Dryad
Published May 1, 2023 | Version v3
Software Open

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

Creators

  • 1. Harvard University
  • 2. Florida International University
  • 3. Stanford University
  • 4. Australian Museum
  • 5. École Normale Supérieure
  • 6. National Taiwan Ocean University
  • 7. Chinese University of Hong Kong
  • 8. George Washington University
  • 9. Stellenbosch University
  • 10. University of Louisiana at Lafayette
  • 11. Natural History Museum of Los Angeles County
  • 12. National University of Singapore
  • 13. University of Łódź
  • 14. Autonomous University of Campeche
  • 15. Jackson State University
  • 16. Smithsonian Institution

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.

--

Notes

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
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1856679

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-1856667

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-EF-0531603

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-EF-0531616

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: DEB-EF-0531762

Files

4_scripts.zip

Files (14.5 kB)

Name Size Download all
md5:76d6f470ab930d84e4428026ccef79a0
14.5 kB Preview Download

Additional details

Related works

Is cited by
10.1101/2022.12.09.519815 (DOI)
Is source of
10.5061/dryad.tmpg4f52z (DOI)