Phylogenetic and Taxonomic Relationships of Northern Far Eastern Phoxinin Minnows, Phoxinus and Rhynchocypris (Pisces, Cyprinidae), as Inferred from Allozyme and Mitochondrial 16S rRNA Sequence Analyses

Analyses of allozyme (18 loci) and partial mitochondrial DNA (mtDNA) sequences (1295 bp, 16S rRNA) support the classification of phoxinin minnows from the northern Far East into 2 genera of 8 species: Phoxinus phoxinus, Rhynchocypris oxycephalus, R. perenurus, R. czekanowskii, R. kumgangensis, R. semotilus, R. lagowskii and R. sp. (bergi ?). Although R. lagowskii from Japan and the Amur basin and R. sp. from Vladivostok region to Korea have been classified into a single species by many authors as R. lagowskii, they form separate clusters in both analyses, suggesting different specific status. Some R. oxycephalus and R. perenurus had the mtDNA haplotypes of R. lagowskii and R. czekanowskii, respectively, which probably indicates that local introgression of mtDNA occurred through inter-specific hybridization. Rhynchocypris forms a monophyletic cluster with dace genera Tribolodon and Pseudaspius, not with Phoxinus. Eurasian and American Phoxinus are suggested to be paraphyletic

Data from: Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data

Phylogenetic relationships among 41 species of salmonid fish and some aspects of their diversification-time history were studied using the GenBank and original mtDNA data. The position of the root of the Salmonidae phylogenetic tree was uncertain. Among the possible variants, the most reasonable seems to be that in which thymallins are grouped into the same clade as coregonins and the lineage of salmonins occupied a basal position relative to this clade. The genera of Salmoninae formed two distinct clades, i.e., (Brachymystax, Hucho) and (Salmo, Parahucho, (Salvelinus, (Parasalmo, Oncorhynchus)). Furthermore, the genera Parasalmo and Oncorhynchus were reciprocally monophyletic. The congruence of Salmonidae phylogenetic trees obtained using different types of phylogenetic markers is discussed. According to Bayesian dating, ancestral lineages of salmonids and their sister esocoids diverged about 106 million years ago. Sometime after, probably 100–70 million years ago, the salmonid-specific whole genome duplication took place. The divergence of salmonid lineages on the genus level occurred much later, within the time interval of 42–20 million years ago. The main wave of the diversification of salmonids at the species level occurred during the last 12 million years. The possible effect of genome duplication on the Salmonidae diversification pattern is discussed

Data from: Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of nuclear RAG1 gene

The phylogenetic relationships among 26 species of salmonid fishes (family Salmonidae) were studied using the RAG1 gene as phylogenetic marker. No unambiguous relationships between thymallins, coregonins, and salmonins it was possible to establish. It seems likely, that divergence of these lineages took place during rather short time interval (about 3 to 4 million years). The thymallins are thought to be the first radiated lineage. The genera of the subfamily Salmoninae form two distinct monophyletic groups, represented by (1) Brachymystax and Hucho and (2) Salmo, Parahucho, Salvelinus, Parasalmo and Oncorhynchus. Ancestral forms of these two evolutionary lineages could diverge at the Oligocene-Miocene boundary (about 24 million years ago). It is suggested that diversification of the main lineages within the second group was rather rapid, and took place in middle Miocene (about 19-16 million years ago). Moreover, the lineages of Salvelinus, Parasalmo and Oncorhynchus were the latest to diverge. It seems likely that divergence of the Prosopium and Corergonus ancestral lineages occurred during the same time interval

Data from: Complete mitochondrial genome of the poorly known Amur sculpin Mesocottus haitej (Cottoidei: Cottidae)

The complete mitochondrial genome sequence of Mesocottus haitej has been obtained by the next generation sequencing, which contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and non-coding control region with the total length of 16,527 bp. The gene content, arrangement, codon usage and base composition of M. haitej mitogenome have no unusual features that distinguish it from most other teleost fishes. According to the result of a pilot phylogenetic analysis, the freshwater Mesocottus is a sister lineage to the Cottus clade. The new mitogenomic data could provide useful information for the further studies on molecular systematics and conservation genetics of cottids

salmonids.mtDNA.timetree

Bayesian chronogram (NEXUS tree format) of salmonid cladogenesi

salmonids.RAG1.timetree

Bayesian chronogram (NEXUS tree format) of salmonid cladogenesi

mesocottusDATAMATRIXandTREES.x

Data matrix (NEXUS format) used to estimate the phylogenetic position of Mesocottus. The matrix contains alignment of six complete (Clinocottus analis, Trachidermus fasciatus, Mesocottus haitej, Cottus reinii, C. koreanus and C. hangiongensis) and two partly sequenced (Rheopresbe kazika and Leptocottus armatus) mitogenomes of the Cottidae, as well as the mitogenomes of outgroup taxa – Lycodes toyamensis (Zoarcidae), Anoplopoma fimbria (Anaplopomatidae), Arctoscopus japonicus (Trichodontidae) and Aptocyclus ventricosus (Cyclopteridae). In addition, it contains the final phylogenetic trees

Phylogenetic and Taxonomic Relationships of Northern Far Eastern Phoxinin Minnows, Phoxinus and Rhynchocypris (Pisces, Cyprinidae), as Inferred from Allozyme and Mitochondrial 16S rRNA Sequence Analyses

Analyses of allozyme (18 loci) and partial mitochondrial DNA (mtDNA) sequences (1295 bp, 16S rRNA) support the classification of phoxinin minnows from the northern Far East into 2 genera of 8 species: Phoxinus phoxinus, Rhynchocypris oxycephalus, R. perenurus, R. czekanowskii, R. kumgangensis, R. semotilus, R. lagowskii and R. sp. (bergi ?). Although R. lagowskii from Japan and the Amur basin and R. sp. from Vladivostok region to Korea have been classified into a single species by many authors as R. lagowskii, they form separate clusters in both analyses, suggesting different specific status. Some R. oxycephalus and R. perenurus had the mtDNA haplotypes of R. lagowskii and R. czekanowskii, respectively, which probably indicates that local introgression of mtDNA occurred through inter-specific hybridization. Rhynchocypris forms a monophyletic cluster with dace genera Tribolodon and Pseudaspius, not with Phoxinus. Eurasian and American Phoxinus are suggested to be paraphyletic