Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes

Kobayashi, Gorô; Itoh, Hajime; Nakajima, Nobuyoshi

doi:10.2108/zs220063

Cited by 4 publications

(9 citation statements)

References 61 publications

(142 reference statements)

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“…S3 ), deserving of superfamily rank. Earlier studies used a single Cryptochiroidea representative, hence no conclusions about the superfamily status could be drawn based on those trees ( Wetzer, Martin & Boyce, 2009 ; Tsang et al, 2014 ; Tsang et al, 2018 ; Sun et al, 2022 ; Kobayashi, Itoh & Nakajima, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

“…as closely related to an Ocypodoidea lineage (Camptandriidae/Xenophthalmidae/Dotillidae), albeit without full branch support. Furthermore, a recent phylogenetic study conducted by Kobayashi, Itoh & Nakajima (2023) , based on 82 thoracotreme mitogenomes, retrieved Cryptochiridae as a sister to the Grapsidae clade. Our phylogenetic reconstruction, with three additional cryptochirid mitogenomes, retrieved Cryptochiroidea as a separate lineage with full support.…”

Section: Discussionmentioning

confidence: 99%

“…This is in disagreement with the results of Tsang et al (2022) whose phylogenetic arrangement showed both families of symbiotic crabs clustering together—albeit also with inconclusive results—far away from the basal branches in the phylogenetic tree. In a multi-gene and fossil-calibrated phylogenetic reconstruction by Wolfe et al (2022) , Cryptochiridae clustered, again with low support, with Xenograpsidae, whereas Kobayashi, Itoh & Nakajima (2023) retrieved, based on mitogenomic data, a close relationship between Cryptochiridae and Grapsidae.…”

Section: Introductionmentioning

confidence: 97%

“…Although Pinnotheridae and Cryptochiridae are considered reciprocally monophyletic, their phylogenetic position within the Thoracotremata—and thus the origin and evolution of thoracotreme symbiosis—is still unresolved ( Sun et al, 2022 ; Tsang et al, 2022 ; Wolfe et al, 2022 ; Kobayashi, Itoh & Nakajima, 2023 ). Sun et al (2022) retrieved pea crabs at the basis of a phylogenetic tree of the Thoracotremata, whilst gall crabs clustered, without full branch support, with an Ocypodoidea lineage (Camptandriidae/Xenophthalmidae/Dotillidae).…”

Section: Introductionmentioning

confidence: 99%

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Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)

Xu,

Bravo,

van der Meij

2023

PeerJ

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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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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)

Xu,

Bravo,

van der Meij

2023

PeerJ

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“…Recently, the interfamilial relationships of Thoracotremata, using 10 molecular markers and exemplars from all nominal families have been resolved to prepare a new taxonomy consistent with phylogenetic relationships (Tsang et al 2022). In the genetic study of thoracotremes by Kobayashi et al (2023: 7), the phylogenetic placements of Pinnotheridae and Cryptochiridae were not resolved in the ML phylogenies, whereas Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae MacLeay, 1838 were highly supported in the Bayesian phylogenies.…”

Section: Review Of External Morphological Characters In the Seven Sub...mentioning

confidence: 99%

A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system

Guinot

2023

Zoosystema

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A new and revised classification of the small family Dorippidae H. Milne Edwards, 1837, which previously comprised two distinct subfamilies (Dorippinae H. Milne Edwards, 1837 and Ethusinae Guinot, 1977), each of which was subsequently elevated to a familial rank supported by traditional data and genetic phylogenies, is presented on the basis of a morphological analysis involving a large number of characters. The family is in fact highly diverse, at all levels. Several features are described and depicted in detail here for the first time, e.g. the presence of a diversely developed strip along the protrudingly rimmed posterior margin of the carapace; on the dorsally exposed thoracic sternite 8, a process acting as an additional pleonal-retention mechanism in the females of three genera (Dorippe Weber, 1795; Philippidorippe Chen, 1986; Phyllodorippe Manning & Holthuis, 1981); a callosity at the base of the coxa of the third pereiopod, variously shaped, in two genera (Dorippe and Dorippoides Serène & Romimohtarto, 1969). The generic and specific taxonomy masterfully stabilised by Holthuis & Manning (1991) is undisputed and still valid, except for the composition of the genus Heikeopsis Ng, Guinot & Davie, 2008 that may well contain in northern China a form not entirely consistent with the typical Heikeopsis japonica (von Siebold, 1824) of Japan. A second exception concerns the genus Paradorippe Serène & Romimohtarto, 1969 sensu Holthuis & Manning (1991) that may not be monophyletic. The validity of Medorippe crosnieri Chen, 1988, questioned by Holthuis & Manning (1990), could not be confirmed here: its distinctive morphological characters from M. lanata (Linnaeus, 1767) suggest that it could be recognised one day. The synthesis of conventional and new characters allows the traditional taxonomic approach to be updated and modernised, more complete and robust diagnoses to be constructed, and groups of genera to be circumscribed. We propose a new subfamily classification whereby the family Dorippidae is recognised as monophyletic but with seven genera assigned to subfamily-level rank, leading to the recognition of seven distinct subfamilies: the Dorippinae H. Milne Edwards, 1837 n. stat. (Dorippe), Dorippoidinae n. subfam. (Dorippoides), Medorippinae n. subfam. (Medorippe Manning & Holthuis, 1981), Heikeopsinae n. subfam. (Heikeopsis, Neodorippe Serène & Romimohtarto, 1969, Nobilum Serène & Romimohtarto, 1969), Paradorippinae n. subfam. (Paradorippe), Philippidorippinae n. subfam. (Philippidorippe) and Phyllodorippinae n. subfam. (Phyllodorippe). There is a high degree of concordance between several elements of our proposal: 1) the main morphological patterns of the male gonopods lead to the recognition of seven subfamilies; 2) the main morphological patterns of the vulvae correspond to the seven observed gonopod types and lead to the recognition of the same seven subfamilies; 3) the recognition of several subfamilies is supported by the well-defined clades obtained by the molecular analyses; and 4) the female re...

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The complete mitochondrial genome of the sand bubbler crab Scopimera longidactyla Shen 1932 (Decapoda: Dotillidae) and its phylogenetic analysis

Bae,

Kim,

Lim

et al. 2024

Mitochondrial DNA Part B

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Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes

Cited by 4 publications

References 61 publications

Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)

Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae)

A new subfamily classification of the highly diversified Dorippidae H. Milne Edwards, 1837 (Crustacea, Decapoda, Brachyura, Dorippoidea), using morphological, molecular and palaeotonlogical data, with special emphasis on its unique female reproductive system

The complete mitochondrial genome of the sand bubbler crab Scopimera longidactyla Shen 1932 (Decapoda: Dotillidae) and its phylogenetic analysis

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