Papers - FUKAMI Hironobu
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An eDNA metabarcoding system for detecting scleractinian corals to the generic level along the Japanese coast Reviewed
Hisata Kanako, Nagata Tomofumi, Kanai Megumi, Sinniger Frederic, Nagata Fumihiko, Suwa Mayuki, Yoshioka Yuki, Harii Saki, Nonaka Masanori, Fukami Hironobu, Arakaki Seiji, Fujie Manabu, Arakaki Nana, Zayasu Yuna, Narisoko Haruhi, Noda Takeshi, Koseki Aya, Nishitsuji Koki, Inoue Jun, Shinzato Chuya, Satoh Noriyuki
Galaxea, Journal of Coral Reef Studies 27 ( 1 ) 13 - 29 2025
Language：English Publishing type：Research paper (scientific journal) Publisher：日本サンゴ礁学会
Coral reefs possess the highest biodiversity of all marine ecosystems and zooxanthellate scleractinian corals, the keystone organisms of these reefs, are in crisis due to climate change and anthropogenic activities. Future reef conservation requires comprehensive understanding of the present status of scleractinian taxa in each region. Environmental DNA metabarcoding (eDNA-M) is a method to meet such requirements. Still, it requires optimized primers for PCR amplification of eDNA and complete genomic sequence information for bioinformatic analyses. Coral reefs of Japan reportedly host 85 scleractinian genera. Our previous study developed a primer set that can be used to amplify scleractinian mitochondrial 12S rDNA for eDNA-M analysis. However, at present, the NCBI nucleotide database contains only ~60 genera with available 12S rDNA sequences, indicating that nearly 25 genera that should be detected by this system have no sequence information. To overcome this problem and to establish a nearly complete eDNA-M system for generic level detection of Japanese scleractinians, we collected 22 scleractinian genera and sequenced their mitochondrial genomes. In addition, species of another 12 genera were re-sequenced to avoid sequence differences caused by geographic variation. Incorporation of these data into a newly constructed informatic pipeline resulted in an eDNA-M system that can detect 83 of the 85 genera. This provides a tool for comprehensive, generic level detection of scleractinian corals in Japanese waters.
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Isomura N., Inoha K., Shimura A., Yasuda N., Kikuchi T., Iwao K., Kitanobo S., Ohki S., Morita M., Fukami H.
Coral Reefs 43 ( 5 ) 1497 - 1509 2024.10
Authorship：Last author Language：English Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Hybridisation is an evolutionary process that generates genetic diversity in organisms. However, the relationship between reproductive features, such as spawning synchronisation and gamete compatibility, and the degree of introgression leading to hybridisation are poorly understood. The reef-building coral Acropora spp. have a complex evolutionary history, and the link between their ecology, life-history traits, and potential to hybridise is disputed. Here, we examined the relationship among the reproductive features involved in the intercrossing of three species, Acropora florida, Acropora gemmifera, and Acropora intermedia, at two sites: Akajima and the Sesoko islands in southern Japan. Although the examined species showed synchronous spawning and high rates of gamete compatibility, spawning synchronisation and gamete compatibility were less strongly associated with high rates of interbreeding among the three species. Model-based genetic clustering and site-pattern frequency-based tests with single nucleotide polymorphisms supported genetic admixture among the three species in each location. Demographic analyses using fastsimcoal implied that the admixture among the three species in each location might have occurred in the past (> 2,000 generations) and recently (< 50 generations). Furthermore, the recent admixture of these three species is potentially associated with heavy bleaching events and population declines. The principal component analysis, structure, and fastsimcoal showed that the extensive admixture of A. intermedia and A. gemmifera on Sesoko Island occurred recently. Therefore, gamete interactions that lead to hybridisation in the field must be clarified. Furthermore, the connectivity between the two locations needs to be identified; however, our results implied that population fluctuations could be associated with introgression.
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Kishi D., Nomura K., Nozawa Y., Arakaki S., Fukami H.
ZooKeys 1205 205 - 222 2024.6
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：ZooKeys
A new zooxanthellate scleractinian coral, Paragoniastrea variabilis Kishi, Nomura & Fu-kami, sp. nov. (Scleractinia, Merulinidae), is described from non-coral reef regions of Japan and northern Taiwan. This new species was previously recognized as a morphological variant of Paragoniastrea deformis (Veron, 1990) and can be morphologically distinguished from that species by lacking groove-and-tube structures on corallite wall joints, and by having larger calices, numerous septa, and up to three corallites in one valley. The new species also formed an independent clade from its congeners, P. australensis (Milne Edwards & Haime, 1857), P. deformis and P. russelli (Wells, 1954), in the molecular phylogeny based on the mitochondrial intergenic region and nuclear ribosom-al internal transcribed spacers.
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A new species of Sympodium (Octocorallia, Xeniidae) from Miyazaki, Japan Reviewed
Koido T., Imahara Y., Fukami H.
Zootaxa 5443 ( 2 ) 186 - 204 2024.4
Authorship：Last author Language：English Publishing type：Research paper (scientific journal) Publisher：Zootaxa
In this study, a new soft coral species, Sympodium omasum sp. nov. (Malacalcyonacea, Xeniidae), is described from a warm-temperate region in Miyazaki, Japan. This new species has double-heads and platelet sclerites, and the platelets are covered with sinuous rodlets, which are fused and form many nodules at the sclerites surface. Sympodium omasum sp. nov. can be distinguished morphologically from a congeneric species by the double-head sclerites and unique platelet surface architecture.
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Seasonal variation of grazing scars on massive <i>Porites</i> corals in Sekisei Lagoon, Okinawa, Japan Reviewed
Ikeuchi Eri, Iguchi Akira, Nakamura Takashi, Fukami Hironobu
Galaxea, Journal of Coral Reef Studies 26 ( 1 ) 3 - 8 2024.3
Authorship：Last author Language：English Publishing type：Research paper (scientific journal) Publisher：日本サンゴ礁学会
Coral reef ecosystems have high biodiversity and unique species interactions. One example is predation on corals by parrotfish species, known for their grazing on surfaces of massive <i>Porites</i> stony corals. However, factors causing variations of grazing scars on <i>Porites</i> colonies remain largely unknown. In this study, we investigated the relationship between ocean depth of <i>Porites</i> colonies, grazing scar ratios, and photosynthetic efficiency, reflecting the health of coral-zooxanthellae symbiosis in Sekisei Lagoon, the largest coral reef in Japan, with distinct seasonality. We documented seasonal variation in photosynthetic efficiency of symbiotic algae and the frequency of grazing scars. Our results suggest that during the cooler season, <i>Porites</i> colonies with higher photosynthetic efficiency may recover from grazing more quickly than colonies with lower photosynthetic efficiency. We also suggest that fish-coral interactions may vary seasonally, possibly in relation to coral reproductive stages and environmental conditions. Further research is needed to understand the complex dynamics of these interactions in coral reefs.
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Changes of scientific names of the scleractinian corals until 2023 Reviewed
FUKAMI Hironobu, Yuko F. KITANO
Journal of the Japanese Coral Reef Society 25 ( 1 ) 19 - 25 2024.1
Authorship：Lead author, Corresponding author Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
Taxonomic classification of the scleractinian corals underwent major revisions from 2012 to 2014, focusing on the former families Mussidae and Faviidae. Since then, changes in scientific names due to the taxonomic revisions of many other corals have been also reported every year. Especially, Rowlett (2020) reported taxonomic revisions of many families and genera of corals. Thus, in the current situation where the taxonomic classification is changing rapidly, coral researchers need to update the scientific names they use. However, it is difficult for researchers who are not deeply involved in taxonomy to spend time on this task. Therefore, in this article, we introduce the main scleractinian corals at the species rank and the higher taxonomic groups that have undergone the changes of the scientific names due to taxonomic revisions since 2016.
DOI： 10.3755/jcrs.25.19
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Wang S., Mizuno K., Tabeta S., Terayama K., Sakamoto S., Sugimoto Y., Sugimoto K., Fukami H., Jimenez L.A.
Ecological Informatics 78 2023.11
Publishing type：Research paper (scientific journal) Publisher：Ecological Informatics
The semantic segmentation of marine images makes it easier to describe seafloor scenes and track marine organisms. However, creating human-annotated datasets for image segmentation requires significant time and effort. Therefore, this study proposes a semisupervised learning approach that combines the mean-teacher model and U-Net architecture for segmenting seafloor images obtained from the Philippines. The proposed method performs segmentation for categories, including corals, sea urchins, sea stars, and seagrass. Traditional manual labelling methods are used for coral, sea urchins, and sea stars. For the seagrass category, which is challenging to label manually, we used the K-means clustering algorithm to obtain corresponding labelled datasets based on the characteristics of such images and evaluated the feasibility. Compared with the U-Net-based supervised method, the semi-supervised method used in this study achieved good results and accuracy values, even with fewer labelled images.
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Chukaew T., Isomura N., Mezaki T., Matsumoto H., Kitano Y.F., Nozawa Y., Tachikawa H., Fukami H.
Zoological Science 40 ( 4 ) 326 - 340 2023.6
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Zoological Science
The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.
DOI： 10.2108/zs230009
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宮崎県日南市大島周辺海域に生息する貴重なサンゴ類
深見裕伸・福田道喜
宮崎の自然と環境 ( 7 ) 74 - 78 2022.12
Authorship：Lead author, Corresponding author Language：Japanese Publishing type：Research paper (scientific journal)
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長崎県佐世保市黒島海岸域の有藻性イシサンゴ類について Reviewed
出来真由美・深見裕伸・百武可奈子・泉徹耶・両角裕希・鶴留司・永光萌衣・眞鍋勇平・川久保晶博
長崎県生物学会誌 ( 90 ) 1 - 6 2022.6
Language：Japanese Publishing type：Research paper (scientific journal)
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First evidence for backcrossing of F<sub>1</sub> hybrids in Acropora corals under sperm competition. Reviewed
Kitanobo S, Iwao K, Fukami H, Isomura N, Morita M
Scientific reports 12 ( 1 ) 5356 2022.3
Language：English Publishing type：Research paper (scientific journal)
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Koido T., Imahara Y., Fukami H.
ZooKeys 2022 ( 1085 ) 29 - 49 2022.2
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：ZooKeys
A new soft coral species, Xenia konohana sp. nov. (Alcyonacea, Xeniidae), is described from Miyazaki in the warm-temperate region of Japan. This new species has conspicuous and unique spindle sclerites in addition to the simple ellipsoid platelet-shaped sclerites typically found in the genus Xenia. These unique spindles are a specific key morphological characteristic for this new species and for differentiating this species among congeneric species.
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Chen M.H., Huang Y.Y., Huang B.Y., Hsieh H.J., Lee J.N., Neo M.L., Fukami H., Chen C.A.
Frontiers in Marine Science 8 2022.1
Language：English Publishing type：Research paper (scientific journal) Publisher：Frontiers in Marine Science
The east Taiwan Strait is largely fringed by sandy and muddy habitats. However, a massive algal reef made of crustose coralline algae has been found along the coast off Taoyuan city in northwestern Taiwan. The porous structure of Taoyuan Algal Reef harbors high abundance and diversity in marine organisms, including the ferocious reef crab, Eriphia ferox. Such a pivotal geographic location and unique ecological features make Taoyuan Algal Reef a potential stepping stone connecting biotic reefs in the east Taiwan Strait, South China Sea to the south, and even the high latitude of Japan to the north. In this study, we examined the population connectivity and historical demography of E. ferox by analyzing mitochondrial cytochrome oxidase I (COI) fragments of 317 individuals sampled from 21 localities in the northwestern Pacific. Our analyses of haplotype network and pairwise FST comparisons revealed a lack of phylogeographical structure among E. ferox populations, implying the existence of a migration corridor connecting the South and East China Seas through the east Taiwan Strait. Multiple lines of evidence, including significant values in neutrality tests, unimodally shaped mismatch distributions, and Bayesian skyline plots elucidated the rapid population growth of E. ferox following the sea-level rise after Last Glacial Maximum (ca. 2–10 Ka). Such demographic expansion in E. ferox coincided with the time when Taoyuan Algal Reef started to build up around 7,500 years ago. Coalescent migration analyses further indicated that the large and continuous E. ferox population exclusively found in Datan Algal Reef, the heart of Taoyuan Algal Reef, was a source population exporting migrants both northward and southward to the adjacent populations. The bidirectional gene flow should be attributed to larval dispersal by ocean currents and secondary contact due to historical population expansion. Instead of serving as a stepping stone, our results support that Taoyuan Algal Reef is an essential population source for biotic reef-associated species along the east Taiwan Strait, and highlight the importance of conserving such a unique ecosystem currently threatened by anthropogenic development.
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The problem of Japanese names for corals (2): EDA-MIDORIISHI / HIME-EDA-MIDORIISHI
FUKAMI Hironobu, NOMURA Keiichi, MEZAKI Takuma, YOKOCHI Hiroyuki
Journal of the Japanese Coral Reef Society 24 ( 1 ) 9 - 12 2022
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
In this paper, we discuss the current problem of two Japanese names for corals, “Eda-midoriishi” and “Hime-eda-midoriishi”. Previously, the scientific name for “Eda-midoriishi” was <i>Acropora tumida</i>, and the scientific name for “Hime-eda-midoriishi” was <i>Acropora pruinosa</i>. The difference between the two species was thought to be the thickness of the branches. However, since Sugihara et al. (2015), the species traditionally recognized as <i>A. tumida</i> in Japan has been reconsidered to be a morphological variant of <i>A. pruinosa</i> based on reinspection of the type specimen. Furthermore, Nomura et al. (2016) have changed the Japanese name of <i>A. pruinosa</i> from “Hime-eda-midoriishi” to the older name “Eda-midoriishi”. The reinspection of the type specimen of <i>A. tumida</i> also revealed that the colony shape was corymbose forms, not thick arborescent forms as previously recognized. Since the current status of <i>A. tumida</i> in Japan has become unknown, its Japanese name remains undecided. Currently, due to insufficient publicity of these changes, there is some confusion in the use of the Japanese and scientific names. Therefore, this paper reiterates the following recommendations: <i>A. pruinosa</i>, the arborescent (thin to thick branches) species that is unique to the temperate region of Japan should be referred to by its Japanese name “Eda-midoriishi”. On the other hand, the current status of <i>A. tumida</i> in Japan is unknown and it does not have a Japanese name at present.
DOI： 10.3755/jcrs.24.9
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Formulation of “Guidelines for the Proposal and Use of Standard Japanese Names for the Japanese Scleractinian Corals”
FUKAMI Hironobu, NOMURA Keiichi, KAJIWARA Kenji, YOKOCHI Hiroyuki, NONAKA Masanori, TACHIKAWA Hiroyuki, KITANO Yuko F, SUZUKI Go, FUJITA Yoshihisa, YAMANO Hiroya
Journal of the Japanese Coral Reef Society 24 ( 1 ) 1 - 7 2022
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
DOI： 10.3755/jcrs.24.1
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Mitsuki Y., Isomura N., Nozawa Y., Tachikawa H., Huang D., Fukami H.
Invertebrate Systematics 35 ( 8 ) 876 - 891 2021.11
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Invertebrate Systematics
Species identification is key for coral reef conservation and restoration. Recent coral molecular-morphological studies have indicated the existence of many cryptic species. Coelastrea aspera (Verrill, 1866) is a zooxanthellate scleractinian coral that is widely distributed in the Indo-Pacific. In Japan, this species is distributed from the subtropical reef region to the high-latitudinal non-reef region. Previous studies have reported that C. aspera colonies in the non-reef region release egg-sperm bundles (bundle type), whereas those in the reef region release eggs and sperm separately (non-bundle type) and release planula larvae after spawning. This difference in reproduction might be relevant to species differences. To clarify the species delimitation of C. aspera, the reproduction, morphology and molecular phylogeny of C. aspera samples collected from reef and non-reef regions in Japan were analysed, along with additional morphological and molecular data of samples from northern Taiwan. The results show that C. aspera is genetically and morphologically separated into two main groups. The first group is the non-bundle type, distributed only in reef regions, whereas the second group is the bundle type, widely distributed throughout the reef and non-reef regions. Examination of type specimens of the taxon's synonyms leads us to conclude that the first group represents the true C. aspera, whereas the second is Coelastrea incrustans comb. nov., herein re-established, that was originally described as Goniastrea incrustans Duncan, 1886, and had been treated as a junior synonym of C. aspera.
DOI： 10.1071/IS21025
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Fukami Hironobu, Niimura Aoi, Nakamori Toru, Iryu Yasufumi
Galaxea, Journal of Coral Reef Studies 23 ( 1 ) 17 - 35 2021.10
Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：日本サンゴ礁学会
About 80 species of <i>Acropora</i> corals have been recorded in Japan to date. However, there are few information on its diversity in Amami-Oshima Island, which is located in the northern part of the central Ryukyu Islands. Multiple studies, including molecular work, have looked at the species diversity of <i>Acropora</i> in Japan, but many of them have not been effective in successful differentiation at the species. This is the first study reporting the species diversity and molecular phylogeny of the <i>Acropora</i> species in Amami-Oshima Island. We collected 89 <i>Acropora</i> specimens, including 26 species within reef lagoon in the southwestern area (Funakoshi) of the island. We recorded <i>A. spathulata</i> for the first time in Japan, and <i>A. acuminata</i> and <i>A. papillare</i> for the first time in the Amami Islands. For eight species that were uncommon or difficult to identify, we described their morphological characteristics. To infer the phylogenetic relationships between the <i>Acropora</i> species in Amami-Oshima Island and Japan, we also reconstructed the phylongey of the specimens using a mitochondrial putative control region including published DNA data from other Japanese specimens. The results showed that <i>Acropora</i> species were genetically separated into seven clades. As previously reported, <i>A. hyacinthus</i> and <i>A. cytherea</i> were highly polyphyletic; nonetheless, most species were included in specific clades. In combination with previously published ecological data, the present data allowed us to propose a new species grouping (eight groups) for 36 Japanese <i>Acropora</i> species, which have morphological, molecular phylogenetic, and ecological similarities. This grouping will help identify the species and understand the species diversity of <i>Acropora</i> until a formal taxonomic revision of the genus is conducted.
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Terayama K., Mizuno K., Tabeta S., Sakamoto S., Sugimoto Y., Sugimoto K., Fukami H., Sakagami M., Jimenez L.A.
Methods in Ecology and Evolution 2021.10
Language：English Publishing type：Research paper (scientific journal) Publisher：Methods in Ecology and Evolution
Various sampling and monitoring strategies have been developed to assess marine habitats and life-forms. However, the cost-effectiveness of such survey methods (e.g. line intercept transects and autonomous underwater vehicles) is still not high. In this paper, a practical seafloor habitat mapping method combining a cost-effective survey system (P-SSS: portable speedy sea scanner) and a deep learning-based quantification method were proposed. P-SSS is a highly portable transport system and a towed-type system with five cameras arrayed on its platform. The sea trial was conducted at Pujada Bay, Philippines, on 7 December 2019. The high-quality orthophotos of the seafloor with a high resolution of ~3.0 mm/pixel were successfully generated. The attained survey efficiency was 12,900 m2/hr. In addition, in this paper, a segmentation method utilizing the U-Net architecture to estimate the coverage of corals, seagrass and sea urchins using a large-scale 2D image is proposed. Overall, this highly portable survey system is expected to become a promising tool for marine environmental surveys, especially in the areas where the rich nature of the oceans is susceptible to environmental changes, such as the remote islands that lack sufficient survey facilities.
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FUKAMI Hironobu, NOMURA Keiichi, MEZAKI Takuma, SUZUKI Go, YOKOCHI Hiroyuki
Journal of the Japanese Coral Reef Society 23 ( 1 ) 21 - 26 2021.6
Authorship：Lead author Language：Japanese Publishing type：Research paper (other academic) Publisher：The Japanese Coral Reef Society
In order to clear up confusion and explain problems related to coral taxonomy, such as drastic revisions in the taxonomic classification and Japanese names of the zooxanthellate scleractinian corals and problems in coral species identification, we have started a series of articles as "Topics on current taxonomy of corals". To begin with, we will focus on the problem of "KUSHIHADA-MIDORIISHI / NANYOU-MIDORIISHI", whose Japanese names are often confused. As a result of morphological, genetic and taxonomic analysis, all the <i>Acropora hyacinthus</i>-like populations in Japan should be treated as a "species complex" rather than a species unit, and should be referred to as the "<i>Acropora hyacinthus</i> species complex" (simplified version: <i>Acropora hyacinthus</i> complex) and as "KUSHIHADA-MIDORIISHI SHU-GUN" for Japanese name. However, as the "species complex" is generally not used in many cases, it is recommended that "<i>Acropora hyacinthus</i>" and "KUSHIHADA-MIDORIISHI" are used instead of the "<i>Acropora hyacinthus</i> species complex" and "KUSHIHADA-MIDORIISHI SHU-GUN" as a coping strategy until the revision and nomenclature of all species of this species complex is completed.
DOI： 10.3755/jcrs.23.21
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Pipithkul S., Ishizu S., Shimura A., Yokochi H., Nagai S., Fukami H., Yasuda N.
Frontiers in Marine Science 8 2021.5
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Frontiers in Marine Science
Acropora pruinosa is a threatened zooxanthellate scleractinian coral that is distributed in the temperate areas along the coastline of Japan and the northern area of the South China Sea. Since A. pruinosa propagates both asexually and sexually, assessing clonal diversity and genetic connectivity among populations is important for conservation. In addition, high morphological variations in the field create confusion during species identification. To examine the existence of hidden genetic lineages, clonality, and genetic connectivity of A. pruinosa for conservation, we applied microsatellite analysis. Clustering analysis indicated two distinct geographically separated genetic lineages: one is distributed in the west, and the other is distributed in the east. The two lineages co-existed in Nishidomari, Kochi. There was no obvious difference in morphological characteristics between the two lineages. Although the factors influencing the observed distribution patterns remain unknown, there is a possibility that the two lineages might have diverged somewhere in the north-western Kyushu and north-eastern Pacific coast habitats in the past, and then periodically colonized the current habitats. A low clonal diversity was observed in most of the populations, indicating a high rate of asexual reproduction associated with their branching morphologies. In addition, there are strong genetic structuring in this species, indicating weak connectivity among populations. These results indicated a low larval dispersal potential among populations and that populations are basically sustained by a high rate of clone propagation and self-seeding. The existence of cryptic lineages and genetically isolated populations with high clonality emphasized the importance of conservation of A. pruinosa.
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Mizuno K., Terayama K., Hagino S., Tabeta S., Sakamoto S., Ogawa T., Sugimoto K., Fukami H.
Scientific Reports 10 ( 1 ) 12416 2020.12
Language：English Publishing type：Research paper (scientific journal) Publisher：Scientific Reports
© 2020, The Author(s). Over the last 3 decades, a large portion of coral cover has been lost around the globe. This significant decline necessitates a rapid assessment of coral reef health to enable more effective management. In this paper, we propose an efficient method for coral cover estimation and demonstrate its viability. A large-scale 3-D structure model, with resolutions in the x, y and z planes of 0.01 m, was successfully generated by means of a towed optical camera array system (Speedy Sea Scanner). The survey efficiency attained was 12,146 m2/h. In addition, we propose a segmentation method utilizing U-Net architecture and estimate coral coverage using a large-scale 2-D image. The U-Net-based segmentation method has shown higher accuracy than pixelwise CNN modeling. Moreover, the computational cost of a U-Net-based method is much lower than that of a pixelwise CNN-based one. We believe that an array of these survey tools can contribute to the rapid assessment of coral reefs.
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Differences in spawning time drive cryptic speciation in the coral Acropora divaricata Reviewed
Furukawa M., Ohki S., Kitanobo S., Fukami H., Morita M.
Marine Biology 167 ( 11 ) 2020.11
Language：English Publishing type：Research paper (scientific journal) Publisher：Marine Biology
Most of the reef-building Acropora corals around Okinawa Island spawn in May and/or June. We found that two morphotypes of Acropora divaricata spawned in August and/or September. The “robust” and “slender” morphotypes differed in branch width and in the diameter of axial corallites. Histological analyses showed that the onset of gamete production/maturation occurred from June onwards. Most of the other Acropora species spawned from late May to early June. A. florida, which spawned in May/June, initiated gamete production in early April. We assumed that the two morphotypes of A. divaricata were reproductively isolated from most of the other Acropora species because of differences in the spawning seasons. We found that the spawning seasons of the two morphotypes slightly overlapped in 2015 but not in 2019, and inter-morphotype gamete compatibility was high. However, population genetics analyses and a phylogeny of the mitochondrial d-loop region showed that they were genetically distinct and rarely hybridized. Thus, the broadcast-spawning coral A. divaricata might have speciated when there might have been only a low possibility of interspecific gamete interaction.
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Mizuno K., Terayama K., Tabeta S., Sakamoto S., Matsumoto Y., Sugimoto Y., Ogawa T., Sugimoto K., Fukami H., Sakagami M., Deki M., Kawakubo A.
IEEE Journal of Oceanic Engineering 45 ( 4 ) 1386 - 1395 2020.10
Language：English Publishing type：Research paper (scientific journal) Publisher：IEEE Journal of Oceanic Engineering
Various methods have been developed and used for monitoring marine benthic habitats, such as coral reefs and seagrass meadows. However, the efficiency of general survey methods [e.g., line intercept transects and autonomous underwater vehicles (AUVs)] still is not high. In this article, we propose a practical coral-coverage estimation method combining an effective survey system [Speedy Sea Scanner (SSS)] and a deep-learning-based estimation method. The SSS is a towed-type system with six cameras arrayed on the platform. The depth rating of the system in our trial was 50 m. The length of the array baseline was 4.4 m, and six cameras were placed on the platform with equal spacing. The sea trial was conducted at Kujuku-Shima, Japan, on September 30, 2017. We successfully generated 3-D models and high-quality orthophotos of the seafloor with high resolution of about 1.5 mm/pixel. The survey efficiency of the SSS was about 7000 m2/h. In addition, the experimental results of coral-coverage estimation showed that the corals can be distinguished with accuracy of about 80% in places with relatively high transparency, and the error of coverage estimation was 10% or less. The proposed coral-coverage estimation method is more efficient than other survey techniques and costs less than AUV surveying; therefore, it is expected to become a promising tool for marine environmental surveying.
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Oku Y., Iwao K., Hoeksema B.W., Dewa N., Tachikawa H., Koido T., Fukami H.
Contributions to Zoology 89 ( 2 ) 188 - 209 2020.3
Language：English Publishing type：Research paper (scientific journal) Publisher：Contributions to Zoology
© 2020 Brill Academic Publishers. All rights reserved. Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: Attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxonomic positions. Molecular data revealed that F. fungites consists of two genetically distinct clades (A and B). Clade A is sister to a lineage including Danafungia scruposa and Halomitra pileus, while clade B formed an independent lineage genetically distant from these three species. The two morphs were also found to be included in both clades, although the attached morph was predominantly found in clade A. Morphologically, both clades were statistically different in density of septal dentation, septal number, and septal teeth shape. These results indicate that F. fungites as presently recognized is actually a species complex including at least two species. After checking type specimens, we conclude that specimens in clade A represent true F. fungites with two morphs (unattached and attached) and that all of those in clade B represent an unknown species and genus comprising an unattached morph with only one exception. These findings suggest that more unrecognized taxa with hitherto unnoticed morphological differences can be present among scleractinian corals.
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Morita M., Kitanobo S., Nozu R., Iwao K., Fukami H., Isomura N.
Coral Reefs 38 ( 6 ) 1211 - 1223 2019.12
Language：English Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. Although many sympatric species of the coral Acropora spawns on the same day, hybridization is partly prevented by their species-specific fertilization manner. On the other hand, several species show bidirectional intercrossing, but their hybridization is prevented by slight time differences in their spawning and fertilization preference with conspecific sperm. However, it is scarcely described how the intercrossing species avoid hybridization. Here we demonstrate that hybridization of the intercrossing species Acropora tenuis and A. donei is likely prevented by differences in the timing of spawning, gametogenesis (differences in production numbers of matured sperm and eggs), population density, and fertilization preferences. We investigated three locations in Okinawa, Japan: Aka Island, Sesoko Island, and Oku. The timing of gamete release in the two species overlapped at Aka Island and Oku, but A. donei did not spawn vigorously at Sesoko Island. Histological observations indicated a decrease in the number of mature sperm and eggs in the weakly spawning colonies of A. donei at Sesoko Island. From the population density, as assessed by field surveys, we predicted that the encounter rate with heterospecific gametes for A. donei around Sesoko Island was higher than at the other locations. Thus, one predictable reason for the suppression of their gonadal development may be the avoidance of hybridization. Although synchronous spawning of A. tenuis and A. donei was observed at Aka Island and Oku, hybridization is likely infrequent, because sperm choice experiments demonstrated that the eggs preferred fertilization by conspecific sperm. Moreover, microsatellite analyses suggested that hybridization rarely occurred even at synchronous spawning sites, as the population structures of the two species at both Aka Island and Oku were not mixed. Collectively, the findings of this study highlight several strategies, tactics, and mechanisms of avoiding hybridization that are likely to be active in other species that hybridize in vitro.
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宮崎県日南海岸におけるサンゴ捕食動物によるサンゴの被害とその駆除活動（2011～ 2018年）について
深見 裕伸, 安田 仁奈, 福田 道喜, 秋田 優, 日南海岸サンゴ群集保全協議会
宮崎の自然と環境 ( 4 ) 46 - 51 2019.12
Language：Japanese Publishing type：Research paper (scientific journal)
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Koido T, Imahara Y, Fukami H
ZooKeys 862 1 - 22 2019.7
Language：English Publishing type：Research paper (scientific journal)
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Maternal inheritance of F1 hybrid morphology and colony shape in the coral genus Acropora Reviewed
Fukami H, Iwao K, Kumagai NH, Morita M, Isomura N
PeerJ 7 e6429 2019.2
Language：English Publishing type：Research paper (scientific journal)
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Mizuno K., Tabeta S., Matsumoto Y., Sakamoto S., Sugimoto Y., Ogawa T., Sugimoto K., Jimenez L., Terayama K., Fukami H., Sakagami M., Deki M., Kawakubo A.
2018 OCEANS - MTS/IEEE Kobe Techno-Oceans, OCEANS - Kobe 2018 2018.12
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：2018 OCEANS - MTS/IEEE Kobe Techno-Oceans, OCEANS - Kobe 2018
© 2018 IEEE Various methods have been developed and used for monitoring marine benthic habitats, such as coral reefs and seagrass meadows. Basically, field transects, such as Line Intercept Transect (LIT), Photo Line Intercept Transect (PLIT), and Video Transect (VT), are the most widely used methods as it is easy and simple to conduct as well as less costly 1. However, these in-situ visual method requires long sampling time due to the small coverage of the methods. In addition, 3D information of the seabed cannot be obtained. On the other hand, marine biologists and ecologists have increasingly relied on imagery from platforms such as autonomous underwater vehicles (AUVs) for marine monitoring 2, 3. The underwater imagery obtained by AUVs can be used to make high quality 3D model of seabed, classify and count the abundance of various species in an area. However, the cost for development is still high and expert is necessary for the operation of vehicles. In addition, the AUV systems usually use mono or stereo cameras for the observation, therefore, the coverage of the observation is not wide
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Morpho-Molecular Evidence for Polymorphism in the Mushroom Coral Cycloseris hexagonalis (Scleractinia: Fungiidae), with a New Phylogenetic Position and the Establishment of a New Genus for the Species Reviewed
Oku, Y., Naruse, T., Fukami, H.
Zoological Science 34 ( 3 ) 242 - 251 2017.6
Language：English Publishing type：Research paper (scientific journal)
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Loss and Gain of Group I Introns in the Mitochondrial Cox1 Gene of the Scleractinia (Cnidaria; Anthozoa). Reviewed
Chuang, Y., Kitahara, M., Fukami, H., Tracey, D., Miller, D. J., Chen, C. A.
Zoological Studies 56 ( 9 ) 2017.4
Language：English Publishing type：Research paper (scientific journal)
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放卵精型のサンゴにおける受精（２）－ミドリイシ属サンゴを中心に－ Invited
北乃坊誠也, 磯村尚子, 深見裕伸, 守田昌也
みどりいし ( 28 ) 7 - 13 2017.3
Language：Japanese Publishing type：Research paper (bulletin of university, research institution)
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阿嘉島でのサンゴの交配実験 Invited
深見裕伸
みどりいし ( 28 ) 1 - 6 2017.3
Language：Japanese Publishing type：Research paper (bulletin of university, research institution)
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<i>Drupella</i> outbreak in a large coral community off the coast of Cape Toi, Miyazaki, Japan
KOIDO Tatsuki, OKU Yutaro, FUKUDA Michiyoshi, NAKANO Ayami, FUKAMI Hironobu
Galaxea, Journal of Coral Reef Studies 19 ( 1 ) 31 - 32 2017
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：日本サンゴ礁学会
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Taxonomic classification of the reef coral family Lobophylliidae (Cnidaria: Anthozoa: Scleractinia). Reviewed
Huang D, Arrigoni R, Benzoni F, Fukami H, Knowlton N, Smith ND, Stolarski J, Chou LM, Budd AF
Zoological Journal of the Linnean Society 178 436 - 481 2016.10
Language：English Publishing type：Research paper (scientific journal)
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Spawning and fertility of F<inf>1</inf>hybrids of the coral genus Acropora in the Indo-Pacific
Isomura N., Iwao K., Morita M., Fukami H.
Coral Reefs 35 ( 3 ) 851 - 855 2016.9
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
� 2016, Springer-Verlag Berlin Heidelberg. The role of hybridization through multi-specific synchronous spawning in the evolution of reef-building corals has been discussed since the 1990s, particularly for the genus Acropora. However, F1hybrids have been reported as common in only one case in the Caribbean, with no evidence of mechanisms that would allow continuous reproduction of the hybrids. In this study, we report for the first time the fecundity of two F1hybrid colonies produced experimentally from two Indo-Pacific species, A. intermedia and A. florida. These F1hybrids spawned at the same time as the parental corals. Backcrossing and F1hybrid crossing were successful in both directions. Furthermore, more than 90% self-fertilization was achieved in an F1hybrid, although it was negligible in the parental corals. While it is possible that the F1hybrid was a chimera, these results suggest that some products of interspecific hybridization may persist as the offspring of self-fertilizing F1hybrids.
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The reef building coral Acropora conditionally hybridize under sperm limitation. Reviewed
Kitanobo S, Isomura N, Fukami H, Iwao K, Morita M
Biology Letters 2016.8
Language：English Publishing type：Research paper (scientific journal)
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Genetic evidence of peripheral isolation and low diversity in marginal populations of the Acropora hyacinthus complex. Reviewed
Suzuki G, Keshavmurthy S, Hayashibara T, Wallace CC, Shirayama Y, Chen CA, Fukami H
Coral Reefs 35 1419 - 1432 2016.6
Language：English Publishing type：Research paper (scientific journal)
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When forms meet genes: revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of twonew species and one new genus. Reviewed
Arrigoni R, Benzoni F, Huang D, Fukami H, Chen CA, Berumen ML, Hoogenboom M, Thomson D, Hoeksema B, Zayasu Y, Budd AF, Terraneo TI, Kinota YF, Baird AH
Contributions to Zoology 85 ( 4 ) 2016.6
Language：English Publishing type：Research paper (scientific journal)
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Outbreak of white syndrome in Acropora spp., temperate region of Japan. Reviewed
Yamashiro H, Fukuda M, Fukami H
Marine Biodiversity 46 321 - 322 2016.6
Language：English Publishing type：Research paper (scientific journal)
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The new systematics of scleractinia: Integrating molecular and morphological evidence
Kitahara M.V., Fukami H., Benzoni F., Huang D.
The Cnidaria, past, present and Future: The World of Medusa and her Sisters 41 - 59 2016.1
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Cnidaria, past, present and Future: The World of Medusa and her Sisters
© Springer International Publishing Switzerland 2016. The taxonomy of scleractinian corals has traditionally been established based on morphology at the “macro” scale since the time of Carl Linnaeus. Taxa described using macromorphology are useful for classifying the myriad of growth forms, yet new molecular and small-scale morphological data have challenged the natural historicity of many familiar groups, motivating multiple revisions at every taxonomic level. In this synthesis of scleractinian phylogenetics and systematics, we present the most current state of affairs in the field covering both zooxanthellate and azooxanthellate taxa, focusing on the progress of our phylogenetic understanding of this ecologically-significant clade, which today is supported by rich sets of molecular and morphological data. It is worth noting that when DNA sequence data was first used to investigate coral evolution in the 1990s, there was no concerted effort to use phylogenetic information to delineate problematic taxa. In the last decade, however, the incompatibility of coral taxonomy with their evolutionary history has become much clearer, as molecular analyses for corals have been improved upon technically and expanded to all major scleractinian clades, shallow and deep. We describe these methodological developments and summarise new taxonomic revisions based on robust inferences of the coral tree of life. Despite these efforts, there are still unresolved sections of the scleractinian phylogeny, resulting in uncertain taxonomy for several taxa. We highlight these and propose a way forward for the taxonomy of corals.
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IMAMIYA Noriko, MORI Yukiko, TSUZUKI Akiko, UENO Ryo, FUKAMI Hironobu, NAKAYAMA Hayashi
Proceedings of the Annual Meeting of Japan Society for Science Education 40 ( 0 ) 431 - 432 2016
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Japan Society for Science Education
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Influence of sperm dilution and gamete contact time on the fertilization rate of scleractinian corals Reviewed
Nozawa Y, Isomura N, Fukami H
Coral Reefs 34 ( 4 ) 1199 - 1206 2015.8
Language：English Publishing type：Research paper (scientific journal)
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Huang D., Benzoni F., Arrigoni R., Baird A., Berumen M., Bouwmeester J., Chou L., Fukami H., Licuanan W., Lovell E., Meier R., Todd P., Budd A.
Zoologica Scripta 43 ( 5 ) 531 - 548 2014.9
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Zoologica Scripta
Recent advances in scleractinian systematics and taxonomy have been achieved through the integration of molecular and morphological data, as well as rigorous analysis using phylogenetic methods. In this study, we continue in our pursuit of a phylogenetic classification by examining the evolutionary relationships between the closely related reef coral genera Merulina, Goniastrea, Paraclavarina and Scapophyllia (Merulinidae). In particular, we address the extreme polyphyly of Favites and Goniastrea that was discovered a decade ago. We sampled 145 specimens belonging to 16 species from a wide geographic range in the Indo-Pacific, focusing especially on type localities, including the Red Sea, western Indian Ocean and central Pacific. Tree reconstructions based on both nuclear and mitochondrial markers reveal a novel lineage composed of three species previously placed in Favites and Goniastrea. Morphological analyses indicate that this clade, Paragoniastrea Huang, Benzoni & Budd, gen. n., has a unique combination of corallite and subcorallite features observable with scanning electron microscopy and thin sections. Molecular and morphological evidence furthermore indicates that the monotypic genus Paraclavarina is nested within Merulina, and the former is therefore synonymised. © 2014 Royal Swedish Academy of Sciences.
DOI： 10.1111/zsc.12061
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A phylogeny reconstruction of the Dendrophylliidae (Cnidaria, Scleractinia) based on molecular and micromorphological criteria, and its ecological implications Reviewed
R Arrigoni, YF Kitano, J Stolarski, BW Hoeksema, H Fukami, F Stefani, P Galli, S Montano, E Castoldi, F Benzoni
Zoologica Scripta 43 661 - 688 2014.6
Language：English Publishing type：Research paper (scientific journal)
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A Phylogeny of the Family Poritidae (Cnidaria, Scleractinia) Based on Molecular and Morphological Analyses Reviewed
YF Kitano, F Benzoni, R Arrigoni, Y Shirayama, CC Wallace, H Fukami
PloS one 9 e98406 2014.5
Language：English Publishing type：Research paper (scientific journal)
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Taxonomic classification of the reef coral families Merulinidae, Montastraeidae, and Diploastraeidae (Cnidaria: Anthozoa: Scleractinia) Reviewed
H Danwei, F Benzoni, H Fukami, N Knowlton, ND Smith, AF Budd
Zoological Journal of the Linnean Society 171 277 - 355 2014.5
Language：English Publishing type：Research paper (scientific journal)
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Lin M., Kitahara M., Luo H., Tracey D., Geller J., Fukami H., Miller D., Chen C.
Genome Biology and Evolution 6 ( 5 ) 1086 - 1095 2014.5
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Genome Biology and Evolution
Corallimorpharia is a small Order of skeleton-less animals that is closely related to the reef-building corals (Scleractinia) and of fundamental interest in the context of understanding the potential impacts of climate change in the future on coral reefs. The relationship between the nominal Orders Corallimorpharia and Scleractinia is controversial the former is either the closest outgroup to the Scleractinia or alternatively is derived from corals via skeleton loss. This latter scenario, the "naked coral" hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences. The "naked coral" hypothesis seeks to link skeleton loss in the putative ancestor of corallimorpharians with a period of elevated oceanic CO2during the Cretaceous, leading to the idea that these skeleton-less animals may be harbingers for the fate of coral reefs under global climate change. In an attempt to better understand their evolutionary relationships, we examined mt genome organization in a representative range (12 species, representing 3 of the 4 extant families) of corallimorpharians and compared these patterns with other Hexacorallia. The most surprising finding was that mt genome organization in Corallimorphusprofundus, a deep-water species that is the most scleractinian-like of all corallimorpharians on the basis of morphology, was much more similar to the common scieractinian pattern than to those of other corallimorpharians. This finding is consistent with the idea that C. profundus represents a key position in the coral-corallimorpharian transition. © 2014 The Author(s).
DOI： 10.1093/gbe/evu084
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Taguchi T., Mezaki T., Iwase F., Sekida S., Kubota S., Fukami H., Okuda K., Shinbo T., Oshima S., Liguni Y., Testa J., Tominaga A.
Zoological Science 31 ( 2 ) 89 - 94 2014.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Zoological Science
We performed a molecular cytogenetic investigation of the scleractinian coral Acropora solitaryensis, which is dominant in the temperate region of Japan (30-35°N). Molecular cytogenetic analysis, using fluorescence in situ hybridization (FISH), was carried out for karyotyping and gene mapping. We propose the karyotype of this coral (2n = 30) based on C-banding and FISH analyses. FISH mapping of the rRNA gene was carried out with a probe generated by PCR amplification using rRNA gene primers. Furthermore, the telomeres and centromeres of all chromosomes were visualized using FISH. By comparative genomic hybridization using DNA from sperm and unfertilized eggs of this coral, we offer evidence suggesting the existence of sex chromosomes in this species. Collectively, these data advance our understanding of coral genetics. © 2014 Zoological Society of Japan.
DOI： 10.2108/zsj.31.89
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Distribution and reproduction of the temperate-specific morphotype of the coral Favites flexuosa in the subtropical region, Lyudao, Taiwan Reviewed
N Isomura, Y Nozawa, H Fukami
Invertebrate Reproduction & Development 58 176 - 178 2014.1
Language：English Publishing type：Research paper (scientific journal)
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Comparative Embryology of Eleven Species of Stony Corals (Scleractinia) Reviewed
N Okubo, T Mezaki, Y Nozawa, Y Nakano, Y-T Lien, H Fukami, DC Hayward, EE Ball
PLoS ONE 8 ( 12 ) e84115 2013.12
Language：English Publishing type：Research paper (scientific journal)
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Y F Kitano, M Obuchi, D Uyeno, K Miyazaki, H Fukami
Zoological Studies 52 25 2013.10
Language：English Publishing type：Research paper (scientific journal)
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Y-T Lien, H Fukami, Y Yamashita
Fisheries Science 2013.4
Language：English Publishing type：Research paper (scientific journal)
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Species-diverse coral communities on an artificial substrate at a tuna farm in Amami, Japan Reviewed
H Hata, I Hirabayashi, H Hamaoka, Y Mukai, K Omori, H Fukami
Marine Environmental Reseach 85 45 - 53 2013.4
Language：English Publishing type：Research paper (scientific journal)
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Isomura N., Iwao K., Fukami H.
PLoS ONE 8 ( 2 ) 2013.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：PLoS ONE
Natural hybridization of corals in the Indo-Pacific has been considered rather rare. However, field studies have observed many corals with intermediate interspecific or unusual morphologies. Given that the existence of F1 hybrids with intermediate interspecific morphologies has been proven in the Caribbean, hybrids may also inhabit the Indo-Pacific and occur more frequently than expected. In this study, we focused on two morphologically different species, Acropora florida and A. intermedia, and performed crossing experiments at Akajima Island, Japan. Results showed that these species could hybridize in both directions via eggs and sperm, but that fertilization rates significantly differed according to which species provided eggs. These results are similar to those reported from the Caribbean. Although all embryos developed normally to the planular larval stage, the developmental processes of some hybrid embryos were delayed by approximately 1 h compared with conspecific embryos, suggesting that fertilization occurred 1 h later in interspecific crosses than in intraspecific crosses. More successful hybridization could occur under conditions with low numbers of conspecific colonies. Additionally, a comparison of survival rates between hybrid and intraspecific larvae revealed that intra- and interspecific larvae produced from eggs of A. florida survived for significantly longer than those produced from eggs of A. intermedia. Considering these data, under specific conditions, hybrids can be expected to be produced and survive in nature in the Pacific. Furthermore, we identified one colony with intermediate morphology between A. florida and A. intermedia in the field. This colony was fertilized only by eggs of A. florida, with high fertilization rates, suggesting that this colony would be a hybrid of these two species and might be backcrossed. © 2013 Isomura et al.
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Lien Y., Keshavmurthy S., Nakano Y., Plathong S., Huang H., Hsu C., Fukami H., Yamashita Y., Hsieh H., Wang J., Chen C.
Marine Ecology Progress Series 473 163 - 177 2013.1
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Marine Ecology Progress Series
Determination of the genetic diversity and structure of coral populations across their biogeographic range must include the investigation of the coral host and its associated Symbiodinium. We examined the genetic similarity of the stress-tolerant coral Oulastrea crispata and the diversity of Symbiodinium D across part of their geographic distribution, which ranges across 5800 km in the West Pacific from tropical Thailand (̃7° N) to the outlying regions of temperate Japan (36°N). FST-statistics and AMOVA of directly sequenced coral ribosomal internal transcribed spacer (ITS) DNA sequences showed a high genetic homogeneity between temperate and subtropical populations, but showed a significant difference between temperate and subtropical populations and their tropical counterparts. Denaturing gradient gel electrophoresis (DGGE) of ITS DNA sequences identified 4 major O. crispata-associated Symbiodinium D types: D8, D8-12, D12-13, and D15; these were found in the regions extending from tropical Thailand towards the high latitude regions of Japan. FST-statistics and AMOVA of Symbiodinium ITS showed significant differences between tropical, subtropical, and temperate regions, with the D8 and D8-12 dominant in the tropical and subtropical regions, the D12-13 endemic in the subtropical northern South China Sea, and D15 restricted to the high-latitudinal outlying coral communities. Consistent variation in environmental factors, such as temperature and light, may have driven the regional -specific divergence of the Symbiodinium D types, suggesting that habitat-specific Symbiodinium types can assist O. crispata in acclimating to the environmental fluctuations found in the marginal range of coral distribution. © Inter-Research 2013.
DOI： 10.3354/meps10041
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Relationship between host genetics and Symbiodinium D diversity in a stress-tolerant scleractinian coral, Oulastrea crispata, in the West Pacific Reviewed
Y-T Lien, S Keshavmurthy, Y Nakano, S Plathong, H Huang, C-m Hsu, H Fukami, Y Yamashita, H J Hsieh, J-T Wang, CA Chen
Marine Ecology Progress Series 473 163 - 177 2013.1
Language：English Publishing type：Research paper (scientific journal)
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Taxonomy and ecology of the genus Isopora (Acroporidae, Scleractinia)
FUKAMI Hironobu, ISOMURA Naoko, IWAO Kenji, TACHIKAWA Hiroyuki
Journal of the Japanese Coral Reef Society 15 ( 1 ) 1 - 14 2013
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
The family Acroporidae (Scleractinia) formerly contained four genera such as <i>Acropora</i>, <i>Anacropora</i>, <i>Astreopora</i>, and <i>Montipora</i> (for examples, Veron and Wallace 1984; Nishihira and Veron 1995; Veron 2000). Recently, Wallace et al. (2007) has elevated the subgenus <i>Isopora</i>, which was one of two subgenera in the genus <i>Acropora</i>, to genus, based on the morphological, ecological and molecular data. Then number of genera in the Acroporidae becomes five. Nevertheless, in Japan, this fact is not generally known and the genus name <i>Acropora</i> is still applied to the species, which should belong to the new genus <i>Isopora</i>. In this paper, to make public the name of the genus <i>Isopora</i>, and to propose the Japanese name of this genus, we summarize the morphological and ecological characters of this genus. The contents of this paper are mainly based on Wallace et al. (2007). In addition, we show morphological and ecological data from samples of <i>Isopora</i> that were collected in Japan. On the basis of the International Code of Zoological Nomenclature (Art. 69.2.2), we note that type species of <i>Isopora</i> is <i>Madrepora labrosa</i> Dana, 1846, not <i>Astrea palifera</i> Lamarck, 1816.
DOI： 10.3755/jcrs.15.1
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Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia). Reviewed
A F Budd, H Fukami, N D Smith, N Knowlton
Zoological Journal of the Linnean Society 166 465 - 529 2012.10
Language：English Publishing type：Research paper (scientific journal)
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Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications. Reviewed
M-F Lin, MV Kitahara, H Tachikawa, H Fukami, DJ Miller, CA Chen
Molecular Phylogenetics and Evolution 65 323 - 328 2012.10
Language：English Publishing type：Research paper (scientific journal)
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Goniopora spp. collected at Akajima Island
Hironobu Fukami, Yuko Kitano
( 23 ) 4 - 7 2012.4
Language：Japanese Publishing type：Research paper (other academic)
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Symbiodinium Clade C Dominates Zooxanthellate Corals (Scleractinia) in the Temperate Region of Japan Reviewed
Y.-T. Lien, H. Fukami, Y. Yamashita
Zoological Science 29 173 - 180 2012.3
Language：English Publishing type：Research paper (scientific journal)
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Evidence of Genetic and Reproductive Isolation between Two Morphs of Subtropical-Dominant Coral Acropora solitaryensis in the Non-Reef Region of Japan Reviewed
Go Suzuki, Hironobu Fukami
Zoological Science 29 134 - 140 2012.2
Language：English Publishing type：Research paper (scientific journal)
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Preface : Introduction of Dr. Siro Kawaguti (1908-2004)
YAMASHIRO Hideyuki, FUKAMI Hironobu
Galaxea, Journal of Coral Reef Studies 14 ( 0 ) 3 - 4 2012
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
DOI： 10.3755/galaxea.14.3
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Volcanic ashfall preserved in the skeleton of Acropora
YAMASHIRO Hideyuki, FUKAMI Hironobu
Galaxea, Journal of Coral Reef Studies 14 ( 1 ) 3 - 4 2012
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
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日本における造礁性イシサンゴ類の同定の現状とその分類学的問題点（共著） Reviewed
深見裕伸, 立川浩之, 鈴木 豪, 永田俊輔, 杉原 薫
日本サンゴ礁学会誌 12 1 - 15 2011.5
Language：Japanese Publishing type：Research paper (scientific journal)
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Huang D., Licuanan W., Baird A., Fukami H.
BMC Evolutionary Biology 11 ( 1 ) 2011.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：BMC Evolutionary Biology
Background. Molecular phylogenetic studies on scleractinian corals have shown that most taxa are not reflective of their evolutionary histories. Based principally on gross morphology, traditional taxonomy suffers from the lack of well-defined and homologous characters that can sufficiently describe scleractinian diversity. One of the most challenging clades recovered by recent analyses is 'Bigmessidae', an informal grouping that comprises four conventional coral families, Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae, interspersed among one another with no apparent systematic pattern. There is an urgent need for taxonomic revisions in this clade, but it is vital to first establish phylogenetic relationships within the group. In this study, we reconstruct the evolutionary history of 'Bigmessidae' based on five DNA sequence markers gathered from 76 of the 132 currently recognized species collected from five reef regions in the central Indo-Pacific and the Atlantic. Results. We present a robust molecular phylogeny of 'Bigmessidae' based on the combined five-gene data, achieving a higher degree of resolution compared to previous analyses. Two Pacific species presumed to be in 'Bigmessidae' are more closely related to outgroup clades, suggesting that other unsampled taxa have unforeseen affinities. As expected, nested within 'Bigmessidae' are four conventional families as listed above, and relationships among them generally corroborate previous molecular analyses. Our more resolved phylogeny supports a close association of Hydnophora (Merulinidae) with Favites + Montastraea (Faviidae), rather than with the rest of Merulinidae, i.e., Merulina and Scapophyllia. Montastraea annularis, the only Atlantic 'Bigmessidae' is sister to Cyphastrea, a grouping that can be reconciled by their septothecal walls, a microstructural feature of the skeleton determined by recent morphological work. Characters at the subcorallite scale appear to be appropriate synapomorphies for other subclades, which cannot be explained using macromorphology. Indeed, wide geographic sampling here has revealed more instances of possible cryptic taxa confused by evolutionary convergence of gross coral morphology. Conclusions. Numerous examples of cryptic taxa determined in this study support the assertion that diversity estimates of scleractinian corals are erroneous. Fortunately, the recovery of most 'Bigmessidae' genera with only minor degrees of paraphyly offers some hope for impending taxonomic amendments. Subclades are well defined and supported by subcorallite morphological features, providing a robust framework for further systematic work. © 2011 Huang et al; licensee BioMed Central Ltd.
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Seasonal changes in fish assemblages in an area of hermatypic corals in Yokonami, Tosa Bay, Japan.
Hirata Tomonori, Oguri Sosuke, Hirata Shiori, Fukami Hironobu, Nakamura Yohei, Yamaoka Kosaku
Jpn. J. Ichthyol. 58 ( 1 ) 49 - 64 2011
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Ichthyological Society of Japan
A monthly underwater visual census was conducted in the coral-dominated habitat of Yokonami, Tosa Bay, Japan, from June 2006 to January 2009. A total of 12,586 individuals belonging to 168 species in 43 families were recorded during the study period. The number of species and individuals increased from June-August (summer), the highest numbers occurring in September-December (autumn), thereafter decreasing from January (winter) to the lowest point in May (spring). Labridae was the most dominant family in terms of species numbers (28 species), followed by Chaetodontidae (21 species) and Pomacentridae (18 species). In terms of individual numbers, Chaetodontidae was the most abundant (56.3% of total individual numbers), followed by Labridae (15%) and Pomacentridae (12.5%). The most dominant species were Chaetodon speculum (33.4%), Pomacentrus coelestis (11.1%), and C. lunulatus (8.2%). The fish assemblage was divided into 4 groups: (1) temperate fishes (1877 individuals in 26 species), (2) (sub-)tropical fishes (10,648 individuals in 136 species), (3) temperate-tropical fishes (28 individuals in 2 species), (4) unknown fishes (33 individuals in 4 species). Species and individual numbers of temperate fishes were high in summer and low in winter, whereas those of tropical fishes were high in summer and autumn and low in spring, suggesting that typhoons in summer and autumn, and low water temperatures in winter might affect fish recruitment and community density. Moreover, at least 44 tropical species were observed throughout the year during the study period.
DOI： 10.11369/jji.58.49
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和歌山産ヒラタオオトゲキクメイシに見られる生時の形態多型は種内変異か種間変異か？（共著） Reviewed
座安佑奈, 野村恵一, 鈴木豪, 白山義久, 深見裕伸
日本サンゴ礁学会誌 11 25 - 31 2010.8
Language：Japanese Publishing type：Research paper (scientific journal)
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和歌山産タカクキクメイシMontastraea valenciennesi（Milne Edwards and Haime, 1848）の隠蔽種の存在（共著） Reviewed
深見裕伸, 野村恵一
日本サンゴ礁学会誌 11 25 - 31 2010.8
Language：Japanese Publishing type：Research paper (scientific journal)
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FUKAMI Hironobu, TACHIKAWA Hiroyuki, SUZUKI Go, NAGATA Shunsuke, SUGIHARA Kaoru
Journal of the Japanese Coral Reef Society 12 17 - 31 2010
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：The Japanese Coral Reef Society
Morphological classification of zooxanthellate (hermatypic) corals (hereafter corals) in the Screlactinia is currently based on skeletal features of the corallite and colony forms. These corals, however, have few taxonomically significant morphological characteristics because such characters show polymorphism, intraspecific variation, and phenotypic plasticity in response to environmental factors. Quantitative description of taxonomic features that comprise differences between morphologically similar genera and/or species is challenging. Recently in Japan, picture books and identification guides of the corals that focus mainly on their living features have become popular. These publications promote awareness of the corals, but they have decreased attention to the skeletal features of corals. A number of these publications do not adhere to the International Code of Zoological Nomenclature, especially with regard to scientific names, thereby reducing the current stability of coral taxonomy. This complicates the effort to obtain a consensus on the taxonomic identification of coral species, which is important for comparing results of studies, past and present. Application of molecular phylogenetic analyses to corals has provided useful information for understanding the relationships among closely related families and/or genera as well as neighboring species in the same genus. These analyses should be used to revise the traditional taxonomic scheme, which is based only on morphological characteristics. Compounding the difficulty, past studies may also have used misidentified coral species. To establish greater taxonomic consistency among coral species, the morphological characteristics used for traditional taxonomy should be quantitatively compared among closely related species. Identification of new morphological characteristics of the external or internal skeletal structures of colony and/or corallite that are consistent with available phylogenetic evidence is also necessary. Because of the possibility of misidentification, efforts should be taken to retain samples of soft tissues of these species as well as skeletal specimens of their corallite and/or colonies.
DOI： 10.3755/jcrs.12.17
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Fukami H., Chen C., Budd A., Collins A., Wallace C., Chuang Y., Chen C., Dai C., Iwao K., Sheppard C., Knowlton N.
PLoS ONE 3 ( 9 ) 2008.9
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：PLoS ONE
Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (β-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.
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Re-evaluation of the systematics of the endemic corals of Brazil by molecular data
Nunes F., Fukami H., Vollmer S., Norris R., Knowlton N.
Coral Reefs 27 ( 2 ) 423 - 432 2008.6
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Recent genetic work on various coral genera has shown that morphological convergence between Atlantic and Pacific corals obscures evolutionary relationships and inferred levels of endemicity between the regions. Based on DNA sequences from nuclear and mitochondrial loci that provide higher resolution than those previously presented, this study shows that relationships within parts of the Atlantic coral fauna are also in need of substantial revision. The data presented here indicate that (1) the endemic Brazilian genus Mussismilia is a monophyletic clade, (2) Mussismilia is more closely related to the Caribbean Faviidae than Mussidae, the family in which it is currently placed, (3) the Brazilian endemic coral Favia leptophylla is much more closely related to Mussismilia than other species of Favia and has most likely been incorrectly placed in the genus Favia and (4) the other endemic Favia species found in Brazil, Favia gravida, is genetically distinct from Favia fragum, a Caribbean congener with which it is frequently synonymized. The nuclear data also suggest the possible presence of a cryptic species within Mussismilia, but additional sampling and morphological information is required to confirm this finding. © 2008 Springer-Verlag.
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Suzuki G., Hayashibara T., Shirayama Y., Fukami H.
Marine Ecology Progress Series 355 149 - 159 2008.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Marine Ecology Progress Series
One of the most abundant genera of scleractinian corals, Acropora, shows considerable zonation along reef slopes. The zones are thought to be established by both selective larval settlement and post-settlement selection. The latter has been credited as more important, possibly due to the obvious relationship between colony shapes and habitat-specific environmental stress. However, there is no evidence that the former has less influence on the creation of the zones. To test the hypothesis that larvae settle selectively on species-specific suitable habitat, we identified recruits using mitochondrial and nuclear molecular markers. A 2-step molecular sorting process successfully identified the 7 most dominant species in the area. Comparing the species composition of 3 different depths, the distribution of the settlement of the 3 dominant species A. digitifera, A. hyacinthus and A. tenuis was significantly related to adult zonation, suggesting that Acropora larvae selectively settle on the suitable habitat. This is the first in situ evidence showing selective settlement of coral larvae, and from it we can conclude that the initial stage of the life cycle plays an important role in establishing habitat segregation at the species level in Acropora. © Inter-Research 2008.
DOI： 10.3354/meps07253
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Kishida T., Kubota S., Shirayama Y., Fukami H.
Biology Letters 3 ( 4 ) 428 - 430 2007.8
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Biology Letters
An olfactory receptor (OR) multigene family is responsible for the well-developed sense of smell possessed by terrestrial tetrapods. Mammalian OR genes had diverged greatly in the terrestrial environment after the fish-tetrapod split, indicating their importance to land habitation. In this study, we analysed OR genes of marine tetrapods (minke whale Balaenoptera acutorostrata, dwarf sperm whale Kogia sima, Dall's porpoise Phocoenoides dalli, Steller's sea lion Eumetopias jubatus and loggerhead sea turtle Caretta caretta) and revealed that the pseudogene proportions of OR gene repertoires in whales were significantly higher than those in their terrestrial relative cattle and also in sea lion and sea turtle. On the other hand, the pseudogene proportion of OR sequences in sea lion was not significantly higher compared with that in their terrestrial relative (dog). It indicates that secondary perfectly adapted marine vertebrates (cetaceans) have lost large amount of their OR genes, whereas secondary-semi-adapted marine vertebrates (sea lions and sea turtles) still have maintained their OR genes, reflecting the importance of terrestrial environment for these animals. © 2007 The Royal Society.
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Wallace C., Chen C., Fukami H., Muir P.
Coral Reefs 26 ( 2 ) 231 - 239 2007.6
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Many attempts have been made to recognise divisions within Acropora, the most diverse reef building coral genus on modern reefs, but only subgenera Acropora and Isopora are currently recognised. In this paper, morphological and genetic analyses, and study of reproductive mode and anatomy, demonstrate that an endemic Indonesian species A. (Acropora) togianensis, Wallace, 1997, belongs to Isopora. Despite the presence of a clear central axial corallite (indicating sub-genus Acropora), this species has supplementary axial corallites, broods planula larvae rather than broadcast-spawning for external fertilisation and develops stalked ova: all characters in common with the type species of subgenus Isopora A. (Isopora) palifera and the other species for which such data are available, A. (I.) cuneata and A. (I.) brueggemanni. Phylogenies are based on the protein-coding genes, mitochondrial cytochrome b (cytb) and nuclear histone 2a and 2b (h2ab) also group A. togianensis with these Isoporans. High bootstrapping and Bayesian support in the major lineages of the family Acroporidae demonstrate significant differences between Isopora (including A. togianensis) and Acropora. As the type species of both subgenera, A. (Acropora) muricata (Linneaus 1758) and A. (Isopora) palifera (Lamarck, 1816) are used in these analyses, elevation of Isopora Studer, 1878 to genus is formally proposed. © 2007 Springer-Verlag.
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Fukami H., Chen C., Chiou C., Knowlton N.
Journal of Molecular Evolution 64 ( 5 ) 591 - 600 2007.5
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Journal of Molecular Evolution
Analyses of mitochondrial sequences revealed the existence of a group I intron in the cytochrome oxidase subunit 1 (cox1) gene in 13 of 41 genera (20 out of 73 species) of corals conventionally assigned to the suborder Faviina. With one exception, phylogenies of the coral cox1 gene and its intron were concordant, suggesting at most two insertions and many subsequent losses. The coral introns were inferred to encode a putative homing endonuclease with a LAGLI-DADG motif as reported for the cox1 group I intron in the sea anemone Metridium senile. However, the coral and sea anemone cox1 group I introns differed in several aspects, such as the intron insertion site and sequence length. The coral cox1 introns most closely resemble the mitochondrial cox1 group I introns of a sponge species, which also has the same insertion site. The coral introns are also more similar to the introns of several fungal species than to that of the sea anemone (although the insertion site differs in the fungi). This suggests either a horizontal transfer between a sponge and a coral or independent transfers from a similar fungal donor (perhaps one with an identical insertion site that has not yet been discovered). The common occurrence of this intron in corals strengthens the evidence for an elevated abundance of group I introns in the mitochondria of anthozoans. © 2007 Springer Science+Business Media, LLC.
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Lien Y., Nakano Y., Plathong S., Fukami H., Wang J., Chen C.
Coral Reefs 26 ( 1 ) 35 - 44 2007.3
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Biogeographic investigations have suggested that coral-symbiont associations can adapt to higher temperatures by hosting a heat-tolerant Symbiodinium, phylotype D. It is hypothesized that phylotype D is absent in high latitudes due to its heat-tolerant characteristics. In this study, this hypothesis was tested by examining the symbiont diversity in a scleractinian coral, Oulastrea crispata, throughout its entire latitudinal distribution range in the West Pacific. Molecular phylotyping of the 5′-end of the nuclear large subunit of ribosomal DNA (lsu rDNA) indicated that phylotype D was the dominant Symbiodinium in O. crispata from the tropical reefs to the marginal non-reefal coral communities. Several colonies of tropical populations were associated with phylotype C, either alone or simultaneously with phylotype D. Analysis of the polymerase chain reaction products using single-strand conformation polymorphism (SSCP) detected relatively low densities of phylotype C in most of the O. crispata colonies surveyed. These results provide evidence for the occurrence of phylotype D in cold-water outlying coral communities. The dominant occurrence of phylotype C in some O. crispata colonies on tropical reefs and the relatively low densities of phylotype C identified by SSCP in subtropical and temperate populations show that the dominant symbiont type can vary in this coral species and that multiple symbionts can co-occur in the same host. © 2007 Springer-Verlag.
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和歌山県田辺湾沿岸海域で1931年から2005年までに記録された造礁性イシサンゴ類（刺胞動物門、花虫綱、六放サンゴ亜綱）の目録
久保田 信, 深見裕伸, 内田紘臣
瀬戸臨海実験所年報 18 32 - 36 2005.12
Language：Japanese Publishing type：Research paper (bulletin of university, research institution)
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Fukami H., Knowlton N.
Coral Reefs 24 ( 3 ) 410 - 417 2005.11
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Coral Reefs
Complete mitochondrial nucleotide sequences of two individuals each of Montastraea annularis, Montastraea faveolata, and Montastraea franksi were determined. Gene composition and order differed substantially from the sea anemone Metridium senile, but were identical to that of the phylogenetically distant coral genus Acropora. However, characteristics of the non-coding regions differed between the two scleractinian genera. Among members of the M. annularis complex, only 25 of 16,134 base pair positions were variable. Sixteen of these occurred in one colony of M. franksi, which (together with additional data) indicates the existence of multiple divergent mitochondrial lineages in this species. Overall, rates of evolution for these mitochondrial genomes were extremely slow (0.03-0.04% per million years based on the fossil record of the M. annularis complex). At higher taxonomic levels, patterns of genetic divergence and synonymous/nonsynonymous substitutions suggest non-neutral and unequal rates of evolution between the two lineages to which Montastraea and Acropora belong. © Springer-Verlag 2005.
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イシサンゴ類の系統分類：分子系統解析と形態分類の不一致
深見裕伸
みどりいし 16 5 - 9 2005.3
Language：Japanese Publishing type：Research paper (other academic)
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ミドリイシサンゴにおける産卵タイミングと生殖隔離
服田昌之，深見裕伸
みどりいし ( 15 ) 23 - 25 2004.3
Language：Japanese Publishing type：Research paper (other academic)
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Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals
Fukami H., Budd A., Paulay G., Solé-Cava A., Chen C., Iwao K., Knowlton N.
Nature 427 ( 6977 ) 832 - 835 2004.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Nature
Only 17% of 111 reef-building coral genera and none of the 18 coral families with reef-builders are considered endemic to the Atlantic, whereas the corresponding percentages for the Indowest Pacific are 76% and 39%. These figures depend on the assumption that genera and families spanning the two provinces belong to the same lineages (that is, they are monophyletic). Here we show that this assumption is incorrect on the basis of analyses of mitochondrial and nuclear genes. Pervasive morphological convergence at the family level has obscured the evolutionary distinctiveness of Atlantic corals. Some Atlantic genera conventionally assigned to different families are more closely related to each other than they are to their respective Pacific 'congeners'. Nine of the 27 genera of reef-building Atlantic corals belong to this previously unrecognized lineage, which probably diverged over 34 million years ago. Although Pacific reefs have larger numbers of more narrowly distributed species, and therefore rank higher in biodiversity hotspot analyses, the deep evolutionary distinctiveness of many Atlantic corals should also be considered when setting conservation priorities.
DOI： 10.1038/nature02339
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Fukami H., Budd A., Levitan D., Jara J., Kersanach R., Knowlton N.
Evolution 58 ( 2 ) 324 - 337 2004.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Evolution
The three members of the Montastraea annularis complex (M. annularis, M. franksi, and M. faveolata) are dominant reef builders in the western Atlantic whose species status has been controversial for over a decade. Although differences in colony morphology and reproductive characteristics exist, interspecific fertilizations are possible in the laboratory and genetic differentiation is slight. Here we compare the three taxa genetically and morphologically in Panama and the Bahamas, widely separated locations spanning most of their geographic ranges. In Panama, analyses of three AFLP loci, a noncoding region of the mitochondrial genome, and ITS sequences reveal that M. faveolata is strongly differentiated genetically. Discriminant function analysis also indicates no overlap with the other two species in the fine structure of the corallites that comprise the colony. Genetic analyses of larvae from interspecific crosses between M. faveolata and the other two taxa confirmed the hybrid status of the larvae, but no examples of the most probable F1genotype were observed in the field. Although M. annularis and M. franksi were more similar, they also exhibited strong frequency differences at two AFLP loci and in the mitochondrial noncoding region, as well as distinct corallite structure. In the Bahamas, in contrast, the three taxa exhibited overlapping morphologies. Montastraea franksi and M. annularis were indistinguishable genetically, and M. faveolata was distinct at fewer genetic loci. Once again, however, the most probable F1genotype involving M. faveolata was not observed. Geographic differences between Panama and the Bahamas explain why past studies have come to different conclusions concerning the status of the three species. In general, the genetic and morphological data suggest a north to south hybridization gradient, with evidence for introgression strongest in the north. However, reproductive data show no such trend, with intrinsic barriers to gene flow comparable or stronger in the north.
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Levitan D., Fukami H., Jara J., Kline D., McGovern T., McGhee K., Swanson C., Knowlton N.
Evolution 58 ( 2 ) 308 - 323 2004.2
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Evolution
Many coral species spawn simultaneously and have compatible gametes, leading to controversy over the nature of species boundaries and the frequency with which hybridization occurs. Three western Atlantic corals, Montastraea annularis, M. faveolata, and M. franksi, typify this controversy; they all spawn sympatrically on the same evenings after the fall full moons. Here we show, in both Panama and the Bahamas for multiple years, how a variety of mechanisms may act in concert to reproductively isolate all three species. Field studies indicate that M. franksi spawns two hours earlier than the other two species, and the eggs released during this earlier period disperse an average of 500 m by the time the other species spawn. Field measures of fertilization indicate that peak fertilization occurs when spawning synchrony is high and that corals that spawn at the tails of the spawning distributions have greatly reduced fertilization success. Laboratory studies indicate that there is a gametic incompatibility between M. faveolata and the other two species. There are regional differences in the gametic compatibility of M. franksi and M. annularis. In Panama, the two species are completely compatible, whereas in the Bahamas, M. franksi sperm can fertilize M. annularis eggs but the reciprocal cross often fails. Gamete age influences patterns of fertilization, such that very young eggs seem resistant to fertilization and old sperm lose viability after two hours. In sum, the combination of temporal differences in spawning, sperm aging, gamete dispersal and dilution, and gametic incompatibility act in various combinations among the three species, making it unlikely that hybrid fertilization would occur.
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Ecological and genetic aspects of reproductive isolation by different spawning times in Acropora corals Reviewed
H Fukami, M Omori, K Shimoike, T Hayashibara, M Hatta
Marine Biology 142 679 - 684 2003.2
Language：English Publishing type：Research paper (scientific journal)
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Reticulate evolution of corals
M Hatta, H Fukami
Natural Science Report, Ochanomizu University 53 67 - 69 2002.6
Language：English Publishing type：Research paper (bulletin of university, research institution)
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Omori M., Fukami H., Kobinata H., Hatta M.
Limnology and Oceanography 46 ( 3 ) 704 - 706 2001.5
Language：Japanese Publishing type：Research paper (scientific journal) Publisher：Limnology and Oceanography
In June 1999, after devastating coral bleaching in 1998, laboratory fertilization of Acropora nasuta, one of the most abundant reef-building corals in Okinawa, Japan, decreased significantly from usual rates (>94%) to an average of 42% at a sperm concentration of 105ml-1. Similar decreases were observed in four other mass-spawning acroporid corals. We also found a decrease in sperm motility in the laboratory. A series of experiments to determine the effects of sperm concentration on fertilization rates revealed that sperm of 107ml-1was needed to obtain a rate >80%. Sperm concentration in surface seawater during mass spawning was highest within 1.0 h of spawning but decreased sharply thereafter. These results suggest that gamete dilution plays an important role in limiting the fertilization of coral eggs in the sea. As successful fertilization appears to have been much lower in 1999, we suspect that production of new coral recruits was also reduced greatly. Current and future sea-temperature increases thus pose a severe potential threat to coral reefs by increasing the frequency of coral bleaching and consequently leading to further declines of coral recruitment and hence, reef corals.
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Phylogenetic Relationships in the Coral Family Acroporidae, Reassessed by Inference from Mitochondrial Genes Reviewed
H Fukami, M Hatta, M Omori
Zoological Science 17 689 - 696 2000.6
Language：English Publishing type：Research paper (scientific journal)
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Mass spawning facilitates reticulate evolution in reef-building corals
M Hatta, H Fukami
Journal of Reproduction & Development, supplment 46 2000.3
Language：English Publishing type：Research paper (international conference proceedings)
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Reproductive and Genetic Evidence for a Reticulate Evolutionary History of Mass-Spawning Corals Reviewed
M Hatta, H Fukami, W Wang, M Omori, K Shimoike, T Hayashibara, Y Ina, T Sugiyama
Molecular Biology and Evolution 16 1607 - 1613 1999.11
Language：English Publishing type：Research paper (scientific journal)
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New Observations on the Bioluminescence of the Pelagic Shrimp, Sergia lucens (Hansen, 1922) Reviewed
M Omori, MI Latz, H Fukami, M Wada
Zooplankton: Sensory Ecology and Physiology 1997.5
Language：English Publishing type：Research paper (other academic)