DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea).

BACKGROUND: The sperm gene bindin encodes a gamete recognition protein, which plays an important role in conspecific fertilization and reproductive isolation of sea urchins. Molecular evolution of the gene has been extensively investigated with the attention focused on the protein coding regions. Intron evolution has been investigated to a much lesser extent. We have studied nucleotide variability in the complete bindin locus, including two exons and one intron, in the sea urchin Strongylocentrotus intermedius represented by two morphological forms. We have also analyzed all available bindin sequences for two other sea urchin species, S. pallidus and S. droebachiensis. RESULTS: The results show that the bindin sequences from the two forms of S. intermedius are intermingled with no evidence of genetic divergence; however, the forms exhibit slightly different patterns in bindin variability. The level of the bindin nucleotide diversity is close for S. intermedius and S. droebachiensis, but noticeably higher for S. pallidus. The distribution of variability is non-uniform along the gene; however there are striking similarities among the species, indicating similar evolutionary trends in this gene engaged in reproductive function. The patterns of nucleotide variability and divergence are radically different in the bindin coding and intron regions. Positive selection is detected in the bindin coding region. The neutrality tests as well as the maximum likelihood approaches suggest the action of diversifying selection in the bindin intron. CONCLUSIONS: Significant deviation from neutrality has been detected in the bindin coding region and suggested in the intron, indicating the possible functional importance of the bindin intron variability. To clarify the question concerning possible involvement of diversifying selection in the bindin intron evolution more data combining population genetic and functional approaches are necessary.

DNA variation in the phenotypically-diverse brown alga Saccharina japonica.

BACKGROUND: Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica. RESULTS: The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events. CONCLUSION: Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.

Recombinant Mitochondrial Genomes Reveal Recent Interspecific Hybridization between Invasive Salangid Fishes.

The interspecific recombination of the mitochondrial (mt) genome, if not an experimental artifact, may result from interbreeding of species with broken reproductive barriers, which, in turn, is a frequent consequence of human activities including species translocations, habitat modifications, and climate change. This issue, however, has not been addressed for Protosalanx chinensis and other commercially important and, simultaneously, invasive salangid fishes that were the product of successful aquaculture in China. To assess the probability of interspecific hybridization, we analyzed the patterns of diversity and recombination in the complete mitochondrial (mt) genomes of these fishes using the GenBank resources. A sliding window analysis revealed a non-uniform distribution of the intraspecific differences in P. chinensis with four highly pronounced peaks of divergence centered at the COI, ND4L-ND4, and ND5 genes, and also at the control region. The corresponding divergent regions in P. chinensis show a high sequence similarity (99−100%) to the related salangid fishes, Neosalanx tangkahkeii and N. anderssoni. This observation suggests that the divergent regions of P. chinensis may represent a recombinant mitochondrial DNA (mtDNA) containing mt genome fragments belonging to different salangid species. Indeed, four, highly significant (pairwise homoplasy index test, P < 0.00001) signals of recombination have been revealed at coordinates closely corresponding to the divergent regions. The recombinant fragments are, however, not fixed, and different mt genomes of P. chinensis are mosaic, containing different numbers of recombinant events. These facts, along with the high similarity or full identity of the recombinant fragments between the donor and the recipient sequences, indicate a recent interspecific hybridization between P. chinensis and two Neosalanx species. Alternative hypotheses, including taxonomical misidentifications, sequence misalignments, DNA contamination, and/or artificial PCR recombinants, are not supported by the data. The recombinant fragments revealed in our study represent diagnostic genetic markers for the identification and distinguishing of hybrids, which can be used to control the invasive dynamics of hybrid salangid fishes.

Multiple bacterial partners in symbiosis with the nudibranch mollusk Rostanga alisae.

The discovery of symbiotic associations extends our understanding of the biological diversity in the aquatic environment and their impact on the host's ecology. Of particular interest are nudibranchs that unprotected by a shell and feed mainly on sponges. The symbiotic association of the nudibranch Rostanga alisae with bacteria was supported by ample evidence, including an analysis of cloned bacterial 16S rRNA genes and a fluorescent in situ hybridization analysis, and microscopic observations. A total of 74 clones belonging to the phyla α-, ß-, γ-Proteobacteria, Actinobacteria, and Cyanobacteria were identified. FISH confirmed that bacteriocytes were packed with Bradyrhizobium, Maritalea, Labrenzia, Bulkholderia, Achromobacter, and Stenotrophomonas mainly in the foot and notum epidermis, and also an abundance of Synechococcus cyanobacteria in the intestinal epithelium. An ultrastructural analysis showed several bacterial morphotypes of bacteria in epidermal cells, intestine epithelium, and in mucus layer covering the mollusk body. The high proportion of typical bacterial fatty acids in R. alisae indicated that symbiotic bacteria make a substantial contribution to its nutrition. Thus, the nudibranch harbors a high diversity of specific endo- and extracellular bacteria, which previously unknown as symbionts of marine invertebrates that provide the mollusk with essential nutrients. They can provide chemical defense against predators.

DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius.

Strongylocentrotus intermedius (A. Agassiz, 1863) is an economically important sea urchin inhabiting the northwest Pacific region of Asia. The northern Primorye (Sea of Japan) populations of S. intermedius consist of two sympatric morphological forms, "usual" (U) and "gray" (G). The two forms are significantly different in morphology and preferred bathymetric distribution, the G form prevailing in deeper-water settlements. We have analyzed the genetic composition of the S. intermedius forms using the nucleotide sequences of the mitochondrial gene encoding the cytochrome c oxidase subunit I and the nuclear gene encoding bindin to evaluate the possibility of cryptic species within S. intermedius. We have examined the presence of symbiont microorganisms by means of 16S rRNA sequences. The nucleotide sequence divergence between the morphological forms is low: 0.74% and 0.70% for cytochrome c oxidase subunit I and nuclear gene encoding bindin, respectively, which is significantly below average intrageneric sequence divergence among Strongylocentrotus species. We thus have found no genetic evidence of cryptic species within S. intermedius. Phylogenetic analysis shows that the bacteria symbionts of S. intermedius belong to the phylum Bacteroidetes, but the U and G forms predominantly harbor highly divergent bacterial lineages belonging to two different taxonomic classes, Flavobacteria and Sphingobacteria. We propose that the U and G forms of S. intermedius represent distinct ecomorphological adaptations to contrasting shallow- and deep-water marine environments and might be considered incipient species. We also propose that the symbiotic bacteria likely play an important role in the evolution of morphological divergence of S. intermedius.

Genetic Evidence for a Mixed Composition of the Genus Myoxocephalus (Cottoidei: Cottidae) Necessitates Generic Realignment.

Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus. Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus. A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus. The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus, but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus. The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.

Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins.

Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.

Complete mitochondrial genome of the great sculpin Myoxocephalus polyacanthocephalus (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two specimens of the great sculpin Myoxocephalus polyacanthocephalus by high-throughput sequencing technology (Ion S5 platform). The genome sequences are 16,651 and 16,652 bp in size, and the gene arrangement, composition, and size are similar to the other sculpin mitochondrial genomes published previously. Overall base composition of the complete mitochondrial DNA is A (26.9%), G (17.0%), C (29.5%), and T (26.6.0%), the percentage of A and T (53.5%) is higher than G and C (46.5%). The difference between the two genomes studied is low, 0.15%. A relatively low level of divergence (3.48%) is detected between M. polyacanthocephalus and M. scorpius, which however is high enough to consider them as separate biological species.

Complete mitochondrial genome of the Belligerent sculpin Megalocottus platycephalus (Cottoidei: Cottidae).

The complete mitochondrial (mt) genome was sequenced in two specimens of the Belligerent sculpin Megalocottus platycephalus by high-throughput sequencing technology (Ion S5 platform). The sequences are 16,673 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mt genomes published previously. Comparison of the two M. platycephalus mt genomes now obtained with other complete mt genomes available in GenBank reveals an affinity to the sculpin fishes from the genus Myoxocephalus. The intergeneric difference between the Megalocottus and Myoxocephalus is 0.0757 ± 0.0019, which is significantly less than the corresponding value, 0.1240 ± 0.0120, obtained previously for the sculpin fishes based on the COI barcoding marker.

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 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.

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 Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome.

The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information.

Complete mitochondrial genome of the Volk's sculpin Cottus volki (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two individuals of the Volk's sculpin Cottus volki. The genome sequences are 16,519 and 16,536 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mitochondrial genomes published previously. The difference between the two genomes studied is relatively high, 3.42%, which is 30% of the average interspecific divergence (8.76%) detected between seven Cottus species from the GenBank database. The data are consistent with the sedentary lifestyle in C. volki, limiting gene flow even between neighbouring rivers.

Complete mitochondrial genome of the Sakhalin sculpin Cottus amblystomopsis (Cottoidei: Cottidae).

The complete mitochondrial genome was sequenced in two individuals of the Sakhalin sculpin Cottus amblystomopsis. The genome sequences are 16,526 and 16,527 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mitochondrial genomes published previously. The difference between the two genomes studied is low, 0.28%, in spite of the relatively long distance separating the localities. The data are consistent with the amphidromous life history of C. amblystomopsis, promoting gene flow even between distantly located rivers.

Complete mitochondrial genome of the phenotypically-diverse sea urchin Strongylocentrotus intermedius (Strongylocentrotidae, Echinoidea).

The complete mitochondrial genomes are sequenced in two individuals representing two morphological forms, 'usual' (U) and 'gray' (G), of the short-spined sea urchin Strongylocentrotus intermedius. The genome sequences are 15,705 bp in size, and the gene arrangement, composition, and size are very similar to the other sea urchin mitochondrial genomes published previously. A low level of sequence divergence (D xy = 0.0083 ± 0.0007) is detected between the forms. The GenBank (KC490912) mt genome of S. intermedius is much closer to the U form (D xy = 0.0013 ± 0.0003) than to the G form (D xy = 0.0085 ± 0.0006), demonstrating unique evolutionary trajectories for each form, which we previously suggested based on the bindin gene and symbiont analyses.

Complete mitochondrial genome of the Kamchatka grayling Thymallus mertensii (Salmoniformes, Salmonidae).

The complete mitochondrial genome was sequenced in two individuals of the Kamchatka grayling Thymallus mertensii. The genome sequences are 16 662 bp in size, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence (0.92%) detected between the genome of T. mertensii and the GenBank complete mitochondrial genomes of the Arctic grayling T. arcticus (FJ872559) may likely be due to recent divergence of the species and/or historical hybridization and interspecific replacement of mtDNA.

Complete mitochondrial genome of blunt-snouted lenok Brachymystax tumensis (Salmoniformes, Salmonidae).

The complete mitochondrial genomes were sequenced in two individuals of blunt-snouted lenok Brachymystax tumensis. The sizes of the genomes in the two isolates were 16,754 and 16,836; the difference was due to variable number of repeat sequences within the control region. The gene arrangement, base composition, and size of the two sequenced genomes are very similar to the B. lenok and B. lenok tsinlingensis genomes previously published (JQ686730 and JQ686731). However, the level of divergence inferred from 12 protein-coding genes (3.48%) indicated clear species boundaries between the lenok species.

Complete mitochondrial genomes of the Northern (Salvelinus malma) and Southern (Salvelinus curilus) Dolly Varden chars (Salmoniformes, Salmonidae).

The complete mitochondrial genomes were sequenced from the Northern and Southern Dolly Varden chars, Salvelinus malma and S. curilus. The genome sequences are 16,654 bp in size in both species, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The level of sequence divergence between S. malma and S. curilus inferred from the complete mitochondrial genomes is relatively low (1.88%) indicating recent divergence of the species and/or historical hybridization.

Complete mitochondrial genomes of the anadromous and resident forms of the lamprey Lethenteron camtschaticum.

The complete mitochondrial genomes were sequenced in anadromous and resident forms of the lamprey Lethenteron camtschaticum. The sizes of the genomes in the two isolates are 16,245 and 16,295 bp. The gene arrangement, base composition, and size of the two sequenced genomes are similar to the lamprey genomes previously published. The total sequence divergence between the two genomes is very low (0.14%), supporting conspecificity of the anadromous and resident forms of L. camtschaticum. Comparison of the genomes sequenced in the present work with other genomes of lampreys available in GenBank, reveals two distinct evolutionary lineages with a genera level of divergence among the lampreys of eastern Eurasia.