DOI: 10.5061/dryad.7ct1n
title: Data from: The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

description: 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.
description: Nexus file - phenotypic
 and ancestral state reconstruction charactersPhenotypic characters
 (766 total) represent latest revision of the Gauthier et al. (2012) AToL
 squamate matrix. Ancestral state reconstruction characters (11 total)
 collected based on literature searches (see Additional file 8). Matrix
 generated using Mesquite v. 2.75 (build 566).phenotypic_asr_data.nxsNexus file - genetic data onlyGenetic data compiled from NCBI GenBank database (see Additional file 9 for accession numbers) for 21 nuclear loci and one mitochondrial locus. Generated using TextWrangler v. 4.0.1 (build 3152).genetic_data.nxsNexus file - combined phenotypic and genetic charactersDataset combining phenotypic characters (777 total) and genetic characters (18,320 total). Generated using TextWrangler v. 4.0.1 (build 3152).combined_data.nxsList of phenotypic characters and state namesComplete list of phenotypic characters updated from Gauthier et al.'s (2012) AToL squamate matrix.character_states_names.docx