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Xu T, Bravo H, van der Meij SE. Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae). PeerJ 2023; 11:e16217. [PMID: 37868050 PMCID: PMC10586294 DOI: 10.7717/peerj.16217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023] Open
Abstract
Background Thoracotremata belong to the large group of "true" crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved. Methods Here we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi). Results The results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle.
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Affiliation(s)
- Tao Xu
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Henrique Bravo
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Sancia E.T. van der Meij
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, Netherlands
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Lee BY, Ng NK, Ng PKL. On the identities of the sesarmid crabs, Sesarma villosum A. Milne-Edwards, 1869, and Clistocoeloma suvaense Edmondson, 1951, with the description of a new species from the West Pacific (Decapoda, Brachyura, Thoracotremata). Zootaxa 2023; 5318. [PMID: 37518389 DOI: 10.11646/zootaxa.5318.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Indexed: 08/01/2023]
Abstract
The identities of two sesarmid crabs, Clistocoeloma villosum (A. Milne-Edwards, 1869), and C. suvaense Edmondson, 1951, both currently in Clistocoeloma A. Milne-Edwards, 1873, are poorly known and the types have not been studied in detail since their description. Clistocoeloma villosum, supposedly widespread, has been recorded from Madagascar and East Africa to Singapore, Japan, Korea, and Samoa. Clistocoeloma suvaense is only known for certain from one male collected from its type locality, Fiji. The taxonomy of C. villosum, and C. suvaense is clarified on the basis of the type specimens from Samoa and Fiji, respectively. A new species, which has long been confused with C. villosum, is described from Southeast Asia and Western Pacific.
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Affiliation(s)
- Bee Yan Lee
- Tropical Marine Science Institute; National University of Singapore; 18 Kent Ridge Road; Singapore 119227; Republic of Singapore. Systematics and Ecology Laboratory; Department of Biological Sciences; National University of Singapore; Block S3 Level 2; 4 Science Drive 4; Singapore 117543; Republic of Singapore..
| | - Ngan Kee Ng
- Tropical Marine Science Institute; National University of Singapore; 18 Kent Ridge Road; Singapore 119227; Department of Biological Sciences; National University of Singapore; 14.
| | - Peter K L Ng
- Tropical Marine Science Institute; National University of Singapore; 18 Kent Ridge Road; Singapore 119227; Science Drive 4; Singapore 117543. Lee Kong Chian Natural History Museum; National University of Singapore; 2 Conservatory Drive; Singapore 117377.
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3
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Kobayashi G, Itoh H, Nakajima N. Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes. Zoolog Sci 2023; 40:224-234. [PMID: 37256570 DOI: 10.2108/zs220063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/02/2023] [Indexed: 06/01/2023]
Abstract
Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.
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Affiliation(s)
- Genki Kobayashi
- Ishinomaki Senshu University, Minamisakai, Ishinomaki, Miyagi 986-8580, Japan,
| | - Hajime Itoh
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Nobuyoshi Nakajima
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
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Jin X, Guo X, Chen J, Li J, Zhang S, Zheng S, Wang Y, Peng Y, Zhang K, Liu Y, Liu B. The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. Genes Genomics 2023; 45:377-391. [PMID: 36346542 DOI: 10.1007/s13258-022-01319-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed. OBJECTIVE The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. METHODS The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks. RESULTS This mitochondrial genome shows that it was 15,900 bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution. CONCLUSION Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.
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Affiliation(s)
- Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Xingle Guo
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Jian Chen
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Jiasheng Li
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, 510300, Guangdong, China
| | - Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China. .,National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, 316022, Zhejiang, China.
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Mvogo Ndongo PA, von Rintelen T, Clark PF, Shahdadi A, Tchietchui CR, Cumberlidge N. Phylogenetic relationships among the species of the Cameroonian endemic freshwater crab genus Louisea Cumberlidge, 1994 (Crustacea, Brachyura, Potamonautidae), with notes on intraspecific morphological variation within two threatened species. Zookeys 2022; 1122:125-143. [PMID: 36761210 PMCID: PMC9848643 DOI: 10.3897/zookeys.1122.85791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/31/2022] [Indexed: 11/12/2022] Open
Abstract
Louisea Cumberlidge, 1994 (Crustacea, Brachyura, Potamonautidae) currently includes four endemic Cameroonian freshwater crab species whose phylogenetic relationships were previously unresolved. In the present study, phylogenetic analyses are carried out involving three mtDNA loci (COI, 12S rRNA, and 16S rRNA). The COI locus revealed divergence times of 5.6 million years ago (myr) for when L.balssi (Bott, 1959) diverged from L.edeaensis (Bott, 1969); 4.1 myr for when L.edeaensis diverged from L.yabassi Mvogo Ndongo, von Rintelen & Cumberlidge, 2019; and 2.48 myr for when the later species diverged from L.nkongsamba Mvogo Ndongo, von Rintelen & Cumberlidge, 2019. Three genetic lineages were found within L.nkongsamba that are supported by uncorrected p-distances and the haplotype network. Morphological variation in some taxonomically important characters was found within both L.nkongsamba and L.yabassi. No correlation, however, was found between the morphotypes within these species and the uncovered genetic lineages. Recognition of species boundaries and of subpopulations of species will prove valuable when making informed conservation decisions as part of the development of species action plans for these rare and threatened freshwater crabs.
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Affiliation(s)
- Pierre A. Mvogo Ndongo
- Département de Gestion des Écosystèmes Aquatiques, Institut des Sciences Halieutiques, Université de Douala à Yabassi, PO. Box. 7236 Douala-Bassa, CameroonMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany,Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, 10115 Berlin, GermanyUniversité de Douala à YabassDouala-BassaCameroon
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, 10115 Berlin, GermanyUniversité de Douala à YabassDouala-BassaCameroon
| | - Paul F. Clark
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UKDepartment of Life Sciences, The Natural History MuseumLondonUnited Kingdom
| | - Adnan Shahdadi
- Department of Marine Biology, Faculty of Marine Sciences and Technology, University of Hormozgan, Bandar Abbas, IranUniversity of HormozganBandar AbbasIran
| | - Carine Rosine Tchietchui
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, PO Box 24157 Douala, CameroonUniversity of DoualaDoualaCameroon
| | - Neil Cumberlidge
- Department of Biology, Northern Michigan University, Marquette, MI 49855-5376, USANorthern Michigan UniversityMarquetteUnited States of America
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T T Tsang C, Schubart CD, Hou Chu K, K L Ng P, Ming Tsang L. Molecular phylogeny of Thoracotremata crabs (Decapoda, Brachyura): toward adopting monophyletic superfamilies, invasion history into terrestrial habitats and multiple origins of symbiosis. Mol Phylogenet Evol 2022; 177:107596. [PMID: 35914646 DOI: 10.1016/j.ympev.2022.107596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/11/2022] [Accepted: 07/26/2022] [Indexed: 11/27/2022]
Abstract
The Thoracotremata is a large and successful group of "true" crabs (Decapoda, Brachyura, Eubrachyura) with a great diversity of lifestyles and well-known intertidal representatives. The group represents the largest brachyuran radiation into terrestrial and semi-terrestrial environments and comprises multiple lineages of obligate symbiotic species. In consequence, they exhibit very diverse physiological and morphological adaptations. Our understanding of their evolution is, however, largely obscured by their confused classification. Here, we resolve interfamilial relationships of Thoracotremata, using 10 molecular markers and exemplars from all nominal families in order to reconstruct the pathways of lifestyle transition and to propose a new taxonomy corresponding to phylogenetic relationships. The results confirm the polyphyly of three superfamilies as currently defined (Grapsoidea, Ocypodoidea and Pinnotheroidea). At the family level, Dotillidae, Macrophthalmidae, and Varunidae are not monophyletic. Ancestral state reconstruction analyses and divergent time estimations indicate that the common ancestor of thoracotremes already thrived in intertidal environments in the Late Cretaceous and terrestrialization became a major driver of thoracotreme diversification. Multiple semi-terrestrial and terrestrial lineages originated and radiated in the Early Eocene, coinciding with the global warming event at the Paleocene-Eocene Thermal Maximum (PETM). Secondary invasions into subtidal regions and colonizations of freshwater habitats occurred independently through multiple semi-terrestrial and terrestrial lineages. Obligate symbiosis between thoracotremes and other marine macro-invertebrates evolved at least twice. On the basis of the current molecular phylogenetic hypothesis, it will be necessary in the future to revise and recognize seven monophyletic superfamilies and revisit the morphological character states which define them.
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Affiliation(s)
- Chandler T T Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Christoph D Schubart
- Zoology & Evolutionary Biology, University of Regensburg, 93040 Regensburg, Germany
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong SAR, China
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Lü J, Xia L, Liu X, Ma Y, Li J, Ye Y, Guo B. The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura. Sci Rep 2022; 12:2104. [PMID: 35136145 PMCID: PMC8826855 DOI: 10.1038/s41598-022-06080-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and evolutionary traits. In this study, we determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus. It is a typical metazoan mitochondrial genome. The total size is 15,583 bp, contains the entire set of 37 genes, and has an AT-rich region. Then, 23 of the 37 genes were encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. Compared with the pan-crustacean ground pattern, two tRNA genes (tRNA-His and tRNA-Gln) were rearranged and the tandem duplication/random loss model was used to explain the observed gene rearrangements. The phylogenetic results showed that all Grapsidae crabs clustered together as a group. Furthermore, the monophyly of each family was well supported, with the exception of Menippidae. In general, the results obtained in this study will contribute to the better understanding of gene rearrangements in Grapsidae crab mitogenomes and provide new insights into the phylogeny of Brachyura.
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Affiliation(s)
- Jiayin Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Liping Xia
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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Rodriguez-Pilco MA, Leśny P, Podsiadłowski L, Schubart CD, Baeza JA. Characterization of The Complete Mitochondrial Genome of the Bromeliad Crab Metopaulias depressus (Rathbun, 1896) (Crustacea: Decapoda: Brachyura: Sesarmidae). Genes (Basel) 2022; 13:genes13020299. [PMID: 35205344 PMCID: PMC8872168 DOI: 10.3390/genes13020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Metopaulias depressus is a non-marine crab endemic to Jamaica that dwells in rainforest bromeliads and exhibits elaborate active parental care behavior. Current genomic resources on M. depressus are rare, limiting the understanding of its adaptation to terrestrial life in species that evolved from marine ancestors. This study reports the complete mitochondrial genome of M. depressus assembled using Sanger sequencing. The AT-rich mitochondrial genome of M. depressus is 15,765 bp in length and comprises 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. A single 691 bp-long intergenic space is assumed to be the control region (CR) or D-loop. A set of selective pressure analyses indicate that the entirety of the PCGs experience purifying selection. Cox1, cox2, nad5, cox3, and atp6 experience strong purifying selection, and atp8 experiences weak purifying selection compared to the rest of the PCGs. The secondary structures of most tRNA genes exhibit a standard ‘cloverleaf’ structure, with the exception of trnS1, which lacks the dihydroxyuridine (DHU) arm but not the loop, the trnH gene, which lacks the thymine pseudouracil cytosine (T) loop but not the arm, and trnM, which exhibits an overly developed T loop. A maximum likelihood phylogenetic analysis based on all PCGs indicated that M. depressus is more closely related to the genera Clistocoeloma, Nanosesarma, and Parasesarma than to Chiromantes, Geosesarma, and Orisarma. This study contributes to deciphering the phylogenetic relationships within the family Sesarmidae and represents a new genomic resource for this iconic crab species.
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Affiliation(s)
- Milena A. Rodriguez-Pilco
- Facultad de Ciencias Biológicas, Universidad Nacional de San Agustin, Av. Daniel Alcides Carreon s/n, Arequipa 04001, Peru;
| | - Peter Leśny
- Institute for Evolutionary Biology & Animal Ecology, University Bonn, 53121 Bonn, Germany;
| | - Lars Podsiadłowski
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), 53113 Bonn, Germany;
| | | | - Juan Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL 34949, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, Coquimbo 1281, Chile
- Correspondence:
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Xu X, Wang Q, Wu Q, Xu J, Wang J, Wang Z. The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura. Biochem Genet 2021; 59:617-636. [PMID: 33415669 DOI: 10.1007/s10528-020-10025-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (- 0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.
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Affiliation(s)
- Xinyi Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qi Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Qiong Wu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jiayan Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Jie Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, China.
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Insights into the evolution of Brachyura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements. Int J Biol Macromol 2021; 170:717-727. [PMID: 33412200 DOI: 10.1016/j.ijbiomac.2020.12.210] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/29/2020] [Accepted: 12/29/2020] [Indexed: 11/23/2022]
Abstract
Brachyura is one of the most species rich and highly derived groups among extant crustaceans, with over 7250 known species. However, brachyuran phylogeny remains controversial and requires further study. Here, we combined 103 brachyuran mitogenomes from GenBank with 10 new mitogenomes to describe gene rearrangement patterns and explore the internal phylogenetic relationships of Brachyura. Most of the 10 novel mitogenomes had the typical 37 genes, except that of Longpotamon depressum, which lacked trnQ. We discovered 15 gene rearrangement patterns among Brachyura and preliminarily determined their rearrangement mechanisms with the help of CREx. We identified seven putative ancestral family gene orders among the 15 rearrangement patterns and expounded systematically upon the mechanisms of their rearrangement. In our phylogenetic analysis, Raninoida shared a sister relationship with an eubrachyuran clade ((Heterotremata [Potamoidea] + Thoracotremata) + Heterotremata) at maximum nodal support rather than Dromiacea, which did not support monophyly of Podotremata. In addition, Potamoidea (Parathelphusidae + Potamidae) retained a close relationship with Thoracotremata rather than their marine relatives in Heterotremata. Our study provides important information for the evolution of Brachyura by using the large taxon sampling currently available for systematic rearrangement and phylogenetic analyses.
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11
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Krieger J, Hörnig MK, Kenning M, Hansson BS, Harzsch S. More than one way to smell ashore - Evolution of the olfactory pathway in terrestrial malacostracan crustaceans. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 60:101022. [PMID: 33385761 DOI: 10.1016/j.asd.2020.101022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Crustaceans provide a fascinating opportunity for studying adaptations to a terrestrial lifestyle because within this group, the conquest of land has occurred at least ten times convergently. The evolutionary transition from water to land demands various morphological and physiological adaptations of tissues and organs including the sensory and nervous system. In this review, we aim to compare the brain architecture between selected terrestrial and closely related marine representatives of the crustacean taxa Amphipoda, Isopoda, Brachyura, and Anomala with an emphasis on the elements of the olfactory pathway including receptor molecules. Our comparison of neuroanatomical structures between terrestrial members and their close aquatic relatives suggests that during the convergent evolution of terrestrial life-styles, the elements of the olfactory pathway were subject to different morphological transformations. In terrestrial anomalans (Coenobitidae), the elements of the primary olfactory pathway (antennules and olfactory lobes) are in general considerably enlarged whereas they are smaller in terrestrial brachyurans compared to their aquatic relatives. Studies on the repertoire of receptor molecules in Coenobitidae do not point to specific terrestrial adaptations but suggest that perireceptor events - processes in the receptor environment before the stimuli bind - may play an important role for aerial olfaction in this group. In terrestrial members of amphipods (Amphipoda: Talitridae) as well as of isopods (Isopoda: Oniscidea), however, the antennules and olfactory sensilla (aesthetascs) are largely reduced and miniaturized. Consequently, their primary olfactory processing centers are suggested to have been lost during the evolution of a life on land. Nevertheless, in terrestrial Peracarida, the (second) antennae as well as their associated tritocerebral processing structures are presumed to compensate for this loss or rather considerable reduction of the (deutocerebral) primary olfactory pathway. We conclude that after the evolutionary transition from water to land, it is not trivial for arthropods to establish aerial olfaction. If we consider insects as an ingroup of Crustacea, then the Coenobitidae and Insecta may be seen as the most successful crustacean representatives in this respect.
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Affiliation(s)
- Jakob Krieger
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
| | - Marie K Hörnig
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
| | - Matthes Kenning
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
| | - Bill S Hansson
- Max-Planck-Institute for Chemical Ecology, Department of Evolutionary Neuroethology, 07745, Jena, Germany.
| | - Steffen Harzsch
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
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12
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Kobayashi G, Itoh H, Fukuda H, Kojima S. The complete mitochondrial genome of the sand bubbler crab Scopimera globosa and its phylogenetic position. Genomics 2020; 113:831-839. [PMID: 33091547 DOI: 10.1016/j.ygeno.2020.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/29/2020] [Accepted: 10/16/2020] [Indexed: 01/19/2023]
Abstract
The mitochondrial genome has become commonly used for the molecular phylogenetic analysis of animals. Most phylogenetic studies on brachyurans using mitogenome sequences have indicated the paraphyly of superfamilies Grapsoidea and Ocypodoidea but taxon sampling remains limited. The phylogenetic position of Scopimera has been tested in several previous studies using nuclear and/or mitochondrial DNA sequences, but the phylogenetic relationship within the family remains to be resolved. We newly sequenced the complete mitochondrial genome of the sand bubbler crab Scopimera globosa (Ocypodoidea: Dotillidae). Scopimera globosa was clustered with Ilyoplax despite the morphological similarity between Scopimera and Dotilla. The mitochondrial gene order of S. globosa was unique, whereas that of other genera in the family was the same. These results suggest that phylogenetic analysis based on mitogenome sequences and gene order comparison would provide a more robust phylogeny of Dotillidae.
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Affiliation(s)
- Genki Kobayashi
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, 459 Shirahama, Nishimuro, Wakayama 649-2211, Japan.
| | - Hajime Itoh
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
| | - Hideki Fukuda
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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13
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Shahdadi A, Fratini S, Schubart CD. Taxonomic reassessment of Parasesarma (Crustacea: Brachyura: Decapoda: Sesarmidae) based on genetic and morphological comparisons, with the description of a new genus. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Parasesarma is a species-rich genus whose representatives are common in wetlands and mangroves of the Indo-Pacific. Morphologically, the genus is heterogeneous and has been postulated to constitute a polyphyletic taxon. In the present study, most species of Parasesarma are re-evaluated phylogenetically, using mitochondrial and nuclear molecular markers. The results show that the majority of the examined species cluster consistently with the type species Parasesarma plicatum. However, some species, among them the tree-climbing Parasesarma leptosoma, are clearly separated from this main clade of Parasesarma, forming a second stable monophyletic group, distinct from other known genera. Based on these results, and with additional support by morphological diagnoses highlighting consistent differences between the two species groups, we propose a new genus for the species clustering around P. leptosoma, proposing the new name Leptarma gen. nov.
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Affiliation(s)
- Adnan Shahdadi
- Department of Marine Biology, Faculty of Marine Sciences and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Sara Fratini
- Department of Biology, University of Florence, via Madonna del Piano, Sesto Fiorentino, Italy
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14
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Characterization of the complete mitochondrial genome of Uca lacteus and comparison with other Brachyuran crabs. Genomics 2020; 112:10-19. [DOI: 10.1016/j.ygeno.2019.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 01/15/2023]
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15
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Di Muzio G, Mussat Sartor R, Nurra N, Battuello M, Pessani D, Cervella P, Cuesta JA. Morphology of planktonic zoeal stages of Palicus caronii (Decapoda, Brachyura), identified by DNA barcoding, provides novelties to Palicoidea larval systematics. Sci Rep 2019; 9:19132. [PMID: 31836767 PMCID: PMC6910961 DOI: 10.1038/s41598-019-55412-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/28/2019] [Indexed: 11/09/2022] Open
Abstract
The zoeal development of the brachyuran crab, Palicus caronii, comprises two zoeal stages and the morphology is described and illustrated in detail. The zoeae were collected in plankton samples from the Southern Ligurian Sea (Western Mediterranean). Although the morphology of the larval stages of this species was unknown, a combination of characters allowed the zoeae to initially be assigned to the Palicidae, based on the previous unique known first zoeal description of one species of this family. Later, the identification of the larvae as Palicus caronii was confirmed through molecular analysis. The morphological features of the zoeae that characterize the Palicidae and separate them from the Crossotonotidae are confirmed. Also, the larval development comprising only two zoeal stages observed in Palicus caronii, the peculiar and uncommon carapace surface setation, and the presence of anterodorsal and posterodorsal sensory dorsal organs suggest that these characters could be common to the Palicoidea.
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Affiliation(s)
- Giorgia Di Muzio
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy.
| | - Rocco Mussat Sartor
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
- Pelagosphera Soc. Coop. Via U. Cosmo 17/bis 10131, Torino, Italy
| | - Nicola Nurra
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
- Pelagosphera Soc. Coop. Via U. Cosmo 17/bis 10131, Torino, Italy
| | - Marco Battuello
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
- Pelagosphera Soc. Coop. Via U. Cosmo 17/bis 10131, Torino, Italy
| | - Daniela Pessani
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
| | - Piero Cervella
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
| | - Jose A Cuesta
- Instituto de Ciencias Marinas de Andalucía (ICMAN-CSIC), Avda. República Saharaui, 2, 11519, Puerto Real, Cádiz, Spain
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16
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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17
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Phylogenomic analyses of brachyuran crabs support early divergence of primary freshwater crabs. Mol Phylogenet Evol 2019; 135:62-66. [DOI: 10.1016/j.ympev.2019.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 12/23/2018] [Accepted: 02/03/2019] [Indexed: 11/23/2022]
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18
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Pfaller JB, Payton AC, Bjorndal KA, Bolten AB, McDaniel SF. Hitchhiking the high seas: Global genomics of rafting crabs. Ecol Evol 2019; 9:957-974. [PMID: 30805133 PMCID: PMC6374717 DOI: 10.1002/ece3.4694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/04/2022] Open
Abstract
Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next-generation sequencing of genomewide restriction-site-associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species-level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low-likely three closely related species-with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F ST = 0.08-0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic-level resolution for estimating contemporary population structure in organisms with large, highly connected populations.
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Affiliation(s)
- Joseph B. Pfaller
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
- Caretta Research ProjectSavannahGeorgia
| | - Adam C. Payton
- Department of BiologyUniversity of FloridaGainesvilleFlorida
| | - Karen A. Bjorndal
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
| | - Alan B. Bolten
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
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19
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Chen J, Xing Y, Yao W, Xu X, Zhang C, Zhang Z, Liu Q. Phylomitogenomics reconfirm the phylogenetic position of the genus Metaplax inferred from the two grapsid crabs (Decapoda: Brachyura: Grapsoidea). PLoS One 2019; 14:e0210763. [PMID: 30682071 PMCID: PMC6347246 DOI: 10.1371/journal.pone.0210763] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/01/2019] [Indexed: 12/22/2022] Open
Abstract
Two new complete mitogenomes of the grapsids, Metaplax longipes Stimpson, 1858 and Nanosesarma minutum (De Man, 1887) were sequenced using next-generation sequencing (NGS). By analyzing a combination of 75 Brachyura taxa, our phylomitogenomic inferences suggested that Metaplax crab seperated earlier from the sesarmid crabs and closely related to the varunids with respect to Nanosesarma crab. It reconfirmed that the Metaplax should be removed from the Sesarmidae and assinged to the Varunidae. Additional mitogenomic comparisons including gene rearrangement and genomic organization were conducted among the 33 taxa of Grapsoidea and Ocypodoidea, and a shared rearrangement pattern between Metaplax longipes and the varunids were recovered, which also strongly supported the inference for the phylogenetic position of the Metaplax.
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Affiliation(s)
- Jianqin Chen
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
- * E-mail:
| | - Yuhui Xing
- Nanjing Normal University Zhongbei College, Nanjing, China
| | - Wenjia Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xue Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chenling Zhang
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
| | - Zhenhua Zhang
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
| | - Qing Liu
- Institute of Aquatic Biology, Jiangsu Key Laboratory of Biofunctional Molecule, School of Life Sciences, Chemistry & Chemical Engineering, Jiangsu Second Normal University, Nanjing, China
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20
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Liu Y, Yang TT, Xin ZZ, Liu QN, Zhang DZ, Tang BP. The complete mitochondrial genome sequence of Metaplax longipes (Grapsoidea: Varunidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1574626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, China
| | - Ting-Ting Yang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, China
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21
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Fratini S, Cannicci S, Porri F, Innocenti G. Revision of the Parasesarma guttatum species complex reveals a new pseudocryptic species in south-east African mangroves. INVERTEBR SYST 2019. [DOI: 10.1071/is18028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Parasesarma De Man, 1895 is the most speciose genus in the family Sesarmidae (Decapoda: Brachyura: Thoracotremata). In the western Indian Ocean, Parasesarma is represented by five species only, although some genetic evidence suggests that P. guttatum could be a species complex comprising two cryptic species. Accordingly, P. guttatum is here split into two pseudocryptic species, and a new species, Parasesarma capensis, sp. nov., is described. P. capensis, sp. nov. fills the same ecological niche as P. guttatum south of the Mozambique Channel. While variation in mitochondrial DNA and morphological differences clearly distinguish the two species, there is no nuclear genetic variation. This may reflect a short history of reproductive isolation. The distinguishing morphological characters of the new species are the 13–15 rounded tubercles on the movable finger, the upper surface of the palm with three transverse crests (one regularly tuberculate and two pectinated), and the shape of the first gonopod. Phylogenetic inference analyses show a sister-species relationship between P. guttatum and P. capensis, sp. nov., and strongly suggest that at least two East African Parasesarma species need a taxonomic revision. The description of this new sesarmid species from the south-eastern African coast sheds new light on the overall biogeographic patterns and general biodiversity of this taxon within the western Indian Ocean.
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22
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Guinot D, Ng NK, Moreno PAR. Review of grapsoid families for the establishment of a new family for Leptograpsodes Montgomery, 1931, and a new genus of Gecarcinidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Grapsoidea MacLeay, 1838). ZOOSYSTEMA 2018. [DOI: 10.5252/zoosystema2018v40a26] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Danièle Guinot
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, case postale 53, 57 rue Cuvier, F-75231 Paris cedex 05 (France)
| | - Ngan Kee Ng
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Republic of Singapore)
| | - Paula A. Rodríguez Moreno
- Direction générale déléguée aux Collections, Muséum national d'Histoire naturelle, case postale 30, 57 rue Cuvier, F-75231 Paris cedex 05 (France)
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23
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Characterization of four new mitogenomes from Ocypodoidea & Grapsoidea, and phylomitogenomic insights into thoracotreme evolution. Gene 2018; 675:27-35. [PMID: 29960073 DOI: 10.1016/j.gene.2018.06.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/01/2018] [Accepted: 06/25/2018] [Indexed: 11/24/2022]
Abstract
Four new complete mitochondrial genomes (mitogenomes) from the two superfamilies Ocypodoidea and Grapsoidea were sequenced, which represented Uca (Gelasimus) borealis (Ocypodidae: Ucinae), Dotilla wichmani (Dotillidae), Metopograpsus quadridentatus (Grapsidae: Grapsinae), and Gaetice depressus (Varunidae: Gaeticinae). All of the mitogenomes shared the complete set of 37 mitochondrial genes. Mitogenome lengths were 15,659, 15,600, 15,517, and 16,288 bp, respectively, with A + T contents of 69.41%, 68.46%, 70.30%, and 72.96%, respectively. Comparative genomic analyses suggested that they exhibited different genomic rearrangements. In particular, G. depressus shared a major rearrangement pattern present in Eriocheir crabs, while the remainder shared the brachyuran ground genomic rearrangement patterns. Phylomitogenomic inferences provided new evidence for the strongly supported nesting of Thoracotremata within Heterotremata clades. A close phylogenetic relationship was observed between Varunidae and Macrophthalmidae crabs, and between Dotillidae and Grapsidae crabs, which was consistent with mitochondrial genomic rearrangement similarities. Altogether, these results suggest the presence of reciprocal paraphyly for Ocypodoidea and Grapsoidea.
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24
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Wang Z, Wang Z, Shi X, Wu Q, Tao Y, Guo H, Ji C, Bai Y. Complete mitochondrial genome of Parasesarma affine (Brachyura: Sesarmidae): Gene rearrangements in Sesarmidae and phylogenetic analysis of the Brachyura. Int J Biol Macromol 2018; 118:31-40. [PMID: 29908270 DOI: 10.1016/j.ijbiomac.2018.06.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/10/2018] [Accepted: 06/12/2018] [Indexed: 10/14/2022]
Abstract
In this study, the complete mitochondrial DNA (mtDNA) sequence of the crab Parasesarma affine is determined, characterized and compared with other decapod crustaceans. The P. affine mitochondrial genome (mitogenome) is 15,638 bp in size, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a control region (CR). Then, 23 of the 37 genes are encoded by the heavy (+) strand while 14 are encoded by the light (-) strand. All PCGs are initiated by ATN codons and 4 of the 13 PCGs harbored the incomplete termination codon by T or TA. The CR with a high A + T% (82.33%) spans 678 bp. The nucleotide composition of the P. affine mitogenome is also biased toward A + T nucleotides (74.83%). The gene order of P. affine has a difference that trnI-trnQ turns into trnQ-trnI when compared with ancestor of Brachyura, which can also been seen in other Sesarmidae species. Phylogenetic tree based on nucleotide sequences of mitochondrial 13 PCGs from 49 decapod crustaceans and one outgroup using Bayesian inference (BI) and Maximum Likelihood (ML), which determined that P. affine belongs to Sesarmidae and Parasesarma is monophyletic.
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Affiliation(s)
- Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China.
| | - Ziqian Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Xuejia Shi
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Qiong Wu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Yitao Tao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Huayun Guo
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Chenyao Ji
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
| | - Yuze Bai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224001, Jiangsu Province, China
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Kienbaum K, Scholtz G, Becker C. The morphology of the reproductive system in the crab Percnon gibbesi
(Decapoda: Brachyura: Grapsoidea) reveals a new combination of characters in Thoracotremata. J Morphol 2018; 279:883-894. [DOI: 10.1002/jmor.20818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/17/2018] [Accepted: 03/02/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Katja Kienbaum
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie; Berlin 10115 Germany
| | - Gerhard Scholtz
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie; Berlin 10115 Germany
- Cluster of Excellence “Image Knowledge Gestaltung”, Humboldt-Universität zu Berlin; Berlin 10178 Germany
| | - Carola Becker
- Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie; Berlin 10115 Germany
- Cluster of Excellence “Image Knowledge Gestaltung”, Humboldt-Universität zu Berlin; Berlin 10178 Germany
- Queen's University Marine Laboratory; Portaferry Northern Ireland BT22 1PF UK
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26
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Karagozlu MZ, Kim JI, Choi TJ, Dinh TD, Kim CB. The complete mitochondrial genome of Hemigrapsus penicillatus (De Haan, 1835) (Decapoda, Varunidae). Mitochondrial DNA B Resour 2018; 3:261-262. [PMID: 33474135 PMCID: PMC7800518 DOI: 10.1080/23802359.2018.1443037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Hemigrapsus penicillatus is a small grapsoid crab which is found in Japan, Taiwan, Korea, and China coasts. In this study a complete mitogenome of Korean H. penicillatus was analyzed and phylogenetic relationships in the family Varunidae were investigated. The mitogenome size is 16,486 bp with 34.1% A, 18.1% C, 11.4% G, and 36.4% T nucleotide distributions. Genome structure and gene orientations are identical with previous records from the family and mitochondrial protein-coding gene based phylogenetic tree suggested that the closest species to H. penicillatus is H. sanguineus. This is the second complete mitogenome record from the genus Hemigrapsus and the first record for the species.
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Affiliation(s)
| | - Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul, Korea
| | - Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul, Korea
| | - Thinh Do Dinh
- Department of Biotechnology, Sangmyung University, Seoul, Korea.,Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Haiphong, Vietnam
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, Korea
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27
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Lin F, Xie Z, Fazhan H, Baylon JC, Yang X, Tan H, Guan M, Shi X, Ikhwanuddin M, Ma H. The complete mitochondrial genome of Varuna yui (Decapoda: Brachyura: Varunidae) and its phylogeny. Mitochondrial DNA B Resour 2018; 3:263-264. [PMID: 33474136 PMCID: PMC7799475 DOI: 10.1080/23802359.2018.1443043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/13/2018] [Indexed: 11/04/2022] Open
Abstract
The complete mitochondrial genome plays an important role in the research on phylogenetic relationship. Here, we reported the first complete mitochondrial genome sequence of Varuna yui Hwang & Takeda, 1986 (Varunidae). The complete mtDNA (15,915 bp in length) consisted of 13 protein-coding genes, 22 tRNAs, two rRNA genes, and a control region. The gene arrangement was identical to those observed in the Varunidae species. The phylogenetic analysis suggested that V. yui had close relationship with other Varunidae species (Helicetient sinensis, Eriocher sinesis, etc.). The newly described genome may facilitate further comparative mitogenomic analysis within Varunidae species.
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Affiliation(s)
- Fan Lin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhuofang Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Juliana C. Baylon
- Division of Biological Sciences, College of Arts and Sciences, University of the Philippines Visayas, Miagao, Philippines
| | - Xiaolong Yang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Huaqiang Tan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Mengyun Guan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Mhd Ikhwanuddin
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
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28
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Fratini S, Cannicci S, Schubart CD. Molecular phylogeny of the crab genus Metopograpsus H. Milne Edwards, 1853 (Decapoda : Brachyura : Grapsidae) reveals high intraspecific genetic variation and distinct evolutionarily significant units. INVERTEBR SYST 2018. [DOI: 10.1071/is17034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Indo-Pacific genus Metopograpsus belongs to the family Grapsidae and comprises six species of intertidal crabs inhabiting sheltered rocky shores and mangrove forests. All species are opportunistic feeders and four of them are associated with roots and trunks of mangroves. So far, no comprehensive molecular phylogenetic study has been conducted on this genus, despite the fact that some species are not easily separable from a morphological point of view. We performed a phylogenetic and phylogeographic investigation based on sequences corresponding to both ribosomal mitochondrial DNA genes from 44 samples of Metopograpsus spp., covering the distribution ranges of each species. Our main aims were to validate species identification across their respective distribution ranges and depict the phylogeographic patterns within each species. Our phylogenetic inference reconstructions confirmed monophyly of the six species. We also recorded a high intraspecific genetic variation and strong phylogeographic structure within M. thukuhar and M. quadridentatus. This indicates the occurrence of distinct evolutionarily significant units within these two taxa, possibly corresponding to undescribed species. Further nuclear DNA-based phylogeographic analyses, as well as morphological investigations, will be necessary to assign a taxonomic value to the recorded evolutionarily significant units.
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29
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Tsang LM, Ahyong ST, Shih HT, Ng PKL. Further polyphyly of pinnotheroid crabs: the molecular phylogenetic position of the polychaete-associated Aphanodactylidae. INVERTEBR SYST 2018. [DOI: 10.1071/is17038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pea crabs of the superfamily Pinnotheroidea De Haan, 1833 are known for their obligate commensal relationships with other marine invertebrates. The concomitant specialisations and adaptations of pinnotheroids have resulted in superficially similar body forms that include a high degree of structural reduction. This has confounded interpretation of their phylogenetic position in the Brachyura and interrelationships within Pinnotheroidea, though all were nevertheless believed to be united by a monophyletic origin of obligate commensalism. The family Aphanodactylidae Ahyong & Ng, 2009 was proposed for a group of genera associated with tube-dwelling polychaetes formerly classified in Pinnotheridae, and provisionally retained in the Pinnotheroidea. We investigated the phylogenetic position of Aphanodactylidae using molecular data from three markers (mitochondrial 12S and 16S rRNAs, and nuclear histone H3) covering five of the 12 described aphanodactylid species and a total of 15 thoracotreme families. We found Aphanodactylidae to be monophyletic, but widely distant from Pinnotheridae and instead most closely related to Macrophthalmidae (Ocypodoidea) and Varunidae (Grapsoidea). Therefore, the family Aphanodactylidae is corroborated, but its placement in Pinnotheroidea is rejected. Instead, the phylogenetic position of Aphanodactylidae, as clearly distant from other pinnotheroids, demonstrates that obligate commensalism has evolved independently multiple times within Thoracotremata.
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30
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Shahdadi A, Schubart CD. Taxonomic review of Perisesarma (Decapoda: Brachyura: Sesarmidae) and closely related genera based on morphology and molecular phylogenetics: new classification, two new genera and the questionable phylogenetic value of the epibranchial tooth. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Adnan Shahdadi
- Institut für Zoologie & Evolutionsbiologie, Universität Regensburg, Regensburg, Germany
- Department of Biology, Faculty of Science, University of Hormozgan, Bandar Abbas, Iran
| | - Christoph D Schubart
- Institut für Zoologie & Evolutionsbiologie, Universität Regensburg, Regensburg, Germany
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31
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Cannicci S, Schubart CD, Innocenti G, Dahdouh-Guebas F, Shahdadi A, Fratini S. A new species of the genus Parasesarma De Man 1895 from East African mangroves and evidence for mitochondrial introgression in sesarmid crabs. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Complete mitochondrial genome of Clistocoeloma sinensis (Brachyura: Grapsoidea): Gene rearrangements and higher-level phylogeny of the Brachyura. Sci Rep 2017. [PMID: 28646134 PMCID: PMC5482888 DOI: 10.1038/s41598-017-04489-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (−0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm. The two ribosomal RNA genes had 80.2% A+T content. The A+T-rich region spanned 684 bp. The gene order within the complete mitogenome of C. sinensis was identical to the pancrustacean ground pattern except for the translocation of trnH. Additionally, the gene order of trnI-trnQ-trnM in the pancrustacean ground pattern becomes trnQ-trnI-trnM in C. sinensis. Our phylogenetic analysis showed that C. sinensis and Sesarmops sinensis cluster together with high nodal support values, indicating that C. sinensis and S. sinensis have a sister group relationship. The results support that C. sinensis belongs to Grapsoidea, Sesarmidae. Our findings also indicate that Varunidae and Sesarmidae species share close relationships. Thus, mitogenomes are likely to be valuable tools for systematics in other groups of Crustacea.
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33
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Fujiwara SI, Kawai H. Crabs grab strongly depending on mechanical advantages of pinching and disarticulation of chela. J Morphol 2016; 277:1259-72. [DOI: 10.1002/jmor.20573] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/23/2016] [Accepted: 06/10/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Shin-ichi Fujiwara
- Nagoya University Museum, Nagoya University, Furocho; Chikusa-ku Nagoya 464-8601 Japan
| | - Hiroki Kawai
- Department of Earth and Planetary Sciences; Graduate School of Environmental Studies, Nagoya University, Furocho; Chikusa-Ku Nagoya 466-8601 Japan
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34
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Xing Y, Ma X, Wei Y, Pan D, Liu W, Sun H. The complete mitochondrial genome of the semiterrestrial crab, Chiromantes neglectum (Eubrachyura: Grapsoidea: Sesarmidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:461-463. [PMID: 33473520 PMCID: PMC7799694 DOI: 10.1080/23802359.2016.1186509] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The complete mitogenome of the semiterrestrial crab Chiromantes neglectum was sequenced. It contained the entire set of 37 genes. The gene order was basically identical to pancrustacean ground pattern, except for thetrnH and trnQ genes. Phylogenetic inferences based on protein-coding genes (PCGs) provide strong evidence that places C. neglectum within an intermingled 'Grapsoidea & Ocypodoidea' clade.
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Affiliation(s)
- Yuhui Xing
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoping Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuqing Wei
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenliang Liu
- Schoole of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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35
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Krieger J, Braun P, Rivera NT, Schubart CD, Müller CH, Harzsch S. Comparative analyses of olfactory systems in terrestrial crabs (Brachyura): evidence for aerial olfaction? PeerJ 2015; 3:e1433. [PMID: 26713228 PMCID: PMC4690415 DOI: 10.7717/peerj.1433] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/03/2015] [Indexed: 11/30/2022] Open
Abstract
Adaptations to a terrestrial lifestyle occurred convergently multiple times during the evolution of the arthropods. This holds also true for the "true crabs" (Brachyura), a taxon that includes several lineages that invaded land independently. During an evolutionary transition from sea to land, animals have to develop a variety of physiological and anatomical adaptations to a terrestrial life style related to respiration, reproduction, development, circulation, ion and water balance. In addition, sensory systems that function in air instead of in water are essential for an animal's life on land. Besides vision and mechanosensory systems, on land, the chemical senses have to be modified substantially in comparison to their function in water. Among arthropods, insects are the most successful ones to evolve aerial olfaction. Various aspects of terrestrial adaptation have also been analyzed in those crustacean lineages that evolved terrestrial representatives including the taxa Anomala, Brachyura, Amphipoda, and Isopoda. We are interested in how the chemical senses of terrestrial crustaceans are modified to function in air. Therefore, in this study, we analyzed the brains and more specifically the structure of the olfactory system of representatives of brachyuran crabs that display different degrees of terrestriality, from exclusively marine to mainly terrestrial. The methods we used included immunohistochemistry, detection of autofluorescence- and confocal microscopy, as well as three-dimensional reconstruction and morphometry. Our comparative approach shows that both the peripheral and central olfactory pathways are reduced in terrestrial members in comparison to their marine relatives, suggesting a limited function of their olfactory system on land. We conclude that for arthropod lineages that invaded land, evolving aerial olfaction is no trivial task.
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Affiliation(s)
- Jakob Krieger
- Zoological Institute and Museum, Department of Cytology and Evolutionary Biology, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Philipp Braun
- Zoological Institute and Museum, Department of Cytology and Evolutionary Biology, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Nicole T. Rivera
- Institute for Zoology, Department of Zoology & Evolution, Universität Regensburg, Regensburg, Germany
| | - Christoph D. Schubart
- Institute for Zoology, Department of Zoology & Evolution, Universität Regensburg, Regensburg, Germany
| | - Carsten H.G. Müller
- Zoological Institute and Museum, Department of General and Systematic Zoology, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
| | - Steffen Harzsch
- Zoological Institute and Museum, Department of Cytology and Evolutionary Biology, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
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36
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Jeena NS, Gopalakrishnan A, Radhakrishnan EV, Kizhakudan JK, Basheer VS, Asokan PK, Jena JK. Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2700-9. [PMID: 26065848 DOI: 10.3109/19401736.2015.1046160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lobsters constitute low-volume high-value crustacean fishery resource along Indian coast. For the conservation and management of this declining resource, accurate identification of species and larvae is essential. The objectives of this work were to generate species-specific molecular signatures of 11 commercially important species of lobsters of families Palinuridae and Scyllaridae and to reconstruct a phylogeny to clarify the evolutionary relationships among genera and species included in this study. Partial sequences were generated for all the candidate species from sampling sites along the Indian coast using markers like Cytochrome oxidase I (COI), 16SrRNA, 12SrRNA, and 18SrRNA genes, and analyzed. The genetic identities of widely distributed Thenus species along the Indian coast to be Thenus unimaculatus and the sub-species of Panulirus homarus to be P. homarus homarus were confirmed. Phylogeny reconstruction using the individual gene and concatenated mtDNA data set were carried out. The overall results suggested independent monophyly of Scyllaridae and Stridentes of Palinuridae. The interspecific divergence was found to be highest for the 12SrRNA compared with other genes. Significant incongruence between mtDNA and nuclear 18SrRNA gene tree topologies was observed. The results hinted an earlier origin for Palinuridae compared with Scyllaridae. The DNA sequence data generated from this study will aid in the correct identification of lobster larvae and will find application in research related to larval transport and distribution.
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Affiliation(s)
- N S Jeena
- a National Bureau of Fish Genetic Resources (NBFGR) Cochin Unit , Cochin , India .,b Central Marine Fisheries Research Institute (CMFRI) , Cochin , India , and
| | - A Gopalakrishnan
- b Central Marine Fisheries Research Institute (CMFRI) , Cochin , India , and
| | - E V Radhakrishnan
- b Central Marine Fisheries Research Institute (CMFRI) , Cochin , India , and
| | - Joe K Kizhakudan
- b Central Marine Fisheries Research Institute (CMFRI) , Cochin , India , and
| | - V S Basheer
- a National Bureau of Fish Genetic Resources (NBFGR) Cochin Unit , Cochin , India
| | - P K Asokan
- b Central Marine Fisheries Research Institute (CMFRI) , Cochin , India , and
| | - J K Jena
- c National Bureau of Fish Genetic Resources (NBFGR) , Lucknow , India
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37
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Ip BHY, Schubart CD, Tsang LM, Chu KH. Phylogeny of the shore crab family Grapsidae (Decapoda: Brachyura: Thoracotremata) based on a multilocus approach. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Brian H. Y. Ip
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong China
| | | | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong China
- Institute of Marine Biology; National Taiwan Ocean University; No. 2, Pei-Ning Road Keelung 202-24 Taiwan
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Hong Kong China
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38
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Ozawa T, Yin W, Fu C, Claremont M, Smith L, Reid DG. Allopatry and overlap in a clade of snails from mangroves and mud flats in the Indo-West Pacific and Mediterranean (Gastropoda: Potamididae:Cerithideopsilla). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12401] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Tomowo Ozawa
- Department of World Heritage; Cyber University; Nagoya Office, Ikegami-cho 2-7-1, Ikegami Jyutaku R203, Chikusa-ku Nagoya 464-0029 Japan
| | - Wei Yin
- Institute of Biodiversity Science; Fudan University; Handan Road 220 Shanghai 200433 China
| | - Cuizhang Fu
- Institute of Biodiversity Science; Fudan University; Handan Road 220 Shanghai 200433 China
| | - Martine Claremont
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
| | - Lisa Smith
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
| | - David G. Reid
- Department of Life Sciences; Natural History Museum; London SW7 5BD UK
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39
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Tsang LM, Schubart CD, Ahyong ST, Lai JC, Au EY, Chan TY, Ng PK, Chu KH. Evolutionary History of True Crabs (Crustacea: Decapoda: Brachyura) and the Origin of Freshwater Crabs. Mol Biol Evol 2014; 31:1173-87. [DOI: 10.1093/molbev/msu068] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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van der Meij SET, Schubart CD. Monophyly and phylogenetic origin of the gall crab family Cryptochiridae (Decapoda : Brachyura). INVERTEBR SYST 2014. [DOI: 10.1071/is13064] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The enigmatic gall crab family Cryptochiridae has been proposed to be phylogenetically derived from within the Grapsidae (subsection Thoracotremata), based on the analysis of 16S mtDNA of one cryptochirid, Hapalocarcinus marsupialis, among a wide array of thoracotremes, including 12 species of the family Grapsidae. Here, we test the monophyly and phylogenetic position of Cryptochiridae using the same gene, but with an extended representation of cryptochirids spanning nine species in eight of 21 genera, in addition to further thoracotreme representatives. The results show that gall crabs form a highly supported monophyletic clade within the Thoracotremata, which evolved independently of grapsid crabs. Therefore, the Cryptochiridae should not be considered as highly modified Grapsidae, but as an independent lineage of Thoracotremata, deserving its current family rank. Further molecular and morphological studies are needed to elucidate the precise placement of the cryptochirids within the Eubrachyura.
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Schubart CD. Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA. ZOOL ANZ 2011. [DOI: 10.1016/j.jcz.2011.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Brösing A, Türkay M. Gastric teeth of some thoracotreme crabs and their contribution to the brachyuran phylogeny. J Morphol 2011; 272:1109-15. [DOI: 10.1002/jmor.10967] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/14/2011] [Accepted: 03/12/2011] [Indexed: 11/11/2022]
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Description of a new species of Parasesarma (Crustacea; Decapoda; Brachyura; Sesarmidae) from the Persian Gulf, based on morphological and genetic characteristics. ZOOL ANZ 2010. [DOI: 10.1016/j.jcz.2010.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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SILVA INÊSC, MESQUITA NATACHA, PAULA JOSÉ. Genetic and morphological differentiation of the mangrove crab Perisesarma guttatum (Brachyura: Sesarmidae) along an East African latitudinal gradient. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01338.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yin W, Fu C, Guo L, He Q, Li J, Jin B, Wu Q, Li B. Species delimitation and historical biogeography in the genus Helice (Brachyura: Varunidae) in the northwestern Pacific. Zoolog Sci 2009; 26:467-75. [PMID: 19663641 DOI: 10.2108/zsj.26.467] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The genus Helice is comprised of four species, H. formosensis, H. latimera, H. tientsinensis, and H. tridens. A recent molecular analysis identified H. formosensis and H. tientsinensis as junior synonyms of H. latimera. We used three mitochondrial and two nuclear genes to further delineate species boundaries in Helice and to add to knowledge of the historical biogeography of the genus. The molecular data revealed deep divergences between the H. formosensis-latimera-tientsinensis complex and H. tridens. Clear genetic separations with incomplete lineage sorting and convincing morphological divergences were detected among H. formosensis, H. latimera, and H. tientsinensis, and a coalescence analysis revealed negligible gene flow among these species, except for weak unidirectional gene flow from H. formosensis to H. latimera. The estimated divergence time of 1.42-1.92 Ma between the H. formosensis-latimera-tientsinensis complex and H. tridens is consistent with the opening of the Tsushima/Korea Strait (1.71-1.52 Ma). The divergence time (approximately 22-730 ka) among H. formosensis, H. latimera, and H. tientsinensis indicates that the Taiwan Strait acted as a biogeographic barrier during major falls in sea level during the Pleistocene. Our findings indicate that H. formosensis, H. latimera, and H. tientsinensis are valid species, and that straits (Tokara Strait, Tsushima/Korea Strait, and Taiwan Strait), the Okinawa Trough, and currents (Kuroshio Current, Tsushima Current, and Taiwan Strait Warm Current) have acted as geographic barriers resulting in allopatric speciation among onshore marine animals in the northwestern Pacific.
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Affiliation(s)
- Wei Yin
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai 200433, China
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Sun H, Jin Y, Zhang D, Yang S, Li Q, Song D, Zhou K. Mitochondrial sequence data reveals the phylogeny of the AsianHelicegroup of crabs (Decapoda: Brachyura: Varunidae). J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2008.00509.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Huys R, Mackenzie-Dodds J, Llewellyn-Hughes J. Cancrincolidae (Copepoda, Harpacticoida) associated with land crabs: A semiterrestrial leaf of the ameirid tree. Mol Phylogenet Evol 2009; 51:143-56. [DOI: 10.1016/j.ympev.2008.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 12/05/2008] [Accepted: 12/06/2008] [Indexed: 11/29/2022]
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Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology. Mol Phylogenet Evol 2008; 48:986-96. [DOI: 10.1016/j.ympev.2008.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 05/02/2008] [Accepted: 05/03/2008] [Indexed: 11/24/2022]
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Nagahashi R, Kitaura J, Kawane M, Wada K, Nhuong DV. The rare shore crab Pseudogelasimus loii (Brachyura, Thoracotremata) rediscovered in Vietnam and genetic support for its assignment in the family Dotillidae. ACTA ACUST UNITED AC 2007. [DOI: 10.18353/crustacea.36.0_37] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ran Nagahashi
- Department of Biological Science, Faculty of Science, Nara Women's University
| | - Jun Kitaura
- Department of Biological Science, Faculty of Science, Nara Women's University
| | - Masako Kawane
- Department of Biological Science, Faculty of Science, Nara Women's University
| | - Keiji Wada
- Department of Biological Science, Faculty of Science, Nara Women's University
| | - Do Van Nhuong
- Mangrove Ecosystem Research Center, Hanoi University of Education
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