Yu. Ph. Kartavtsev

Analysis of Nucleotide Diversity at the Cytochrome b and Cytochrome Oxidase 1 Genes at the Population, Species, and Genus Levels

Algorithms of nucleotide diversity measures and other measures of genetic divergence at the molecular level are analyzed. Based on a database of p-distances, we have compared genetic divergence of populations (1) and taxa of different rank, such as sibling species (2), species within a genus (3), and species from different genera within a family (4). Based on the theory and algorithms of distance calculation from the primary DNA sequences, as well as the actual distances estimated from literature, it is recommended to use in analysis of experimental data a specific model selected from the eight available ones. The empirical data for more than 24 000 vertebrate and invertebrate species demonstrate that the data series are realistic and interpretable when p-distance or its various estimates are used. This testifies to the applicability of p-distance for most interspecies and intraspecies comparisons of genetic divergence up to the family level by two genes compared. Data on p-distances revealed various and increasing levels of genetic divergence of the sequences of genes Cyt-b and Co-1 in four groups compared. Mean unweighted scores of distances for the four groups were as follows: Cyt-b (1) 1.55 ± 0.56, (2) 5.52 ± 1.34, (3) 10.69 ± 1.34, (4) 18.51 ± 2.09 and Co-1 (1) 0.55 ± 0.19, (2) 4.91 ± 0.83, (3) 9.66 ± 0.72, (4) 14.69 ± 1.02. Differences in divergence between the genes themselves at the four levels were also found, although the total mean distances for the two genes did not show statistically significant differences. This conforms to the ample evidence showing different and nonuniform evolution rates of these and other genes and their various regions. The results of the analysis of the nucleotide and allozyme divergence within species and higher taxa of animals, first, are in a good agreement with these results, including data on protein gene markers, and, second, this evidence suggests that in animals, phyletic evolution is likely to prevail at the molecular level, and speciation mainly corresponds to the type D1 (geographic model). The prevalence of the D1 speciation mode does not mean that the other modes are absent. There are at least seven various modes of speciation. Recognition of speciation modes is a task that seems to require construction of a quantitative genetic model (theory) of speciation. Although, in view of a vast diversity of the possible causes of reproductive isolating barriers (RIBs) and speciation initiation, as well as the “empirical nature” of the formalized approach, proposed in the present work, some newly arising questions may be left without an answer. Their solution probably lied in increasing the number of descriptors and members of equations, proposed in this study, on the basis of DNA markers and other genomic characteristics.

The taxonomic composition and distribution of sand lances from the genus Ammodytes (Perciformes: Ammodytidae) in the North Pacific

An analysis of the variability of 34 sequences of the 5′-region of the Co-1 mitochondrial gene fish of the genus Ammodytes has been performed taking the precise geographic location into account. Among them, seven sequences are original data and 27 were retrieved from the GenBank. Two hypotheses on the taxonomic composition of sand lances of North Pacific have been proposed. The first is preferable to the authors; it assumes that there are four separate species, while the second considers the presence of a complex circumpolar species with four major local geographic races. Both hypotheses suppose a clear delineation and deep divergence of cold-water sand lances from warmer-water southern ones. These data and the analysis of the history of the study of the taxonomy of far-eastern sand lances allowed us to consider that the use of the species name A. personatus is inappropriate for sand lances from the Yellow Sea and the southern part of the Sea of Japan, as well as for some representatives of the Bering sea and the Sea of Okhotsk and adjacent waters, which form a separate monophyletic group with the current name Ammodytes hexapterus.

Phylogenetic analysis of Altai osmans of the genus Oreoleuciscus (Pisces, Cyprinidae, Leuciscinae), based on the analysis of the cytochrome oxidase 1 gene (Co-1) sequence

Molecular genetic analysis of Altai osmans of the genus Oreoleuciscus from two different parts of the range was carried out. In this study, based on the mitochondrial Co-1 gene sequence, a total of 25 fish specimens belonging to four genera were examined: (1) O. humilis, 2 specimens; O. potanini, 13 specimens; (2) Pseudaspius leptocephalus, 1 specimen; (3) Tribolodon brandtii, T. hakonensis, and T. sachalinensis from the GanBank database, 9 speciens; and (4) Leuciscus waleckii, 1 specimen (used as an outgroup). The p-distances were very low both within and between the species: (1) 0.20 ± 0.03%; (2) 0.40 ± 0.12%; and (1–2) 0.80 ± 0.04%. To visualize the relationships among all of the species examined, the neighbor joining (NJ), maximum parsimony (MP), Bayesian (BA), and maximum likelihood (ML) trees were constructed. The results obtained using these methods were very similar. It was demonstrated that species assignment of the individuals (barcoding) with the help Co-1 gene was effective, despite of very low divergence of the two osman taxa, which was comparable with typical intraspecific values in other animal groups. Taxonomic status of O. potanini and O. humilis requires further investigation with paying attention to low genetic distances between these species along with the lack of material from sympatric parts of the ranges.

Phylogenetic and taxonomic analysis of flatfish species (Teleostei, Pleuronectiformes) inferred from the primary nucleotide sequence of cytochrome oxidase 1 gene (Co-1)

Seventeen nucleotide sequences of Co-1 gene from 13 Pleuronectiformes species and 2 Perciformes species served as the outgroup were examined. For divergence comparison, the initial stage involved calculation of pairwise p-distances for all investigated sequences. This allowed to evaluate the nucleotide diversity on four phylogenetically different levels: (1) intraspecific, (2) intrageneric, (3) intrafamilial, and (4) intraordinal. The values of p-distances for the Co-1 gene for the four mentioned categories were (1) 0.93 ± 0.73%, (2) 11.72 ± 1.86%, (3) 12.10 ± 1.10%, and (4) 20.20 ± 0.22%, respectively. An increase in the level of genetic divergence along with an enhancement in taxon rank was previously reported for different species, which might be explained by prevalence of geographic speciation model in nature. Phylogenetic trees were constructed using four approaches: maximum parsimony, Bayesian, maximum likelihood, and neighbor-joining. These trees demonstrated similar results confirming the monophyletic origin of the families studied. The examined representatives of the flatfish species and genera were shown to be sufficiently divergent genetically.

Phylogenetic inferences introduced on cytochrome b gene sequences data for six flatfish species (Teleostei, Pleuronectidae) and species synonymy between representatives of genera Pseudopleuronectes and Hippoglossoides from Far Eastern seas.

Cytochrome b (Cyt-b) gene was sequenced for six flatfish species and compared with seven other species belonging to Pleuronectiformes. Monophyly of the family Pleuronectidae representatives was fine supported by bootstrap or other means in several sequence-based trees on Cyt-b gene data. Results revealed that synonymy must be accepted for Hippoglossoides elassodon, and H. robustus, as well as for Pseudopleuronectes yokohamae, and P. schrenki.

Molecular phylogenetic study of several eelpout fishes (Perciformes, Zoarcoidei) from Far Eastern seas on the basis of the nucleotide sequences of the mitochondrial cytochrome oxidase 1 gene (Co-1)

A total of 95 nucleotide sequences of a Co-1 gene fragment of approximately 650 bp were analyzed for fishes of the orders Perciformes and Scorpaeniformes (outgroup). Gene trees based on four algorithms (BA, NJ, MP, and ML) were similar in topology of solved branches. An emphasis was placed on the species and generic levels, but a significant phylogenetic signal was obtained for higher taxonomic ranks as well. For instance, a monophyletic origin was confirmed for the family Zoarcidae and the subfamily Opisthocentrinae (Stichaeidae). The proportion of different nucleotides in the sequences compared (p-distances) significantly increased with increasing taxonomic rank. The p-distances were estimated for four hierarchic levels and were (1) 0.15 ± 0.06% for the within-species hierarchic level, (2) 6.33 ± 0.37% for the within-genus level, (3) 11.83 ± 0.06% for the within-family level, and (4) 15.22 ± 0.05% for the within-order level. The difference in the Co-1 gene fragments between levels (1) and (2) allows almost errorless species identification on the basis of this kind of a molecular bar code.

Janolus fuscus O’Donoghue, 1924 (Gastropoda: Proctonotidae), a species of a nudibranch family that is new to the marine fauna of Russia

The seaslug Janolus fuscus of the family Proctonotidae, which is new to the Russian fauna, was found in the Sea of Japan for the first time. A small population of this mollusk was found at the northwestern coast on a bank occupying approximately 3000 m2 of the sea bottom south of Rudnaya Bay. Data on the distribution, ecology, radula morphology, and feeding of this mollusk on the bryozoan Microporina articulata are presented. The differences between J. fuscus and similar species of the genus Janolus are discussed. The partial sequences (614 bp) of the mitochondrial COI gene differed in two nucleotide substitutions, suggesting that the population that is found in the Sea of Japan is conspecific to the North American J. fuscus.

Genetic Divergence of Mussels (Mollusca, Mytilidae) Based on the 28S rRNA, 18S rRNA, and H3 Nuclear Gene Sequences

On the basis of nucleotide sequences of three nuclear genes and using molecular phylogenetic and evolutionary genetic approaches, the phylogeny of the main representatives of one of the largest taxa of bivalve mollusks, the family Mytilidae, was studied, and its system and taxonomy were refined. A phylogenetic system for the family Mytilidae and closely relative taxa of the order Mytilida, which currently has no consensus among specialists on the basis of traditional characters, is presented. Using nucleotide sequences of the 28S rRNA, 18S pRNA, and histone H3 genes, this consensus was established by the study of Mytilidae. Some concerns of mussel systematics were resolved; in particular, the monophyly of the family Mytilidae Rafinesque, 1815 was established with the strongest support for the subfamily Mytilinae Rafinesque, 1815. The data obtained disprove Distel’s conclusion on polyphyly of the subfamily Mytilinae Rafinesque, 1815. Isolation of the taxa in the rank of the Modiolinae G. Termier & H. Termier, 1950 and Bathymodiolinae Kenk & Wilson, 1985 subfamilies in the family Mytilidae and also the family Septiferidae Scarlato et Starobogatov, 1979 was confirmed, although the rank of the later taxon is not universally recognized and it remains to be clarified in an additional study.

Morphometric Differences between Two Smelt Species, Hypomesus japonicus (Brevoort, 1856) and H. nipponensis (McAllister, 1963) (Pisces: Osmeridae) from The Northwestern Part of the Sea of Japan

Two smelt species that inhabit the northwest of the Sea of Japan, Hypomesus japonicus and H. nipponensis (family Osmeridae), which are both currently referred to as Japanese smelt, have been studied in order to clarify the taxonomic value of morphometric characters. Variations between individuals of these species have been revealed using a multivariate analysis of their morphometric characters and indices. The results of the analysis show that H. japonicus is distinguished from H. nipponensis both by the previously known characters (the eye diameter is smaller and the vertical through the beginning of the dorsal fin is closer to the head than that through the beginning of the pelvic fins) and by a greater height of the dorsal and adipose fins in the former species as defined in the paper. Within the species H. japonicus, the individuals sampled from Olga Bay are most similar morphologically to those from the coastal waters off the village of Terney. In contrast, the individuals of this species from the coastal waters off Russky Island and from Olga Bay manifest the greatest differences.

[Relationship between heterozygosity and quantitative traits: intralocus interactions and multiple-locus averaging].

The dependence of the expression of genotypic values (Y) on gene dosage (X) have been analyzed for four types of intralocus interactions (additivity, dominance, overdominance, and neutrality) using a linear model. Artificial numerical examples have been used to demonstrate that X and Y are positively associated with each other in the cases of additivity, dominance, and overdominance and are not associated in the case of neutrality. The averaging of single-locus genotypic values to obtain multiple-locus genotypes yields different results for different types of intralocus interactions. Genotypic values and individual heterozygosity are positively correlated with each other in the cases of dominance and overdominance and are negatively correlated in the case of additivity. In the case of neutrality, there is still no correlation after averaging. The results obtained and their interpretation suggest a new view on the experimental studies and generalizations on the relationship between heterozygosity and quantitative traits.