Jun-Im Song

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record

The phylum Cnidaria is comprised of remarkably diverse and ecologically significant taxa, such as the reef-forming corals, and occupies a basal position in metazoan evolution. The origin of this phylum and the most recent common ancestors (MRCAs) of its modern classes remain mostly unknown, although scattered fossil evidence provides some insights on this topic. Here, we investigate the molecular divergence times of the major taxonomic groups of Cnidaria (27 Hexacorallia, 16 Octocorallia, and 5 Medusozoa) on the basis of mitochondrial DNA sequences of 13 protein-coding genes. For this analysis, the complete mitochondrial genomes of seven octocoral and two scyphozoan species were newly sequenced and combined with all available mitogenomic data from GenBank. Five reliable fossil dates were used to calibrate the Bayesian estimates of divergence times. The molecular evidence suggests that cnidarians originated 741 million years ago (Ma) (95% credible region of 686-819), and the major taxa diversified prior to the Cambrian (543 Ma). The Octocorallia and Scleractinia may have originated from radiations of survivors of the Permian-Triassic mass extinction, which matches their fossil record well.

A phylogenetic study of the Anthozoa (phylum Cnidaria) based on morphological and molecular characters

Abstract. The phylogenetic relationships within the Anthozoa were re-evaluated based on 41 morphological characters and nuclear sequences of 18S ribosomal DNA (29 anthozoans as ingroups and 3 hydrozoans as outgroups). The parsimony trees derived from the morphological data did not coincide closely with the molecular data, and the presence of several polytomies at some nodes of the trees resulted in ambiguities among the systematic relationships. On the other hand, the combined analysis using total evidence presents a more resolved and highly supported topology, as is indicated by higher bootstrap values and decay indices than either analysis alone. However, strict and semi-strict consensus trees derived from taxonomic congruence show a poorer resolution for the phylogeny of Anthozoa. The trees constructed from the molecular data, using neighbor-joining and maximum-likelihood methods, are nearly congruent with the result from the total evidence. Based on these results, Anthozoa is divided into three subclasses: Alcyonaria, Zoantharia, and Ceriantipatharia. The Ceriantipatharia now includes only one order, Ceriantharia, since the order Antipatharia is more closely related to orders within the Zoantharia. The Alcyonaria is a monophyletic group, in which the order Pennatulacea is basal, and orders Alcyonacea and Telestacea branch later. The order Gorgonacea is divided into two suborders, Holaxonia and Scleraxonia. Bellonela is more related to order Stolonifera, forming a monophyletic group. In Zoantharia, the order Zoanthinaria is basal, and the remaining taxa are divided into two clades: one includes the order Actiniaria and the other includes orders Antipatharia, Corallimorpharia, and Scleractinia. The latter two orders form a monophyletic group. This study presents a different phylogeny of actiniarians from the earlier hypothesis of scleractinian ancestry.

Emergent effects of heavy metal pollution at a population level: Littorina brevicula a study case

Changes in genetic variability and allele frequency can be responses from natural populations when encountering a novel contaminated environment. The genetic diversity and population structuring of natural populations of the gastropod Littorina brevicula from heavy-metal polluted and unpolluted environments along the southeast coast of Korea were examined using two mtDNA markers, cyt b and ND6. This study applied a nested clade analysis to test the existence of structuring association of haplotype distribution with environments (polluted and unpolluted). No genetic differences within cyt b mtDNA were detected between environments. On the other hand, differences in population haplotype diversity and structuring were found within ND6 mtDNA between polluted and unpolluted environments. The ND6-mtDNA haplotype (=genetic) diversity was significant lower in polluted environments. This decreased genetic diversity along with differences in the haplotype distribution within heavy-metal polluted environments compared to those unpolluted ones stand out as emergent effects from pollution at a population level. In this study, we propose the use of different approaches, such as the NCA, that takes into account the rare haplotypes, when assessing the effects of pollution on population genetic structuring.

Systematic Relationship of the Anthozoan Orders Based on the Partial Nuclear 18S rDNA Sequences

Systematic relationship of 13 species representing seven orders of anthozoans, and one hydrozoan as an outgroup, were investigated. Distance and parsimony methods were used to analyze nucleotide sequence data obtained from the 18S rDNA. The inferred phylogeny indicates that two orders, Ceriantharia and Antipatharia within subclass Ceriantipatharia, are not closely related to each other. Instead, the former appears to be the most ancestral group among anthozoans but the latter is more closely related to order Actiniaria within subclass Zoantharia. The result also indicates that the actiniarian may not be a monophyletic group, because Epiactis japonica is related more to order Scleractinia. Subclass Octocorallia appears to be a monophyletic group, within which order Pennatulacea diversed at first, and then orders Alcyonacea and Gorgonacea diversed later.

The complete mitochondrial genome of Calicogorgia granulosa (Anthozoa: Octocorallia): potential gene novelty in unidentified ORFs formed by repeat expansion and segmental duplication.

Mitochondrial genomes of many nonbilaterian animals show high diversity of genome size and gene content, revealing many intergenic regions (IGRs), diverse repeats and additional genes. Here we present a new complete mitogenome of the cnidarian sea fan species, Calicogorgia granulosa (Anthozoa: Octocorallia) and its novel genomic features. The 20,246 bp of the complete mitogenome, which is the largest among the nine octocorals sequenced to date, contains 13 protein coding genes, 2 rRNAs and a tRNA within its circular form of mitochondrial DNA. We found an identical segmental duplication (S1 and S2, 913 bp) composed of an ORF (672 bp) coding for a hypothetical protein within which Direct Variant Repeat (DVR) expansions reside in-frame to the coding sequence. Additionally, the duplicated segmental DNA showed no variation in nucleotide sequences both between S1 and S2 and across multiple individual samples. Upon these observations, we discuss plausible causes for the intramitochondrial segmental duplication and the absence of sequence variation, and a need for further investigation of the novel ORF as well. In conclusion the present mitogenome of C. granulosa adds more information to our understanding of the diversity and evolution of mitogenomes of nonbilaterian animals.

Genetic population structure of Littorina brevicula around Korean waters

Because Korean waters are influenced by different minor current systems, this may lead us to expect certain genetic differentiation among populations of marine invertebrates around Korean coastlines. To test this idea, we examined the genetic differentiation of 14 populations of a widely distributed marine gastropod, Littorina brevicula, using mtDNA markers, cyt b and ND6. Sequencing analyses of 500 bp fragment of the cyt b and 501 bp of the ND6 mtDNA revealed the existence of 14 and 24 haplotypes, respectively. Geographic association with population genetic variability was tested using a nested clade analysis (NCA). However, no significant association between geography and haplotype distribution was found, which suggests the existence of a high level of gene flow of L. brevicula around Korean waters. The lack of genetic structure and likely high gene flow among these populations, even under influences of different minor current systems, may be accounted for long periods of dispersal of the planktonic larvae from this gastropod species within major currents on the north western Pacific Ocean.

Reproductive biology of the temperate soft coral Dendronephthya suensoni (Alcyonacea: Nephtheidae)

Abstract The azooxanthellate soft coral Dendronephthya suensoni (Holem, 1895) is distributed mainly around Jejudo Island, Korea. This species was determined as gonochoric with a sex ratio of 2:1 (female:male). Both female and male colonies have one gametogenic cycle a year. The annual reproductive cycle of D. suensoni is dependent on the seawater temperature. In particular, reproduction of the male colony showed a higher positive correlation between seawater temperature and the mean diameter of the spermaries. Gametogenesis in females and males took 6 months and 12 months, respectively. The mean diameter of a mature oocyte was 249.29 ± 36.24 μm, with a maximum size of 354.45 μm. Spawning could have occurred in the fall after the seawater temperature began to decrease.

Alveopora japonica beds thriving under kelp

Alveopora japonica Eguchi, 1968 (Scleractinia, Acroporidae) occurs in shallow benthic communities from Southern Taiwan to high latitude areas of Japan where it is usually rare and nested among algae and soft corals (Dai and Horng 2009). It is also a peculiar species among the scleractinians due to its association with Symbiodinium clades C, E, and F (RodriguezLanetty et al. 2003; Jeong et al. 2012). In October 2012, we found extensive A. japonica beds (Fig. 1a, b) at Biyangdo, located to the northwest of Jeju Island, South Korea (33 24¢5†N, 126 13¢8†E), where it formed a dense and almost monospecific carpet at 10–17 m in depth. These stands were punctuated by the regionally endemic kelp Ecklonia cava. Based on 63 quadrats (0.25 m), A. japonica covered 67 ± 4 % of the benthos over an area of >1 ha. Most of the colonies were <10 cm in diameter. Many recruits occurred where coral cover was low such as around the base of holdfasts of the kelp, which represented 4 % of the benthic community. Other major benthic categories included calcareous crustose coralline algae (18 %) and sand (8 %). Ecklonia cava is usually the dominant benthic species around Jeju Island. Recently, traditional fisherwomen, ‘Haenyeo,’ as well as local divers, have reported orally a gradual decline in the population of this economically and ecologically important kelp to the benefit of A. japonica. Apart from being one of the first reports on high dominance of scleractinian coral species at this latitude, this observation might also indicate a persistent shift from kelp forests to coral dominance, and the potential loss of an economically important endemic taxa.

A New Species of Genus Coeloplana (Ctenophora: Tentaculata: Platyctenida) from Korea

Since November, 2006, the new creeping platyctenid ctenophore, Coeloplana anthostella n. sp., has been collected from twigs and polyp masses of encrusting dendronephthyans at a depth of 26-32 m off the coast of Munseom, Jejudo Island. This new species is distinguished from C. bocki Komai, 1920 and C. komai Utinomi, 1963 by its smaller size, the absence of dorsal papillae, and the deep scarlet colored star-shaped markings on the dorsal plane. This novel addition to ctenophore fauna is presently described and illustrated in detail.

Molecular Phylogeny and Divergence Time Estimation of the Soft Coral Dendronephthya gigantea(Alcyonacea: Nephtheidae)

Soft coral Dendronephthya gigantea (Verrill, 1864) is a conspicuous species dominating shallow sea waters of Jejudo Island, Korea. Recently its whole mitochondrial genome sequencing was completed by us and the sequence information provided an opportunity to test the age of Octocorallia and time of evolutionary separation between some representative orders of the subclass Octocorallia. Molecular phylogenetic analyses based on 13 mitochondrial protein encoding genes revealed a polyphyletic relationship among octocorallians representing two orders (Alcyonacea and Gorgonacea) and four families (Alcyoniidae, Nephtheidae, Briareidae, and Gorgoniidae). Estimates of divergence times among octocorallians indicate that the first splitting might occur around end of or after Cretaceous period (50-79 million years ago (Ma)). The age is relatively young compared to the long history of stony sea corals (¤240 Ma). Taken together our result suggests a possible relatively recent radiating evolution at least in the order Alcyonacea and Gorgonacea. Molecular dating and phylogenetic analysis based on much broader taxon sampling and many genes might give an insight into this interesting hypothesis.