title: Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?
abstract: BACKGROUND
  Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution.
  
  
  RESULTS
  The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20-25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997).
  
  
  CONCLUSIONS
  Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America.
authors.affiliation: Department of Biology, University of Washington, Seattle, Washington, 98195, USA. leache@uw.edu.|Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA. leache@uw.edu.
authors.forename: Adam D
authors.identifier: http://orcid.org/0000-0001-8929-6300
authors.initials: AD
authors.lastname: Leaché
authors.affiliation: Department of Biology, University of Washington, Seattle, Washington, 98195, USA.|Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B402, Seattle, 98109, Washington, USA.
authors.forename: Barbara L
authors.initials: BL
authors.lastname: Banbury
authors.affiliation: Department of Biology, University of Washington, Seattle, Washington, 98195, USA.
authors.forename: Charles W
authors.initials: CW
authors.lastname: Linkem
authors.affiliation: Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México.
authors.forename: Adrián Nieto-Montes
authors.initials: AN
authors.lastname: de Oca
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002875:Chromosomes; D008116:Lizards / Q000145:classification* / Q000235:genetics*; D009656:North America; D010802:Phylogeny; D017422:Sequence Analysis, DNA
keywords: Gene tree; Lizards; Phrynosomatidae; Phylogenomics; Species tree; Systematics