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

Abstract

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 ...

Symbiotic Associations in the Phenotypically-Diverse Brown Alga Saccharina japonica

“…If the settlement depth would be principal factor differentiating the microbial communities we should expect similar symbiont communities for different species collected from the same (or close) depths and more different communities in hosts collected from different depths. This prediction is not supported by the data obtained for the Bacteroidetes symbionts of the sea urchin Strongylocentrotus nudus : shallow-water S. nudus samples have intermingled bacterial distributions belonging to different Bacteroidetes lineages, without clear-cut differentiation among the Bacteroidetes [21]. Our present data are also inconsistent with the hypothesis: (1) the SHA form has closer bacterial composition to the LON form than to the TYP form, even though LON and SHA come from more contrasting depths (0.5 and 15 m); (2) Tauya basicrassa , Arthrothamnus bifidus , and Alaria marginata have intermingled bacterial distributions belonging to different Proteobacteria lineages, without clear-cut differentiation associated with depth.…”

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

“…The procedures for DNA amplification, cloning, and sequencing have been described previously [44]–[45]. The mtDNA fragment (8.1 kb) was amplified with primers designed with the program mitoPrimer, version 1 [46].…”

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

“…Thus, our specimens, collected in close proximity (150 m) but belonging to different morphological forms, are more different than specimens collected from distant regions (separated by 2089.43 km) but belonging to the same morphological form. These discrepancies between genetic differences and geographical distances confirm that the U and G morphological forms of S. intermedius represent distinct evolutionary lineages (incipient species) with low genetic divergence but significant differences in symbiont contents (Balakirev et al 2008(Balakirev et al , 2016.…”

“…There are two sympatric morphological forms, 'usual' (U) and 'gray' (G), which are different in morphology and preferred bathymetric distribution. We detected previously that these two forms harbour highly divergent bacterial symbiont lineages and show distinct patterns of nuclear bindin gene variability but not mitochondrial COI gene (Balakirev et al 2008(Balakirev et al , 2016. The evolutionary history and taxonomical relationships of the S. intermedius morphological forms remain unclear due to limited genetic data.…”