Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end
Stern, David Ben, George Washington University
Breinholt, Jesse, University of Florida
Pedraza-Lara, Carlos, National Autonomous University of Mexico
López-Mejía, Marilú, University of Quintana Roo
Owen, Christopher L., George Washington University
Bracken-Grissom, Heather, Florida International University
Fetzner Jr., James W., Carnegie Museum of Natural History
Crandall, Keith A., George Washington University, Smithsonian Institution
Fetzner, James W., Carnegie Museum of Natural History
Published Jul 27, 2017 on Dryad.
Cite this dataset
Stern, David Ben et al. (2017). Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end [Dataset]. Dryad. https://doi.org/10.5061/dryad.6tc06
Caves are perceived as isolated, extreme habitats with a set of uniquely specialized biota, which long ago led to the idea that caves are ‘evolutionary dead-ends.’ This suggests that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independent cave-dwelling groups. Here we use the freshwater crayfish, a group with dozens of cave-dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave-dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave-adaptation is not a ‘dead-end’ for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.
DatasetS1 - Sequence alignment
Concatenated alignment of six genes used for phylogenetic analysis along with best-fit partitioning scheme
DatasetS2 - Synthetic phylogeny
Synthetic tree file
DatasetS3 - Maximum likelihood phylogeny
Time-calibrated, maximum likelihood molecular phylogeny.
DatasetS4 - Bootstrap phylogenies
Time-calibrated bootstrap phylogenies (N=1000)
TableS1 - GenBank numbers
GenBank accession numbers for all genes used in molecular phylogenetic analysis. Sequences new to this study are in bold
TableS2 - Habitat and range size data
Habitat assignments and log10 range size for taxa in the synthetic tree. Taxa without any data are excluded.
FileS1 - R scripts
R scripts used to execute the state-dependent diversification analyses and model adequacy tests.
FileS2 - treePL config file
Configuration file with fossil calibrations used in treePL
FileS3 - habitats Cave geosse
Habitat state data used for GeoSSE analysis, derived from Table S2
FileS4 - habitats Cave hisse
Habitat state data used for HiSSE analysis, derived from Table S2