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 deeperwater 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.Bacteroidetes ͉ DNA polymorphism ͉ incipient speciation ͉ marine adaptation ͉ sympatric morphological forms T he intermediate (short-spined) sea urchin Strongylocentrotus intermedius (A. Agassiz. 1863) inhabits a wide range of the northwest Pacific region of Asia: the Sea of Japan, Sea of Okhotsk, east coast of Kamtchatka, Southern Kuril Islands, and coast of Japan (1, 2). The full distribution pattern remains uncertain as a result of the difficulty of reliable species identification (2). The species occurs from the littoral and upper sublittoral zone to a depth of 25 m (3); occasional specimens from the west coast of Japan islands have been dredged from depths as great as 150 to 225 m (1).The body of S. intermedius is variable in color. Within the same locality, it can be deep green, reddish, brown, lilac, and white; moreover, the basal and apical parts of spines as well as the primary, secondary, and miliary spines, in adults as well as in juveniles, are frequently variable in color. A milk-white color of spines prevails in deep-water settlements (15-25 m). This color variant is known as the gray (G) morphological form to distinguish it from the ''usual'' (U) form that mostly occurs in shallow-water settlements (5-10 m). The spines of juvenile individuals (age, 1-3 y) belonging to ...

BackgroundThe 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.ResultsThe 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.ConclusionsSignificant 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0374-5) contains supplementary material, which is available to authorized users.

(2017) Complete mitochondrial genome of the phenotypically-diverse sea urchin Strongylocentrotus intermedius (Strongylocentrotidae, Echinoidea), Mitochondrial DNA Part B, 2:2, 613-614,