Molecular phylogeny of the genus Capoeta (Teleostei: Cyprinidae) in Anatolia, Turkey

Capoeta ekmekciae Turan, Kottelat, Kirankaya & Engin, 2006, a junior synonym of Capoeta capoeta (Güldenstädt, 1773) (Teleostei: Cyprinidae)

Some recent works have proposed that Capoeta ekmekciae from the Çoruh River and C. capoeta from the Kura-Aras River system are synonyms based on molecular data, which prompted this study to compare their morphometric, meristic and molecular data to investigate this hypothesis. Based on the results, the C. ekmekciae form displays morphometric and meristic traits quite similar to the C. capoeta form. Since there are no diagnostic traits to distinguish these two allopatric species from each other and they share identical cytb gene, we treat C. ekmekciae as a junior synonym of C. capoeta.

Paracapoeta, a new genus of the Cyprinidae from Mesopotamia, Cilicia and Levant (Teleostei, Cypriniformes)

The molecular and morphological studies carried out within the scope of this study revealed that the scrapers, known as the Mesopotamian group, belong to a different genus. The Paracapoetagen. nov., from the Mesopotomia and Levant, is distinguished from Capoeta and Luciobarbus species by the presence of a strong ligament between the base of the last simple and the first branched rays of the dorsal-fin (vs. no or a very weak ligament). The Paracapoeta further differs from Capoeta by the last simple dorsal-fin ray strongly ossified in adult specimens (more than 75%, vs. less than 75%). The Paracapoeta further differs from Luciobarbus by the lower lip with horny layer (vs. fleshy lips). The molecular phylogeny based on the combined dataset (COI + Cytb, 1312 bp.) showed that the genus Paracapoeta was recovered from the other groups in the subfamily Barbinae with high bootstrap and posterior probability values (BP: 94%, PP: 0.96). Also, Paracapoeta and Capoeta are well differentiated by an average genetic distance of 8.02±0.78%. The morphological and molecular findings have largely overlapped each other. Besides, Capoeta turani is treated as a synonym of Capoeta erhani.

Pliocene-Pleistocene dispersal bring along low inter species diversity between Vimba species based on multilocus analysis

This study investigates phylogenetic and phylogeographic relationships of Vimba species using mitochondrial cytochrome b (cyt b) (1023 bp) and cytochrome c oxidase subunit I (COI) barcoding region (652 bp) genes. Ninety-one samples from 36 populations for the cyt b gene and 67 samples from 20 populations for the COI were analyzed. We identified 29 haplotypes and calculated overall haplotype diversity as Hd: 0.907 ± 0.015 for cyt b. We also identified 13 COI haplotypes and calculated overall haplotype diversity as 0.826 ± 0.026 for this marker. The phylogenetic analysis of Vimba species reveals the presence of four clades, based on concatenated cyt b and COI sequences. The first and second clade consist of Vimba vimba Western lineage, and Vimba vimba Caspian lineage, while the third and fourth clade consist of Vimba mirabilis and Vimba melanops. Based on haplotype network analyses and phylogeographic inferences, the Vimba genus is monophyletic, and its species dispersed in the Pleistocene era.

Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)

BACKGROUND

The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of the population genetic structure of this species is limited by the low number of molecular markers currently described.

METHODS AND RESULTS

In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16 (average = 7.89). The results showed that, the polymorphism information content (PIC) of these simple sequence repeat (SSR) loci varied from 0.254 to 0.888. The observed heterozygosity (H_O) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (H_E) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05).

CONCLUSIONS

These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate and other closely related species.

Distribution and diversity of fish from Seyhan, Ceyhan and Orontes river systems

In this study, the current ichthyofauna of the Seyhan, Ceyhan and Orontes River drainages were presented and actual taxonomic positions of the species were assessed. Sixty-seven species belonging to 32 genera and 17 families of fishes were reported from these river drainages in Turkey and Syria. Acanthobrama centisquama and Tinca tinca could not be observed in the study area and Alburnus sellal and Esox lucius are recorded for the first time respectively in the Lake Gölbaşı (connected to the Ceyhan River) and Seyhan 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).

Possible species-flock scenario for the evolution of the cyprinid genus Capoeta (Cypriniformes: Cyprinidae) within late Neogene lake systems of the Armenian Highland

We studied 4 Ma old isolated pharyngeal teeth from lake sediments of Çevirme (Tekman Palaeolake, Erzurum Province). Based on shape characters defined for 3D models of modern species, we found that the Pliocene lake constitutes sympatric occurrence of four Capoeta species (C. cf. umbla, C. cf. baliki, C. cf. sieboldi and C. sp. sevangi/capoeta), whose modern relatives belong to a monophyletic clade inhabiting today three different drainage systems of this region (Euphrates River, Kura River and Black Sea). We interpreted this high local diversity of closely related species in terms of the species-flock model. The Tekman palaeolake was a part of an unrecognized extended late Miocene to Pliocene palaeolake system in the present-day Armenian Highland, which has been disrupted by Pliocene tectonic activities. Surface uplift of the Armenian Highland contributed to the very characteristic biogeographic distribution and endemism of Capoeta in West Asian drainage systems. Thus, we proposed a species-flock scenario for the evolution and dispersal of the cyprinid genus Capoeta in a huge unrecognized palaeolake system in the present-day Armenian Highland.

Phylogenetic analysis of sooty grunter and other major freshwater fishes in the suborder Percoidei based on mitochondrial DNA

Perciformes is the largest order of fishes and vertebrates. Sooty grunter (Hephaestus fuliginosus) is an economic fish species in the Terapontidae family of Percoidei, a suborder within Perciformes. To conduct molecular-level analysis of the phylogenetic relationships between sooty grunter and major freshwater fishes in Percoidei, we analysed the entire sooty grunter mitochondrial genome sequence and obtained the mitochondrial genome information of 19 fishes from Terapontidae, Serranidae, and Centrarchidae families in Percoidei from GenBank. The complete length of the sooty grunter mitochondrial genome was 16,770 bp; it encoded 13 proteins, 2 rRNAs, 22 tRNAs, and a displacement loop (D-loop). Other than ND6 and eight tRNA genes that are encoded by the light strand, the majority of genes are encoded by the heavy strand. The sequence and distribution of sooty grunter mitochondrial-encoded genes and non-coding segment were similar to those of most vertebrates. The results of neighbour joining, maximum parsimony, and Bayesian inference analyses of the complete mitochondrial genome and six genes, including cytochrome oxidase I, cytochrome B, 12S rRNA, ND2, ND4, and ND5, were consistent. In the phylogenetic trees, fishes in Terapontidae and Centrarchidae formed monophyletic clades, whereas those in Serranidae were divided into two clades, each containing Lateolabrax and Siniperca species. Among the three freshwater fish species in Terapontidae, the freshwater Terapontidae were more closely related to jade perch than with silver perch, suggesting that freshwater Terapontidae fishes originate from marine fishes. In addition, the phylogenetic results indicated that Micropterus salmoides salmoides and Micropterus salmoides floridanus in Centrarchidae should be designated as two independent species, and Siniperca in Serranidae should be considered an independent family. The sooty grunter mitochondrial genome sequence obtained in this study could be used to conduct population genetic diversity and germplasm resource studies. Furthermore, the phylogenetic analysis results of freshwater fishes in Percoidei could provide a molecular basis for cross-breeding.