Background Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation. Methodology We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared. Results P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs. Conclusion This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).

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The estimation of larval dispersal on an ecological timescale is significant for conservation of marine species. In 2018, a semi-population outbreak of crown-of-thorns sea star, Acanthaster cf. solaris, was observed on a relatively isolated oceanic island, Ogasawara. The aim of this study was to assess whether this population outbreak was caused by large-scale larval recruitment (termed secondary outbreak) from the Kuroshio region. We estimated larval dispersal of the coral predator A. cf. solaris between the Kuroshio and Ogasawara regions using both population genomic analysis and simulation of oceanographic dispersal. Population genomic analysis revealed overall genetically homogenized patterns among Ogasawara and other Japanese populations, suggesting that the origin of the populations in the two regions is the same. In contrast, a simulation of 26-year oceanographic dispersal indicated that larvae are mostly self-seeded in Ogasawara populations and have difficulty reaching Ogasawara from the Kuroshio region within one generation. However, a connectivity matrix produced by the larval dispersal simulation assuming a Markov chain indicated gradual larval dispersal migration from the Kuroshio region to Ogasawara in a stepping-stone manner over multiple years. These results suggest that the 2018 outbreak was likely the result of self-seeding, including possible inbreeding (as evidenced by clonemate analysis), as large-scale larval dispersal from the Kurishio population to the Ogasawara population within one generation is unlikely. Instead, the population in Ogasawara is basically sustained by self-seedings, and the outbreak in 2018 was also most likely caused by successful self-seedings including possible inbreeding, as evidenced by clonemate analysis. This study also highlighted the importance of using both genomic and oceanographic methods to estimate larval dispersal, which provides significant insight into larval dispersal that occurs on ecological and evolutionary timescales.

Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.

The blue coral (Heliopora coerulea, Pallas 1766) is a reef-building coral, which is recently been classified as a threatened species. Recent population genetic analyses have found two genetically distinct, cryptic lineages of this coral (types A and B). However, the ecological differences between them, as well as the drivers of this speciation, are still unclear. The aim of this study was to examine the possible differentiation in the reproductive timing of the two lineages, as a plausible cause of speciation. We subjected both formalin-and ethanol-preserved samples of the coral, collected from sympatric H. coerulea populations, for tissue and genetic analyses. Samples were collected every one or two months, from June 2014 to September 2017, around Sekisei Lagoon, southwest Okinawa, Japan. We also conducted field observations of the coral's reproductive behavior (larval brooding) in mid-June and July. As a result we could observe larval brooding behavior from mid-to late-July in type B; however no such behavior was observed in type A during the observation and sampling period. After examining a total of 468 histological samples, we found that the diameters of the oocytes and spermaries peaked from May to June in type A, whereas in type B they peaked from June to July, after which the spermaries disappeared or diminished. Our study demonstrates that the two H. coerulea lineages, under the same environmental conditions, exhibit different reproductive timings. This gap in reproductive timing, which possibly stemmed from endogenous differences, might have promoted their genetic differentiation and speciation into two distinct lineages.