論文 - 深見 裕伸
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An eDNA metabarcoding system for detecting scleractinian corals to the generic level along the Japanese coast 査読あり
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年
記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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年10月
担当区分：最終著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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年6月
担当区分：責任著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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 査読あり
Koido T., Imahara Y., Fukami H.
Zootaxa 5443 ( 2 ) 186 - 204 2024年4月
担当区分：最終著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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 査読あり
Ikeuchi Eri, Iguchi Akira, Nakamura Takashi, Fukami Hironobu
Galaxea, Journal of Coral Reef Studies 26 ( 1 ) 3 - 8 2024年3月
担当区分：最終著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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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サンゴ分類の話 連載 第4回 イシサンゴ類の学名の変更 2023 査読あり
深見 裕伸, 北野 裕子
日本サンゴ礁学会誌 25 ( 1 ) 19 - 25 2024年1月
担当区分：筆頭著者, 責任著者 記述言語：日本語 掲載種別：研究論文（学術雑誌） 出版者・発行元：日本サンゴ礁学会
2012～2014年にかけて旧オオトゲサンゴ科と旧キクメイシ科を中心に分類体系が大きく変更され，それ以降も毎年分類の変更に伴う学名の変更が報告されている。最近ではRowlett（2020）によって多数の科や属の分類の変更が報告された。このように，分類体系の変更が激しい現状において，サンゴ研究者は使用する学名を最新の情報を踏まえて把握する必要がある。しかしながら，分類学に深く関わっていない研究者にとってその作業に時間を費やすことが困難である。そこで，今回は，2016年以降の分類改変に伴う学名の変更があった主なイシサンゴ類の種や高次分類群について紹介する。
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年11月
掲載種別：研究論文（学術雑誌） 出版者・発行元：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年6月
担当区分：責任著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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年12月
担当区分：筆頭著者, 責任著者 記述言語：日本語 掲載種別：研究論文（学術雑誌）
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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 査読あり
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年6月
記述言語：日本語 掲載種別：研究論文（学術雑誌）
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First evidence for backcrossing of F<sub>1</sub> hybrids in Acropora corals under sperm competition. 査読あり
Kitanobo S, Iwao K, Fukami H, Isomura N, Morita M
Scientific reports 12 ( 1 ) 5356 2022年3月
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Koido T., Imahara Y., Fukami H.
ZooKeys 2022 ( 1085 ) 29 - 49 2022年2月
担当区分：責任著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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年1月
記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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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サンゴ分類の話 連載 第3回 サンゴの和名問題（2）「エダミドリイシ／ヒメエダミドリイシ」
深見 裕伸, 野村 恵一, 目﨑 拓真, 横地 洋之
日本サンゴ礁学会誌 24 ( 1 ) 9 - 12 2022年
記述言語：日本語 掲載種別：研究論文（学術雑誌） 出版者・発行元：日本サンゴ礁学会
今回，サンゴの和名問題として，日本温帯域に特異的に生息している樹枝状の種であるエダミドリイシとヒメエダミドリイシを取り上げる。従来，エダミドリイシの学名は<i>Acropora tumida</i>，ヒメエダミドリイシの学名は<i>Acropora pruinosa</i>とされており，この2種は枝の太さの違いにより識別されていた。しかしながら，タイプ標本の観察の結果，杉原ら（2015）は，日本でこれら2種として認識されてきたものは同一種の形態変異形であり，どちらも<i>A. pruinosa</i>であると判断した。さらに，野村ら（2016）により， <i>A. pruinosa</i>の和名は，従来のヒメエダミドリイシからより古い和名であるエダミドリイシに変更された。一方，<i>A. tumida</i>はタイプ標本の観察から群体形がコリンボース状であることが分かり，従来認識されていた太い枝の樹枝状ではないことが判明した。これにより，日本国内での<i>A. tumida</i>の実態は不明となったため，和名については未定となっている。現在，これらの変更の周知が不十分であるため，和名および学名の使用で混乱が見られる。そのため，本稿では改めて次の提言を行う：「日本温帯域に特異的に生息している樹枝状のミドリイシ属の種は（枝の太さに関係なく）<i>A. pruinosa</i>であり，和名にはエダミドリイシを用いる。<i>A. tumida</i>については国内の実態が不明であり，現在，和名はない。」
DOI： 10.3755/jcrs.24.9
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「日本産イシサンゴ目の標準和名の提唱と使用のガイドライン」の策定について
深見 裕伸, 野村 恵一, 梶原 健次, 横地 洋之, 野中 正法, 立川 浩之, 北野 裕子, 鈴木 豪, 藤田 喜久, 山野 博哉
日本サンゴ礁学会誌 24 ( 1 ) 1 - 7 2022年
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Mitsuki Y., Isomura N., Nozawa Y., Tachikawa H., Huang D., Fukami H.
Invertebrate Systematics 35 ( 8 ) 876 - 891 2021年11月
担当区分：責任著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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年10月
担当区分：筆頭著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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年10月
記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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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サンゴ分類の話 連載 第1回 サンゴの和名問題（1）「クシハダミドリイシ／ナンヨウミドリイシ」 査読あり
深見 裕伸, 野村 恵一, 目﨑 拓真, 鈴木 豪, 横地 洋之
日本サンゴ礁学会誌 23 ( 1 ) 21 - 26 2021年6月
担当区分：筆頭著者 記述言語：日本語 掲載種別：研究論文（その他学術会議資料等） 出版者・発行元：日本サンゴ礁学会
有藻性イシサンゴ類の分類体系および和名の大幅な変更，また，サンゴの種同定問題などに起因するサンゴの分類関連の混乱の解消および問題の解決のため，「解説：サンゴ分類の話 連載」を開始する。手始めにサンゴの和名問題を取り上げ，特に和名の混乱が認められるクシハダミドリイシ／ナンヨウミドリイシについて解説する。形態や遺伝子解析，記載論文やタイプ標本の調査から判断した結果，日本国内の全てのクシハダミドリイシ様集団は，種単位ではなく「種群」として扱い，"<i>Acropora hyacinthus</i> species complex"（簡易版：<i>Acropora hyacinthus </i>complex）「クシハダミドリ種群」とするのが適切であると結論付けた。しかしながら，一般的に「種群」が使用されない場合が多いため，次善策としては，本種群の整理が完了するまで，和名のナンヨウミドリイシは使用せず，<i>Acropora hyacinthus</i> クシハダミドリイシの使用を推奨する。
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年5月
担当区分：責任著者 記述言語：英語 掲載種別：研究論文（学術雑誌） 出版者・発行元：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.