title: Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time.
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.
authors.affiliation: Department of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, Texas, United States of America. shannon.hedtke@gmail.com
authors.forename: Shannon M
authors.initials: SM
authors.lastname: Hedtke
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Morgan
authors.forename: David C
authors.initials: DC
authors.lastname: Cannatella
authors.forename: David M
authors.initials: DM
authors.lastname: Hillis
mesh_terms: D000818:Animals; D001001:Anura / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics*; D014644:Genetic Variation; D016678:Genome / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013997:Time Factors