Data from: More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
Data files
May 18, 2012 version files 224.53 MB
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turtles-all-probes.fasta
865.45 KB
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turtles-computer-code-README.txt
642 B
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turtles-contigs-enriched-from-taxa.fasta
11.32 MB
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turtles-genetrees-1000-bootreps-from-cloudforest.nex.bz2
72.77 MB
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turtles-genetrees-from-cloudforest.tar.bz2
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turtles-genetrees-no-snake-1000-bootreps-from-cloudforest.bz2
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turtles-genetrees-no-snake-from-cloudforest.tar.bz2
115.48 KB
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turtles-individual-nexus-files-for-loci.tar.bz2
711.02 KB
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turtles-individual-nexus-files-for-no-snake.tar.bz2
634.77 KB
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turtles-lastz-matches-to-genome-enabled-taxa.tar.bz2
837.82 KB
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turtles-lastz-matches-to-reptiles.tar.bz2
360.49 KB
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turtles-mrbayes-concatenated-nexus-file-no-snake.nex.bz2
726.48 KB
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turtles-mrbayes-concatenated-nexus-file.nex.bz2
814.49 KB
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turtles-mrbayes-substitution-models-from-mraic-no-snake.tar.bz2
1.07 MB
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turtles-mrbayes-substitution-models-from-mraic.tar.bz2
1.36 MB
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turtles-mrbayes-thin-100-output-no-snake.tar.bz2
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turtles-mrbayes-thin-100-output.tar.bz2
21.32 MB
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turtles-mrbayes-thin-1000-output.tar.bz2
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turtles-mrbayes-thin-500-output.tar.bz2
6.16 MB
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turtles-probe-matches-to-genome-enabled-taxa.sqlite
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turtles-probe-matches-to-reptiles.sqlite
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Abstract
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.