Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction

Mass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes—a major clade of predators comprising over 3,700 living species—remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth’s extant vertebrate faunas.

This study consists of a number of different analyses: Phylogenetic analyses: after original construction of a tree in PhyloBayes, different parameterisations were tested in PAML. Each time, at least two chains were run and checked for convergence, and a final sample size of over 2000 was used. Disparity analyses: disparity was estimated based on vertebral measurements, in PAST. Biogeographical analyses: geographical ranges of extant taxa were used to infer biogeographical patterns in the past, accounting for the delayed emergence of the Caribbean and the changing distances between continents, from the Cretaceous to the present.

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Information on extant taxon ranges was gathered from the Reptile Database https://reptile-database.reptarium.cz/. All other data is from published literature (references included in SI) All figures have associated raw data, freely available in the SI.
2 Phylogenetic analyses: an existing dataset of molecular sequences for all squamate species (Zheng & Wiens, 2016) with at least one gene sequenced at the time was used. This was subsampled with a focus on snakes, but maintaining the non-squamate outgroup taxa and other squamate clades, to allow for additional fossil calibrations. Disparity analyses: images of published fossil snake vertebrae were collected, all references available in the supplementary files. Biogeographical analyses: only the ingroup tree was used. All estimations run over 3 time slices and 9 continental areas. Information on extant taxon ranges was gathered from the Reptile Database.
Disparity analyses: all snake fossils represented by mid-trunk vertebrae, dating from the mid-Cretaceous to the Oligocene, and published in peer-reviewed literature, were included. Sample sizes in individual time bins, when data was separated by ecological preference in size through time analyses, reached a minimum of three. Phylogenetic analyses: snake taxa were chosen so as to reflect the different families within snakes and all basal nodes, without compromising on the stability of the tree due to low gene sampling. Sampling was not automated, but conducted as objectively as possible Data was purely collected from the literature. All measurements taken for disparity analyses and geographical ranges were collected by a single person, CGK.
Data collection for disparity analyses occurred in November 2017 to May 2019. Geographical ranges were recorded on 27 April 2018 Exclusion criteria were pre-established -only some snake vertebrae were excluded from disparity analyses, when the position along the vertebral column could not be established, or specimen was described as juvenile.
All molecular clock analyses were run at least twice, successfully converging on similar dates. All other analyses can be reproduced successfully.
Searches of tree space were started in random locations. For all other analyses, randomization tests were implemented, as we did not have control over the grouping of data -for disparity analyses species were allocated to groups in relation to their temporal range We deal with a single history of life. This is not a manipulative experimental set up or design, so blinding was not relevant. nature research | reporting summary