title: Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae).
abstract: A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).
authors.affiliation: Brigham Young University, Department of Biology LSB 4102, Provo, UT 84602, USA. Electronic address: Derek_tucker@byu.edu.
authors.forename: Derek B
authors.initials: DB
authors.lastname: Tucker
authors.affiliation: Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília DF, Brazil.
authors.forename: Guarino R
authors.initials: GR
authors.lastname: Colli
authors.affiliation: Departamento de Genética e Morfologia, Universidade de Brasília, 70910-900 Brasília DF, Brazil.
authors.forename: Lilian G
authors.initials: LG
authors.lastname: Giugliano
authors.affiliation: Center for Biodiversity, Temple University, 1925 N. 12th Street, Suite 502, Philadelphia, PA 19122, USA.
authors.forename: S Blair
authors.initials: SB
authors.lastname: Hedges
authors.affiliation: Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA.
authors.forename: Catriona R
authors.initials: CR
authors.lastname: Hendry
authors.affiliation: Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA.
authors.forename: Emily Moriarty
authors.initials: EM
authors.lastname: Lemmon
authors.affiliation: Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306-4120, USA.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
authors.affiliation: Brigham Young University, Department of Biology LSB 4102, Provo, UT 84602, USA.
authors.forename: Jack W
authors.initials: JW
authors.lastname: Sites
authors.affiliation: Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA.
authors.forename: R Alexander
authors.initials: RA
authors.lastname: Pyron
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics; D020224:Expressed Sequence Tags; D056426:Genetic Loci; D008116:Lizards / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics; D010802:Phylogeny
keywords: Anchored phylogenomics; Concatenation; Species tree; Systematics; Tegu; Whiptail