DOI: 10.5061/dryad.75nv22qj
title: Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

description: We present the first genomic-scale analysis addressing the phylogenetic
 position of turtles, using over 1,000 loci from representatives of all
 major reptile lineages including tuatara. Previously, studies of
 morphological traits positioned turtles either at the base of the reptile
 tree or with lizards, snakes, and tuatara (lepidosaurs), whereas molecular
 analyses typically allied turtles with crocodiles and birds (archosaurs).
 A recent analysis of shared microRNA families found that turtles are more
 closely related to lepidosaurs. To test this hypothesis with data from
 many single-copy nuclear loci dispersed throughout the genome, we used
 sequence capture, high-throughput sequencing and published genomes to
 obtain sequences from 1,145 ultraconserved elements (UCEs) and their
 variable flanking DNA. The resulting phylogeny provides overwhelming
 support for the hypothesis that turtles evolved from a common ancestor of
 birds and crocodilians, rejecting the hypothesized relationship between
 turtles and lepidosaurs.
description: turtles-all-probes.fastaFasta 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)turtles-contigs-enriched-from-taxa.fastaFASTA file of contigs assembled from raw reads generated by sequencing enriched libraries of several reptile species.turtles-lastz-matches-to-reptiles.tar.bz2LASTZ matches of probes to species-specific contigs in turtle-contigs-enriched-from-taxa.turtles-probe-matches-to-reptiles.sqliteSQLITE 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.turtles-lastz-matches-to-genome-enabled-taxa.tar.bz2LASTZ matches of probes to data from genome-enabled taxa.turtles-probe-matches-to-genome-enabled-taxa.sqliteSQLITE 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.turtles-individual-nexus-files-for-loci.tar.bz2NEXUS alignment files for all taxa used to generate the tree in Figure 2.turtles-mrbayes-substitution-models-from-mraic.tar.bz2MRAIC 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).turtles-mrbayes-concatenated-nexus-file.nexMRBAYES 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).turtles-mrbayes-thin-100-output.tar.bz2MRBAYES 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.turtles-mrbayes-thin-500-output.tar.bz2MRBAYES 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.turtles-mrbayes-thin-1000-output.tar.bz2MRBAYES 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.turtles-genetrees-from-cloudforest.tar.bz2Genetrees generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2 using Cloudforest (map-reduce Phybase).turtles-genetrees-1000-bootreps-from-cloudforest.bz2Genetree bootstrap replicates generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2 using Cloudforest (map-reduce Phybase).turtles-genetrees-1000-bootreps-from-cloudforest.nex.bz2turtles-computer-code-READMEREADME describing source of computer code and snapshot of code used to analyze these data.turtles-individual-nexus-files-for-no-snake.tar.bz2NEXUS alignment files for all taxa (DROPPING SNAKE) for additional analysis requested by referee.turtles-mrbayes-substitution-models-from-mraic-no-snake.tar.bz2MRAIC substitution models estimated for NEXUS alignment (DROPPING SNAKE) for analysis requested by referee.turtles-mrbayes-concatenated-nexus-file-no-snake.nex.bz2MRBAYES 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).turtles-mrbayes-thin-100-output-no-snake.tar.bz2MRBAYES output following 5,000,000 iterations (thin=100) after inputting turtles-mrbayes-concatenated-nexus-file-no-snake.nex.bz2.turtles-genetrees-no-snake-from-cloudforest.tar.bz2STAR & STEAC Genetrees generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2, dropping snake, using Cloudforest (map-reduce Phybase).turtles-genetrees-no-snake-1000-bootreps-from-cloudforest.bz2Genetree bootstrap replicates generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2, dropping snake, using Cloudforest (map-reduce Phybase).