Abstract
Estimated phylogenies of evolutionarily diverse taxa will be well supported and more likely to be historically accurate when the analysis contains large amounts of data–many genes sequenced across many taxa. Inferring such phylogenies for non-model organisms is challenging given limited resources for whole-genome sequencing. We take advantage of genomic data from a single species to test the limits of hybridization-based enrichment of hundreds of exons across frog species that diverged up to 250 million years ago. Enrichment success for a given species depends greatly on the divergence time between it and the reference species, and the resulting alignment contains a significant proportion of missing data. However, our alignment generates a well-supported phylogeny of frogs, suggesting that this technique is a practical solution towards resolving relationships across deep evolutionary time.
Highlights
Biologists have made great strides in reconstructing the evolutionary history of Life
Useful for phylogenetic analyses, transcriptome sequencing requires mRNA from fresh tissues, and cannot be used with genetic resource collections, museum specimens, or tissues that have been stored in ethanol
We found that reads simulated on the target regions only very rarely mapped to the wrong target exon, even when the average p-distance between the reference and simulated reads was as high as 24%
Summary
Biologists have made great strides in reconstructing the evolutionary history of Life. The number of available orthologous sequences for many taxa has greatly increased by comparing whole genomes [7,8,9,10] or expressed sequenced tags (ESTs; e.g., [11,12,13,14]) These two approaches have proven useful, generating the initial sequence data typically requires high-quality tissue samples and considerable effort for each species. Messenger RNA is extracted from fresh tissue and used to produce cDNA libraries, which are sequenced and used to build phylogenies (as in [16,17,18]) These data sets are enriched for expressed genes, and contain only exon sequences. Useful for phylogenetic analyses, transcriptome sequencing requires mRNA from fresh tissues, and cannot be used with genetic resource collections, museum specimens, or tissues that have been stored in ethanol
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