Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

Zhang, Ying; Gong, Li; Lu, Xinting; Miao, Zengliang; Jiang, Lihua; Liu, Bingjian; Liu, Liqin; Li, Pengfei; Zhang, Xu; Lü, Zhen-Ming

doi:10.1007/s13131-021-1927-7

Cited by 8 publications

(7 citation statements)

References 56 publications

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“…The utilization of the genetic distance analysis reveals that the distance between Gecarcinidae or Sesarmidae and Ocypodoidea 4 is greater than between Gecarcinidae and Sesarmidae, providing evidence to support the closer relationship between Gecarcinidae and Sesarmidae and thus justifying the N-tree topology. Additionally, comparisons made with previous studies lent further credence to this result [44,45]. Third, despite the lack of substantial differences in the overall status of the superfamily, the distribution of individual families within it has resulted in significant variations.…”

Section: Mictyris Thailandensissupporting

confidence: 55%

Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences

Wang

Zheng

Zhao

et al. 2023

Biology

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Tuerkayana is of particular interest because it has been separated, in recent years, from Cardisoma and Discoplax but studies of its taxonomic status, especially from a whole mitochondrial genome perspective, have been lacking. In this study, the mitogenomes of four species (Tuerkayana magnum, Tuerkayana rotundum, Tuerkayana hirtipes, and Tuerkayana celeste) of Tuerkayana are sequenced and contrasted with other species in Brachyura for the first time. The phylogenetic tree of Brachyura, which includes 206 crab species (189 species of Brachyuran and 17 Anomura species) with a complete mitogenome, was constructed to evaluate the phylogenetic position of Tuerkayana and Gecarcinidae within Brachyuran, and explore the monophyly of Gecarcinidae. Furthermore, two single gene trees based on cox1 and 16SrRNA separately within interspecies of Gecarcinidae were reconstructed, providing molecular evidence for Tuerkayana and further clarifying the division of genera in Gecarcinidae. Based on the mitogenome dataset of 206 crabs, the branch-site model was utilized to explore selective pressure in individual codons with CodeML. The strong selective pressure shown in nad6 indicates that it may have played a significant role in the evolution of Gecarcinidae.

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Section: Mictyris Thailandensissupporting

confidence: 55%

Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences

Wang

Zheng

Zhao

et al. 2023

Biology

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“…The inclusion of Hymenosomatidae (pillbox crabs) with the African and Eurasian freshwater groups in our results is novel, as it is the first analysis to incorporate this family in a larger tree. The grouping of African and Eurasian freshwater crabs with thoracotremes is otherwise fairly well supported Zhang et al 2022). We contradict previous analyses, where the Neotropical Pseudothelphusoidea were closely related to the freshwater group (Tsang et al 2014) and share a number of morphological synapomorphies (Cumberlidge et al 2021).…”

Section: Discussionmentioning

confidence: 99%

“…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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“…Pachygrapsus is phylogenetically well nested within crown Grapsidae, close to Grapsus (e.g., Karasawa and Kato, 2001;Chen et al, 2019;Lü et al, 2022;Tsang et al, 2022;Wolfe et al, 2022;Zhang et al, 2022).…”

Section: Phylogenetic Justification Morphological and Molecular Phylo...mentioning

confidence: 99%

“…Molecular and morphological phylogenetics are key to better understanding the evolutionary relationships through common ancestry among and within brachyurans, allowing us to quantitatively examine previous views and hypotheses largely based on traditional alpha taxonomy. This is particularly important when considering problematic groups such as the so-called podotremes and the heterotreme eubrachyurans, now widely recognized as paraphyletic groups, as well as the relationships among primary freshwater groups (e.g., Tan et al, 2018;Wang et al, 2018;Luque et al, 2019b;Ma et al, 2019;Tang et al, 2020;Wang et al, 2020;Luque et al, 2021;Tsang et al, 2022;Wolfe et al, 2022;Zhang et al, 2022;Poore and Ahyong, 2023).…”

Section: Introductionmentioning

confidence: 99%

Fossil calibrations for molecular analyses and divergence time estimation for true crabs (Decapoda: Brachyura)

Luque

Bracken‐Grissom

Ortega‐Hernández

et al. 2023

Preprint

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True crabs, or Brachyura, comprise over 7,300 known species and are among the most ecologically dominant, economically significant, and popularly recognized group of extant crustaceans. There are over 3,000 fossil brachyuran species known from mid and upper Jurassic, Cretaceous, and Cenozoic deposits across the globe, many of preserved in exquisite detail, but the origins and early evolution of true crabs remain unresolved. This uncertainty hinders the identification of the stratigraphically earliest occurrence of major brachyuran groups in the fossil record, obscuring our understanding of their phylogenetic relationships and thus the ability to estimate divergence times to answer large scale macroevolutionary questions. Here, we present 36 vetted fossil node calibration points for molecular phylogenetic analysis of crabs (one Anomura and 35 Brachyura) and reassess the earliest occurrences of several key clades based on recent fossil discoveries or re-examination of previous studies. For each calibrated node, we provide the minimum and tip maximum ages for the stratigraphically oldest fossil that can be reliably assigned to the group. Disentangling the anatomical disparity of fossil forms and their phylogenetic relationships is crucial to recognize the earliest branching members among brachyuran groups. This represents a critical first step understanding the evolution of carcinization and decarcinization in true crabs, the appearance of key adaptations, and the transition from sea to land and freshwater. The identification of reliable fossils for deep time calibrations, both as tips and nodes, is pivotal to ensure not only precise but more accurate divergence time estimations when reconstructing the crab tree of life

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Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

Cited by 8 publications

References 56 publications

Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences

Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences

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

Fossil calibrations for molecular analyses and divergence time estimation for true crabs (Decapoda: Brachyura)

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