Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships

Author(s):Show less -

Burbrink, Frank T. ^[1] ; Grazziotin, Felipe G. ^[2] ; Pyron, R. Alexander ^[3] ; Cundall, David ^[4] ; Donnellan, Steve ^{[5, 6]} ; Irish, Frances ^[7] ; Keogh, J. Scott ^[8] ; Kraus, Fred ^[9] ; Murphy, Robert W. ^[10] ; Noonan, Brice ^[11] ; Raxworthy, Christopher J. ^[1] ; Ruane, Sara ^[12] ; Lemmon, Alan R. ^[13] ; Lemmon, Emily Moriarty ^[14] ; Zaher, Hussam ^{[15, 16]}

Affiliation:Show less -

^[1] Amer Museum Nat Hist, Dept Herpetol, 79th St, Cent Pk West, New York, NY 10024 - USA

^[2] Inst Butantan, Lab Colecoes Zool, Ave Vital Brasil, 1500 Butanta, BR-05503900 Sao Paulo, SP - Brazil

^[3] George Washington Univ, Dept Biol Sci, Washington, DC 20052 - USA

^[4] Lehigh Univ, Dept Biol Sci, 1 W Packer Ave, Bethlehem, PA 18015 - USA

^[5] South Australian Museum, Adelaide, SA 5000 - Australia

^[6] Univ Adelaide, Sch Biol Sci, Adelaide, SA 5005 - Australia

^[7] Moravian Coll, Dept Biol Sci, 1200 Main St, Bethlehem, PA 18018 - USA

^[8] Australian Natl Univ, Res Sch Biol, Div Ecol & Evolut, Canberra, ACT 2601 - Australia

^[9] Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 - USA

^[10] Royal Ontario Museum, Dept Nat Hist, 100 Queens Pk, Toronto, ON M5S 2C6 - Canada

^[11] Univ Mississippi, Dept Biol, Oxford, MS 38677 - USA

^[12] Rutgers State Univ, Dept Biol Sci, 206 Boyden Hall, 195 Univ Ave, Newark, NJ 07102 - USA

^[13] Florida State Univ, Dirac Sci Lib, Dept Sci Comp, Tallahassee, FL 32306 - USA

^[14] Florida State Univ, Dept Biol Sci, 319 Stadium Dr, Tallahassee, FL 32306 - USA

^[15] Univ Sao Paulo, Museu Zool, BR-04263000 Sao Paulo, SP - Brazil

^[16] Sorbonne Univ, Ctr Rech Paleobiodiversite & Paleoenvironm CR2P, UMR 7207, CNRS, MNHN, Museum Natl Hist Nat, 8 Rue Buffon, CP 38, F-75005 Paris - France

• Document type: Journal article
• Source: Systematic Biology; v. 69, n. 3, p. 502-520, MAY 2020.
• Web of Science Citations: 3

Abstract

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families). (AU)

• FAPESP's process: 11/50206-9 - Origin and evolution of snakes and their diversification in the Neotropics: a multidisciplinary approach
• Grantee: Hussam El Dine Zaher
• Support Opportunities: BIOTA-FAPESP Program - Thematic Grants