Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

Stern DB, Breinholt J, Pedraza C, López-Mejía M, Owen CL, Bracken-Grissom H, Fetzner Jr. JW, Crandall KA

Date Published: July 27, 2017

DOI: http://dx.doi.org/10.5061/dryad.6tc06

 

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Title DatasetS1 - Sequence alignment
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Description Concatenated alignment of six genes used for phylogenetic analysis along with best-fit partitioning scheme
Download DatasetS1.nex (3.736 Mb)
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Title DatasetS2 - Synthetic phylogeny
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Description Synthetic tree file
Download DatasetS2.tre (21.20 Kb)
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Title DatasetS3 - Maximum likelihood phylogeny
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Description Time-calibrated, maximum likelihood molecular phylogeny.
Download DatasetS3.tre (19.52 Kb)
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Title DatasetS4 - Bootstrap phylogenies
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Description Time-calibrated bootstrap phylogenies (N=1000)
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Title TableS1 - GenBank numbers
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Description GenBank accession numbers for all genes used in molecular phylogenetic analysis. Sequences new to this study are in bold
Download TableS1.xls (95.74 Kb)
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Title TableS2 - Habitat and range size data
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Description Habitat assignments and log10 range size for taxa in the synthetic tree. Taxa without any data are excluded.
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Title FileS1 - R scripts
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Description R scripts used to execute the state-dependent diversification analyses and model adequacy tests.
Download FileS1.R_scripts.R (14.40 Kb)
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Title FileS2 - treePL config file
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Description Configuration file with fossil calibrations used in treePL
Download FileS2.treePL.txt (889 bytes)
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Title FileS3 - habitats Cave geosse
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Description Habitat state data used for GeoSSE analysis, derived from Table S2
Download FileS3.habitats_Cave.geosse.csv (9.318 Kb)
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Title FileS4 - habitats Cave hisse
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Description Habitat state data used for HiSSE analysis, derived from Table S2
Download FileS4.habitats_Cave.hisse.tsv (6.979 Kb)
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When using this data, please cite the original publication:

Stern DB, Breinholt J, Pedraza C, López-Mejía M, Owen CL, Bracken-Grissom H, Fetzner JW, Crandall KA (2017) Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end. Evolution, online in advance of print. http://dx.doi.org/10.1111/evo.13326

Additionally, please cite the Dryad data package:

Stern DB, Breinholt J, Pedraza C, López-Mejía M, Owen CL, Bracken-Grissom H, Fetzner Jr. JW, Crandall KA (2017) Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6tc06
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