Relationships of osmerid fishes (Osmeridae) of Russia: divergence of nucleotide sequences of mitochondrial and nuclear genes

Photoreceptors, visual pigments and intraretinal variability in spectral sensitivity in two species of smelts (Pisces, Osmeridae)

The main goal of this study was to clarify whether the spectral properties of retinal photoreceptors reflect the features of behaviour of closely related fish species cohabiting shallow marine and fresh waters. The spectral sensitivity of photoreceptors was compared between two smelt species, Hypomesus japonicus and Japanese smelt Hypomesus nipponensis. The spectral absorption of the visual pigments was measured using microspectrophotometry. In H. japonicus, a mostly marine species, all photoreceptors contained visual pigments based on retinal and were distributed differently in specific retinal areas. The absorbance maxima (λ_max ) of rods and long-wave-sensitive members of double cones throughout the retina amounted to 507 and 573 nm, respectively, but the λ_max value of the short-wave-sensitive members of double cones and single cones in the temporal hemiretina showed a significant blue shift compared to the nasal hemiretina: 485 vs. 516 nm and 375 vs. 412 nm, respectively, thus enhancing the short-wave sensitivity of the temporal hemiretina. In H. nipponensis, an euryhaline species, the estimated λ_max value of both rods and cones significantly varied between the groups caught in different localities (sea, river or estuary) because of the presence of rhodopsin/porphyropsin mixtures. The long-wavelength shift in rod and cone photoreceptors was observed because of changes in the chromophore complement in closely related but ecologically different species dwelling in freshened bodies of water. Considering the data available in the literature, several putative common opsin genes have been suggested for species under study.

Analysis of the relationship between geography and body color with the genetic diversity in the Echiura worm Urechis unicinctus based on the mitochondrial COI and D-loop sequences

Urechis unicinctus is the only Echiurini species distributed in Bohai Gulf of China. The wild populations of this species have sharply declined in China due to overfishing. Over 150 samples from Bohai Gulf were collected in the present study, which were classified into five populations according to their geographic areas and body colors. The genetic diversity and population structure of these populations were investigated by mitochondiral COI and D-loop sequences. The haplotype diversity of U. unicinctus based on COI and D-loop sequences were still high. In addition, the evolution rate of D-loop region could faster than the COI gene of U. unicinctus. Meanwhile, over 99% genetic diversity was contributed by different individuals within populations. Moreover, phylogenetic trees did not show clear geographic or color cluster. Our findings indicated that this species in Bohai Gulf of China should be treated as a whole population.

Cycles of trans-Arctic dispersal and vicariance, and diversification of the amphi-boreal marine fauna

The amphi-boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans-Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent inter-oceanic vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further trans-Arctic dispersal have risen at times, however, and molecular data now expose more complex patterns of inter-oceanic affinities and dispersal histories. For a general view on the trans-Arctic dynamics and of the roles of potential dispersal-vicariance cycles in generating systematic diversity, we produced new phylogeographic data sets for amphi-boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 inter-oceanic comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond to a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene-Pleistocene-Holocene time frame. Repeated inter-oceanic exchange was inferred for 23 taxa, and the latest connection was usually post-glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late- or post-glacial exchange was inferred in 46% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the North Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter-oceanic vicariance scenario underlying amphi-boreal speciation, the data expose complex patterns of reinvasion and reticulation that complicate the interpretation of taxon boundaries in the region.

Complete mitochondrial genome of the surf smelt Hypomesus japonicus (Osmeriformes, Osmeridae)

The complete mitochondrial genome was sequenced in two individuals of the surf smelt Hypomesus japonicus. The genome sequences are 16,762 and 16,771 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mitochondrial genomes published previously. The difference between two H. japonicus genomes studied is 0.37%, which is noticeably higher in comparison with other osmerid fishes. The level of sequence divergence between H. japonicus and related osmerids belonging to genera Hypomeus, Osmerus, and Mallotus varies within a very narrow range (12.31-13.72%) indicating poor phylogenetic resolution of this complex fish group.

Complete mitochondrial genome of the Arctic rainbow smelt Osmerus dentex (Osmeriformes, Osmeridae)

The complete mitochondrial genome was sequenced in two individuals of the Arctic rainbow smelt Osmerus dentex. The genome sequences are 16,615 and 16,616 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mitochondrial genomes published previously. The difference between the two O. dentex genomes studied is 0.25%, that is, 5.0 times higher in comparison with close species, the European smelt O. eperlanus studied previously. The level of mitochondrial genome divergence between O. dentex and close osmerid fishes, O. eperlanus, and O. mordax is high enough (6.86-7.54%) to consider all of them as separate biological species.

Complete mitochondrial genome of the European smelt Osmerus eperlanus (Osmeriformes, Osmeridae)

The complete mitochondrial (mt) genome was sequenced in two individuals of the European smelt Osmerus eperlanus. The genome sequences are 16,608 and 16,609 bp in size, and the gene arrangement, composition, and size are very similar to the other smelt mt genomes previously published. The difference between the two genomes studied is low, 0.05%. The difference is significantly higher (6.95%) between the O. eperlanus genomes studied here and the genome of the congeneric species, O. mordax (HM106493.1) available in GenBank. The distribution of divergence is non-uniform along the genomes. There is a continuous segment (≈2.5 kb) encompassing tRNA-Phe, complete 12S rRNA gene, tRNA-Val, and partial 16S rRNA gene, which demonstrates significantly lower levels of divergence than on average for the whole genome. The 12S rRNA and 16S rRNA genes are frequently used for phylogenetic and molecular taxonomy analyses and could underestimate the level of divergence between osmerid fishes.