title: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record.
abstract: BACKGROUND
  The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes.
  
  
  RESULTS
  Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group - approximated by the Coniophis node - is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia.
  
  
  CONCLUSIONS
  Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.
authors.affiliation: Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. allison.hsiang@yale.edu.
authors.forename: Allison Y
authors.initials: AY
authors.lastname: Hsiang
authors.affiliation: Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. daniel.field@yale.edu.|Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA. daniel.field@yale.edu.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Field
authors.affiliation: Department of Anthropology, Yale University, New Haven, Connecticut, 06520, USA. timothy.h.webster@yale.edu.
authors.forename: Timothy H
authors.initials: TH
authors.lastname: Webster
authors.affiliation: Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. adam.behlke@yale.edu.
authors.forename: Adam D B
authors.initials: AD
authors.lastname: Behlke
authors.affiliation: Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. matthew.davis@yale.edu.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Davis
authors.affiliation: Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. rachel.racicot@yale.edu.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Racicot
authors.affiliation: Department of Geology and Geophysics, Yale University, New Haven, Connecticut, 06520, USA. jacques.gauthier@yale.edu.|Yale Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06520, USA. jacques.gauthier@yale.edu.
authors.forename: Jacques A
authors.initials: JA
authors.lastname: Gauthier
mesh_terms: D000818:Animals; D005075:Biological Evolution; D004463:Ecology; D019143:Evolution, Molecular; D053476:Extinction, Biological; D005580:Fossils; D023281:Genomics; D010802:Phylogeny; D012911:Snakes / Q000145:classification* / Q000235:genetics* / Q000502:physiology