title: A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification.
abstract: Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using (*)BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for >10Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.
authors: Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195-1800, USA. Electronic address: leache@uw.edu.
authors: Adam D
authors: AD
authors: Leaché
authors: Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D53113 Bonn, Germany; Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA.
authors: Philipp
authors: P
authors: Wagner
authors: Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195-1800, USA.
authors: Charles W
authors: CW
authors: Linkem
authors: Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D53113 Bonn, Germany.
authors: Wolfgang
authors: W
authors: Böhme
authors: Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
authors: Theodore J
authors: TJ
authors: Papenfuss
authors: Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA.
authors: Rebecca A
authors: RA
authors: Chong
authors: Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA.
authors: Brian R
authors: BR
authors: Lavin
authors: Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA.
authors: Aaron M
authors: AM
authors: Bauer
authors: Department of Biology, Box 1848, University of Mississippi, University, MS 38677, USA.
authors: Stuart V
authors: SV
authors: Nielsen
authors: Department of Biological Sciences, University of Texas at El Paso, 500 West University Ave., El Paso, TX 79968, USA.
authors: Eli
authors: E
authors: Greenbaum
authors: Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, 10115 Berlin, Germany.
authors: Mark-Oliver
authors: MO
authors: Rödel
authors: Department of Herpetology and Ichthyology, Natural History Museum of Geneva, C.P. 6434, CH-1211, Geneva 6, Switzerland.
authors: Andreas
authors: A
authors: Schmitz
authors: Muséum National d'Histoire Naturelle, Départment Systématique et Evolution (Reptiles), ISYEB (Institut Systématique, Evolution, Biodiversité, UMR 7205 CNRS/EPHE/MNHN), Paris, France.
authors: Matthew
authors: M
authors: LeBreton
authors: Muséum National d'Histoire Naturelle, Départment Systématique et Evolution (Reptiles), ISYEB (Institut Systématique, Evolution, Biodiversité, UMR 7205 CNRS/EPHE/MNHN), Paris, France.
authors: Ivan
authors: I
authors: Ineich
authors: Muséum National d'Histoire Naturelle, Départment Systématique et Evolution (Reptiles), ISYEB (Institut Systématique, Evolution, Biodiversité, UMR 7205 CNRS/EPHE/MNHN), Paris, France.
authors: Laurent
authors: L
authors: Chirio
authors: Forestry Research Institute of Ghana, P.O. Box 63, Fumesua, Kumasi, Ghana.
authors: Caleb
authors: C
authors: Ofori-Boateng
authors: Department of Forestry and Wildlife, University of Uyo, Akwa Ibom State, Nigeria.
authors: Edem A
authors: EA
authors: Eniang
authors: Nature Conservation Sector, Egyptian Environmental Affairs Agency, 3 Abdalla El Katib, Apt. 3, Dokki, Cairo, Egypt.
authors: Sherif
authors: S
authors: Baha El Din
authors: Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA.
authors: Alan R
authors: AR
authors: Lemmon
authors: Department of Biology, The College of Staten Island, The City University of New York, Staten Island, NY 10314, USA.
authors: Frank T
authors: FT
authors: Burbrink
mesh_terms: D000349:Africa; D000818:Animals; D001499:Bayes Theorem; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D016013:Likelihood Functions; D008116:Lizards / Q000145:classification* / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: Africa; Agamidae; Anchored phylogenomics; Next-generation sequencing; Sequence capture; Xenagama