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.
turtles-all-probes.fasta
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)
turtles-contigs-enriched-from-taxa.fasta
FASTA file of contigs assembled from raw reads generated by sequencing enriched libraries of several reptile species.
turtles-lastz-matches-to-reptiles.tar.bz2
LASTZ matches of probes to species-specific contigs in turtle-contigs-enriched-from-taxa.
turtles-probe-matches-to-reptiles.sqlite
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.
turtles-lastz-matches-to-genome-enabled-taxa.tar.bz2
LASTZ matches of probes to data from genome-enabled taxa.
turtles-probe-matches-to-genome-enabled-taxa.sqlite
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.
turtles-individual-nexus-files-for-loci.tar.bz2
NEXUS alignment files for all taxa used to generate the tree in Figure 2.
turtles-mrbayes-substitution-models-from-mraic.tar.bz2
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).
turtles-mrbayes-concatenated-nexus-file.nex
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).
turtles-mrbayes-thin-100-output.tar.bz2
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.
turtles-mrbayes-thin-500-output.tar.bz2
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.
turtles-mrbayes-thin-1000-output.tar.bz2
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.
turtles-genetrees-from-cloudforest.tar.bz2
Genetrees generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2 using Cloudforest (map-reduce Phybase).
turtles-genetrees-1000-bootreps-from-cloudforest.bz2
Genetree 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.bz2
turtles-computer-code-README
README describing source of computer code and snapshot of code used to analyze these data.
turtles-individual-nexus-files-for-no-snake.tar.bz2
NEXUS alignment files for all taxa (DROPPING SNAKE) for additional analysis requested by referee.
turtles-mrbayes-substitution-models-from-mraic-no-snake.tar.bz2
MRAIC substitution models estimated for NEXUS alignment (DROPPING SNAKE) for analysis requested by referee.
turtles-mrbayes-concatenated-nexus-file-no-snake.nex.bz2
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).
turtles-mrbayes-thin-100-output-no-snake.tar.bz2
MRBAYES 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.bz2
STAR & 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.bz2
Genetree bootstrap replicates generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2, dropping snake, using Cloudforest (map-reduce Phybase).