scholarly journals Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7769 ◽  
Author(s):  
Kenji Takata ◽  
Hiroki Taninaka ◽  
Masanori Nonaka ◽  
Fumihito Iwase ◽  
Taisei Kikuchi ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Deep Sea ◽  
Nuclear Dna ◽  
Genotyping By Sequencing ◽  
Inter Simple Sequence Repeat ◽  
Mitochondrial Haplotype ◽  
Ryukyu Islands ◽  
The Ryukyu Islands ◽  
Principle Coordinate Analysis ◽  
Species Specific

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

scholarly journals Evolutionary Relationship between Two Firefly Species,Curtos costipennisandC. okinawanus(Coleoptera, Lampyridae), in the Ryukyu Islands of Japan Revealed by the Mitochondrial and Nuclear DNA Sequences

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Masahiko Muraji ◽  
Norio Arakaki ◽  
Shigeo Tanizaki
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Nuclear Dna ◽  
Evolutionary Relationship ◽  
Early Pleistocene ◽  
Ryukyu Islands ◽  
Mtdna Sequences ◽  
Northern Half ◽  
The Ryukyu Islands ◽  
History Of

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species,Curtos costipennisandC. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups,C. costipennisin the Amami region,C. okinawanusin the Okinawa region, andC. costipennisin the Sakishima region. Their mtDNA sequences suggested that ancestralC. costipennispopulation was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided betweenC. costipennisin the Amami andC. okinawanusin the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

Late Pleistocene lineage divergence among populations of Neolitsea sericea (Lauraceae) across a deep sea-barrier in the Ryukyu Islands

2012 ◽  
Vol 39 (7) ◽  
pp. 1347-1360 ◽  
Author(s):  
Sheng-Nan Zhai ◽  
Hans Peter Comes ◽  
Koh Nakamura ◽  
Hai-Fei Yan ◽  
Ying-Xiong Qiu
Keyword(s):  
Late Pleistocene ◽  
Deep Sea ◽  
Ryukyu Islands ◽  
The Ryukyu Islands ◽  
Lineage Divergence

scholarly journals Extensive gene flow among populations of the cavernicolous shrimp at the northernmost distribution margin in the Ryukyu Islands, Japan

2020 ◽  
Vol 7 (10) ◽  
pp. 191731
Author(s):  
Takefumi Yorisue ◽  
Akira Iguchi ◽  
Nina Yasuda ◽  
Masaru Mizuyama ◽  
Yuki Yoshioka ◽  
...  
Keyword(s):  
Gene Flow ◽  
Flow Pattern ◽  
Population Genetic ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Genotyping By Sequencing ◽  
Flow Patterns ◽  
Ryukyu Islands ◽  
Effective Population ◽  
The Ryukyu Islands

Marine cave habitats in the Ryukyu Islands, Indo-West Pacific, are located at the northern edge of the distribution of many cave-dwelling species. At distribution margins, gene flow is often more restricted than that among core populations due to the smaller effective population size. Here, we used high-throughput sequencing technology to investigate the gene flow pattern among three sampling sites of a marine cave-dwelling species at the margin of its distribution range. We collected individuals of the barbouriid shrimp Parhippolyte misticia from three marine caves in the Ryukyu Islands and performed population genetic analyses by means of multiplexed inter-simple sequence repeat genotyping by sequencing. Based on 62 single-nucleotide polymorphism markers, no clear population structure or directional gene flow pattern was found among the three sites. These results were unexpected because previous studies of other stygobitic shrimps in this region did find significant population genetic structures and northward directional gene flow patterns . Together, these inconsistent findings imply that marine cave-dwelling species in the region have different mechanisms of larval dispersal. Future studies on larval ecology and the biotic and abiotic factors influencing gene flow patterns are needed to clarify the mechanisms underlying the population dynamics of marine cave-dwelling species.

Redescription of the pagurid hermit crab Catapaguroides fragilis (Melin, 1939) and descriptions of two new species from deep-sea off the Ryukyu Islands, Japan (Crustacea: Decapoda: Anomura)

Zootaxa ◽  
2017 ◽  
Vol 4273 (2) ◽  
pp. 235
Author(s):  
TOMOYUKI KOMAI
Keyword(s):  
New Species ◽  
Hermit Crab ◽  
Deep Sea ◽  
Distal Portion ◽  
Ryukyu Islands ◽  
Additional Material ◽  
Characteristic Shape ◽  
The Ryukyu Islands ◽  
Two New Species ◽  
Japanese Waters

Three species of the pagurid hermit crab genus Catapaguroides A. Milne-Edwards & Bouvier, 1892, all from Japanese waters, are reported. Catapaguroides fragilis (Melin, 1939) is redescribed on the basis of the holotype and additional material from southern Japan. Diagnostic characters of this poorly known species are fully assessed. Two new species, C. bythos and C. rubromaculatus, are described and illustrated on the basis of material from upper bathyal depths off the Ryukyu Islands. Catapaguroides rubromaculatus n. sp. resembles C. fragilis and C. hirsutus Komai & Rahayu, 2013, but the characteristic shape of the ocular peduncle and the elongate male right sexual tube with an anteriorly directed distal portion readily separate C. rubromaculatus n. sp. from the latter two congeners. Catapaguroides bythos n. sp. appears close to C. mortenseni de Saint Laurent, 1968 and C. pectinipes (Lewinsohn, 1969), but the different armature of the chelipeds distinguishes C. bythos n. sp. from the latter two allies. Catapaguroides is now represented by 30 species. 

New records of six deep-sea caridean shrimps (Crustacea: Decapoda) from the Ryukyu Islands and its adjacent waters, southwestern Japan

Zootaxa ◽  
2018 ◽  
Vol 4457 (1) ◽  
pp. 114
Author(s):  
TOMOYUKI KOMAI ◽  
SUSUMU OHTSUKA ◽  
SHUHEI YAMAGUCHI ◽  
KAZUMITSU NAKAGUCHI
Keyword(s):  
Deep Sea ◽  
New Records ◽  
Biological Science ◽  
Ryukyu Islands ◽  
West Pacific ◽  
The North ◽  
South West ◽  
The Ryukyu Islands ◽  
Japanese Waters ◽  
First Time

Six species of caridean shrimps from four families are recorded from Japanese waters for the first time on the basis of material from the Ryukyu Islands and its adjacent waters, collected during research cruises of the T/RV “Toyoshio-maru” of Faculty of Applied Biological Science, Hiroshima University: two species of Crangonidae, Lissosabinea unispinosa Komai, 2006 and Pseudopontophilus serratus Komai, 2004; one species of Oplophoridae, Systellaspis pellucida (Filhol, 1885); one species of Pandalidae, Calipandalus elachys Komai & Chan, 2003; and two species of Pasiphaeidae, Pasiphaea debitusae Hayashi, 1999 and P. gracilis Hayashi, 1999. Of them, L. unispinosa, Pseudopontophilus serratus, Pasiphaea debitusae and P. gracilis are heretofore known from the South-West Pacific localities, and then the geographical ranges of these four species are greatly extended to the north and west. Illustrations and/or colour images are provided for each species to supplement previous descriptions and to give evidence for identification.

A new squat lobster species of the genus Munida (Decapoda, Anomura, Munididae) from the deep-sea off the Ryukyu Islands, Japan

Crustaceana ◽  
2017 ◽  
Vol 90 (7-10) ◽  
pp. 969-979
Author(s):  
Tomoyuki Komai
Keyword(s):  
New Species ◽  
Deep Sea ◽  
The Philippines ◽  
Ryukyu Islands ◽  
Single Male ◽  
Okinawa Island ◽  
Male Specimen ◽  
Squat Lobster ◽  
The Ryukyu Islands ◽  
Japanese Waters

Munida michaeli, a new species of deep-sea squat lobster (Munididae), is described and illustrated on the basis of a single male specimen collected off Okinawa Island, Ryukyu Islands, Japan, at depths of 641-650 m. It closely resemblesM. sacksiMacpherson, 1993 known with certainty only from the Philippines, but different spination of the carapace dorsum and the greatly reduced armature of the flexor margins of the ambulatory dactyli distinguish the new species from the latter. With the addition of the present new species, 41 species ofMunidaLeach, 1820 are now known from Japanese waters.

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