Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments
Creators: name: Wolfe, Joanna M.
name: Ballou, Lauren
name: Luque, Javier
name: Watson-Zink, Victoria
name: Ahyong, Shane
name: Barido-Sottani, Joëlle
name: Chan, Tin-Yam
name: Chu, Ka Hou
name: Crandall, Keith
name: Daniels, Savel
name: Felder, Darryl
name: Mancke, Harrison
name: Martin, Joel
name: Ng, Peter
name: Ortega-Hernández, Javier
name: Palacios Theil, Emma
name: Pentcheff, Dean
name: Robles, Rafael
name: Thoma, Brent
name: Tsang, Ling Ming
name: Wetzer, Regina
name: Windsor, Amanda
name: Bracken-Grissom, Heather
Publisher: name: Zenodo
Year: 2023
Subjects: Brachyura
Crustaceans
convergent evolution
Terrestrialization
molecular phylogeny
divergence times
Fossil calibration
threshold model

description: 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 tips spanning 88 of 109 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 seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. 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 extensive new 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.
description: Fasta (.fasta) is a file type for sequence data and multiple sequence alignments. Nexus (.nex) is a common file type for phylogenetic data and multiple sequence alignments, and the required runfile to use MrBayes for phylogenetic analysis. Newick (.tre, .trees, .treefile) files are phylogenetic tree and chronogram outputs from multiple programs, which can be visualized directly e.g. with Figtree. XML (.xml) files are used to set up the run parameters for divergence time analysis in BEAST2. Log (.log) files in this instance are output from the independent chains run by BEAST2, and can be visualized by Tracer.Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB-1856679Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB-1856667Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB-EF-0531603Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB-EF-0531616Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001<br>Award Number: DEB-EF-0531762
description: Please see preprint.