ribosomal RNA from Northren areas of Pakistan.

We assessed the relationship of Schizothoracinae species with other subfamilies Alburninae, Xenocyprinae, Cultrinae and Squaliobarbinae of family Cyprinidae by creating the phylogenetic trees using complete mitogenome and 12S and 16S RNA. Our representative species show the great affiliation with other but separated from a group composed of Metzia mesembrinum, Metzia longinasus, Metzia lineata and Metzia formosae of subfamily Alburninae while other subfamilies formed distinct group. The members of subfamily Schizothoracinae shows separate line of evolution from subfamily Barbinae.