Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title turtles-all-probes.fasta
Downloaded 127 times
Description Fasta file of probe sequences commercially synthesized to target UCE loci in reptiles. Probes are identical to those used in Faircloth et al. 2012 (Systematic Biology; doi: 10.1093/sysbio/sys004)
Download turtles-all-probes.fasta (865.4 Kb)
Details View File Details
Title turtles-contigs-enriched-from-taxa.fasta
Downloaded 114 times
Description FASTA file of contigs assembled from raw reads generated by sequencing enriched libraries of several reptile species.
Download turtles-contigs-enriched-from-taxa.fasta (11.31 Mb)
Details View File Details
Title turtles-lastz-matches-to-reptiles.tar.bz2
Downloaded 101 times
Description LASTZ matches of probes to species-specific contigs in turtle-contigs-enriched-from-taxa.
Download turtles-lastz-matches-to-reptiles.tar.bz2 (360.4 Kb)
Details View File Details
Title turtles-probe-matches-to-reptiles.sqlite
Downloaded 104 times
Description SQLITE database of LASTZ matches (from turtles-lastz-matches-to-reptiles.tar.bz2) between assembled contigs in turtle-contigs-enriched-from-taxa.fasta and the UCE probes in turtles-all-probes.fasta. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.
Download turtles-probe-matches-to-reptiles.sqlite (496.6 Kb)
Details View File Details
Title turtles-lastz-matches-to-genome-enabled-taxa.tar.bz2
Downloaded 93 times
Description LASTZ matches of probes to data from genome-enabled taxa.
Download turtles-lastz-matches-to-genome-enabled-t...ar.bz2 (837.8 Kb)
Details View File Details
Title turtles-probe-matches-to-genome-enabled-taxa.sqlite
Downloaded 90 times
Description SQLITE database of LASTZ matches between data from genome-enabled taxa and the UCE probes in turtles-all-probes.fasta. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.
Download turtles-probe-matches-to-genome-enabled-ta...qlite (295.9 Kb)
Details View File Details
Title turtles-individual-nexus-files-for-loci.tar.bz2
Downloaded 121 times
Description NEXUS alignment files for all taxa used to generate the tree in Figure 2.
Download turtles-individual-nexus-files-for-loci.tar.bz2 (711.0 Kb)
Details View File Details
Title turtles-mrbayes-substitution-models-from-mraic.tar.bz2
Downloaded 72 times
Description MRAIC substitution models estimated for NEXUS alignment files for all taxa used to generate the tree in Figure 2 (those in turtles-individual-nexus-files-for-loci.tar.bz2).
Download turtles-mrbayes-substitution-models-from-...ar.bz2 (1.358 Mb)
Details View File Details
Title turtles-mrbayes-concatenated-nexus-file.nex
Downloaded 121 times
Description MRBAYES input file built from partitioning loci by substitution models (in turtles-mrbayes-substitution-models-from-mraic.tar.bz2) and concatenating loci (in turtles-individual-nexus-files-for-loci.tar.bz2).
Download turtles-mrbayes-concatenated-nexus-file.nex.bz2 (814.4 Kb)
Details View File Details
Title turtles-mrbayes-thin-100-output.tar.bz2
Downloaded 95 times
Description MRBAYES output following 5,000,000 iterations (thin=100) after inputting turtles-mrbayes-concatenated-nexus-file.nex.bz2. We thinned this output to generate the "thin-500" and "thin-1000" data sets by keeping every 500th and 1000th records, respectively.
Download turtles-mrbayes-thin-100-output.tar.bz2 (21.32 Mb)
Details View File Details
Title turtles-mrbayes-thin-500-output.tar.bz2
Downloaded 75 times
Description MRBAYES output following 5,000,000 iterations (thin=500) after inputting turtles-mrbayes-concatenated-nexus-file.nex.bz2. We generated this output from the "thin-100" data set (turtles-mrbayes-thin-100-output.tar.bz2) by keeping every 500th record.
Download turtles-mrbayes-thin-500-output.tar.bz2 (6.157 Mb)
Details View File Details
Title turtles-mrbayes-thin-1000-output.tar.bz2
Downloaded 75 times
Description MRBAYES output following 5,000,000 iterations (thin=1000) after inputting turtles-mrbayes-concatenated-nexus-file.nex.bz2. We generated this output from the "thin-100" data set (turtles-mrbayes-thin-100-output.tar.bz2) by keeping every 1000th record.
Download turtles-mrbayes-thin-1000-output.tar.bz2 (3.709 Mb)
Details View File Details
Title turtles-genetrees-from-cloudforest.tar.bz2
Downloaded 95 times
Description Genetrees generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2 using Cloudforest (map-reduce Phybase).
Download turtles-genetrees-from-cloudforest.tar.bz2 (130.9 Kb)
Details View File Details
Title turtles-genetrees-1000-bootreps-from-cloudforest.bz2
Downloaded 76 times
Description Genetree bootstrap replicates generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2 using Cloudforest (map-reduce Phybase).
Download turtles-genetrees-1000-bootreps-from-clou...ex.bz2 (72.77 Mb)
Details View File Details
Title turtles-computer-code-README
Downloaded 90 times
Description README describing source of computer code and snapshot of code used to analyze these data.
Download turtles-computer-code-README.txt (642 bytes)
Details View File Details
Title turtles-individual-nexus-files-for-no-snake.tar.bz2
Downloaded 71 times
Description NEXUS alignment files for all taxa (DROPPING SNAKE) for additional analysis requested by referee.
Download turtles-individual-nexus-files-for-no-sna...ar.bz2 (634.7 Kb)
Details View File Details
Title turtles-mrbayes-substitution-models-from-mraic-no-snake.tar.bz2
Downloaded 72 times
Description MRAIC substitution models estimated for NEXUS alignment (DROPPING SNAKE) for analysis requested by referee.
Download turtles-mrbayes-substitution-models-from-...ar.bz2 (1.067 Mb)
Details View File Details
Title turtles-mrbayes-concatenated-nexus-file-no-snake.nex.bz2
Downloaded 72 times
Description MRBAYES input file built from partitioning no-snake loci by substitution models (in turtles-mrbayes-substitution-models-from-mraic-no-snake.tar.bz2) and concatenating loci (in turtles-individual-nexus-files-for-no-snake.tar.bz2).
Download turtles-mrbayes-concatenated-nexus-file-n...ex.bz2 (726.4 Kb)
Details View File Details
Title turtles-mrbayes-thin-100-output-no-snake.tar.bz2
Downloaded 576 times
Description MRBAYES output following 5,000,000 iterations (thin=100) after inputting turtles-mrbayes-concatenated-nexus-file-no-snake.nex.bz2.
Download turtles-mrbayes-thin-100-output-no-snake.tar.bz2 (20.24 Mb)
Details View File Details
Title turtles-genetrees-no-snake-from-cloudforest.tar.bz2
Downloaded 75 times
Description STAR & STEAC Genetrees generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2, dropping snake, using Cloudforest (map-reduce Phybase).
Download turtles-genetrees-no-snake-from-cloudfore...ar.bz2 (115.4 Kb)
Details View File Details
Title turtles-genetrees-no-snake-1000-bootreps-from-cloudforest.bz2
Downloaded 80 times
Description Genetree bootstrap replicates generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2, dropping snake, using Cloudforest (map-reduce Phybase).
Download turtles-genetrees-no-snake-1000-bootreps-...st.bz2 (80.59 Mb)
Details View File Details

When using this data, please cite the original publication:

Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC (2012) More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Biology Letters 8(5): 783-786. http://dx.doi.org/10.1098/rsbl.2012.0331

Additionally, please cite the Dryad data package:

Crawford NG, Faircloth BC, McCormack JE, Brumfield RT, Winker K, Glenn TC (2012) Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.75nv22qj
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: