Mitogenomes Provide Insights Into the Evolution of Thoracotremata (Brachyura: Eubrachyura)

Sun, Shao'e; Jiang, Wei; Yuan, Ziming; Sha, Zhongli

doi:10.3389/fmars.2022.848203

Cited by 13 publications

(35 citation statements)

References 65 publications

(108 reference statements)

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“…Previous molecular phylogenies of Brachyura have been constructed from eight to 10 Sanger loci (Tsang et al 2014, 2022), mitochondrial genomes (Tang et al 2017; Tan et al 2019; Wang et al 2021; Jennings et al 2021; Lau et al 2021; Sun et al 2022; Zhang et al 2022), transcriptomics (Ma et al 2019) and genomic target capture (Wolfe et al 2019). However, the deep relationships among families and superfamilies remain uncertain, as the most extensive study (Tsang et al 2014) sampled only 58 of 104 families with eight genes and low support at deep nodes, and more extensive gene sampling was coupled with even lower taxon sampling (Timm and Bracken-Grissom 2015; Wolfe et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

Wolfe

Ballou

Luque

et al. 2022

Preprint

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For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 species spanning 88 of 104 families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least five and up to 15 times convergently, and returned to the sea from non-marine environments three or four times. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and newly compiled fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

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Section: Discussionmentioning

confidence: 99%

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

Wolfe

Ballou

Luque

et al. 2022

Preprint

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“…The variation in mitochondrial gene order is informative in understanding the evolution of invertebrates (Akasaki et al, 2006; Sun et al, 2022a; Yuan et al, 2012; Zheng et al, 2018). The ancestral gene order reconstruction (MGLO analysis, Figure 3b) recovered the gene order found in all sampled Ophiuridae as the most likely ancestral order of all Ophiuroidea.…”

Section: Resultsmentioning

confidence: 99%

Mitogenomes provide insights into the phylogeny and evolution of brittle stars (Echinodermata, Ophiuroidea)

2022

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Ophiuroidea is the most speciose of all classes of Echinoderma. It is an important component in benthic ecosystems, occurring in almost all ecological niches of modern seas. To date, the phylogeny and complete evolutionary history of the ophiuroids have not yet been fully resolved. In this study, we sequenced the complete mitochondrial genomes (mitogenomes) of Ophiothrix (Ophiothrix) exigua and two deep‐sea species Histampica sp. CS049 and Ophioplinthaca sp. M5261. These two deep‐sea ophiuroids displayed reversed strand‐compositional bias and rearranged gene orders. Thirteen distinct patterns of mitochondrial gene order among ophiuroid mitogenomes were detected, with two gene order newly found in Ophiuroidea. Our data supported the gene order found in all sampled Ophiuridae as the most likely ancestral order of all Ophiuroidea. To improve phylogenetic accuracy based on nucleotide differences, two different criteria were used for the analyses: (i) nucleotide sequence from all codon positions (PCG123); (ii) the NTE method (“Neutral Transitions Excluded”) for ameliorating the misleading effects of a reverse strand bias in the data. The two methods confirmed the polyphyly of the orders Ophiacanthida and Amphilepidia. At family and genus level, Ophiuridae, Ophionotus and Ophioplinthus were not monophyletic. The most notable exception was that the NTE phylogeny showed low variation of branch length. NTE dataset generated younger age for most lower‐level nodes than that from PCG123 dataset. All analyses suggested that the ophiuroids radiation occurred around the Permian–Triassic mass extinction event, and the divergence time of the deep‐sea lineages was during the Cretaceous.

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“…The invasives have significantly more AT rich mitogenomes than the natives, while natives have a higher GC content. This indicates that invasive species might have longer non-coding regions or that the native species have longer protein-coding genes, overall indicating more compact mitogenomes in the latter [75,76]. How and if this relates to invasion ability remains to be seen, but this strong differentiation can potentially open new avenues for research.…”

Section: Discussionmentioning

confidence: 99%

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

Macher

Šidagytė-Copilas

Copilaş‐Ciocianu

2023

Preprint

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European inland surface waters harbor an extensive diversity of native amphipod crustaceans with many species facing threats from invasive counterparts of Ponto-Caspian origin. Herein, we examine mitochondrial genomes to infer phylogenetic relationships and compare gene order and nucleotide composition between representative native European and invasive Ponto-Caspian taxa belonging to five families, ten genera, and 20 species (13 newly sequenced herein). We observe diverse gene rearrangement patterns in the phylogenetically disparate native species pool.Pallaseopsis quadrispinosaandSynurella ambulansshow significant departures from the typical organization, with extensive translocations of tRNAs and thenad1gene, as well as a tRNA-F polarity switch in the latter. The monophyletic alien Ponto-Caspian gammarids display a conserved gene order, mainly differing from the native species by a tRNA-E and tRNA-R translocation, which strengthens previous findings. However, extensive rearrangement is observed inChaetogammarus warpachowskyiwith translocations of six tRNAs. The alien corophiid,Chelicorophium curvispinum, displays a very conserved gene order despite its distant phylogenetic position. We also find that native species have a significantly higher GC and lower AT content than invasive ones. The observed mitogenomic differences between native and invasive amphipods need further investigation and could shed light on the mechanisms underlying invasion success.

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Mitogenomes Provide Insights Into the Evolution of Thoracotremata (Brachyura: Eubrachyura)

Cited by 13 publications

References 65 publications

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments

Mitogenomes provide insights into the phylogeny and evolution of brittle stars (Echinodermata, Ophiuroidea)

Comparative mitogenomics of native European and alien Ponto-Caspian amphipods

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