title: Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes.
abstract: Ultraconserved elements (UCEs) have become popular markers in phylogenomic studies because of their cost effectiveness and their potential to resolve problematic phylogenetic relationships. Although UCE datasets typically contain a much larger number of loci and sites than more traditional datasets of PCR-amplified, single-copy, protein coding genes, a fraction of UCE sites are expected to be part of a nearly invariant core, and the relative performance of UCE datasets versus protein coding gene datasets is poorly understood. Here we use phylogenetic informativeness (PI) to compare the resolving power of multi-locus and UCE datasets in a sample of percomorph fishes with sequenced genomes (genome-enabled). We compare three data sets: UCE core regions, flanking sequence adjacent to the UCE core and a set of ten protein coding genes commonly used in fish systematics. We found the net informativeness of UCE core and flank regions to be roughly ten-fold and 100-fold more informative than that of the protein coding genes. On a per locus basis UCEs and protein coding genes exhibited similar levels of phylogenetic informativeness. Our results suggest that UCEs offer enormous potential for resolving relationships across the percomorph tree of life.
authors.affiliation: Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA. Electronic address: ps.gilbert@ucla.edu.
authors.forename: Princess S
authors.initials: PS
authors.lastname: Gilbert
authors.affiliation: Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Chang
authors.affiliation: Department of Medicine, University of California, Los Angeles, CA, USA.
authors.forename: Calvin
authors.initials: C
authors.lastname: Pan
authors.affiliation: Department of Human Genetics, University of California, Los Angeles, CA, USA.
authors.forename: Eric M
authors.initials: EM
authors.lastname: Sobel
authors.affiliation: Department of Biomathematics, University of California, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Biostatistics, University of California, Los Angeles, CA, USA.
authors.forename: Janet S
authors.initials: JS
authors.lastname: Sinsheimer
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA.
authors.forename: Brant C
authors.initials: BC
authors.lastname: Faircloth
authors.affiliation: Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA. Electronic address: michaelalfaro@ucla.edu.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Alfaro
mesh_terms: D000818:Animals; D016001:Confidence Intervals; D017124:Conserved Sequence / Q000235:genetics*; D030541:Databases, Genetic; D005399:Fishes / Q000235:genetics*; D056426:Genetic Loci; D005819:Genetic Markers; D016678:Genome; D016014:Linear Models; D009711:Nucleotides / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D015203:Reproducibility of Results
chemical_list: D005819:Genetic Markers; D009711:Nucleotides
keywords: Molecular evolution; Next-generation sequencing; Non-coding DNA; Phylogenetic informativeness; Phylogenomics; Ultraconserved elements