Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

Abstract

Background The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. Results Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. Conclusions We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

Sphenofontis velseraegen. et sp. nov., a new rhynchocephalian from the Late Jurassic of Brunn (Solnhofen Archipelago, southern Germany)

“…If the identification of Sphenofontis as a sphenodontine is correct, this mixture of characters may suggest a basal position within the clade. A preliminary phylogenetic analysis based on the matrix recently published by Simões, Caldwell & Pierce (2020) and conducted as a first test for the relationships of Sphenofontis supports this conclusion ( Fig. 12 ; see the Data S1 for further details).…”

“…In the future, further scrutiny will permit a better understanding of its relationships with other rhynchocephalians, especially those from the Solnhofen Archipelago, and also to improve our comprehension of character distribution in less inclusive clades within the group due to its good preservation and the apparent mixture of derived and plesiomorphic features. This gains additional significance in the light of the importance of mosaic evolution in sphenodontian phylogenetic history recently highlighted by Simões, Caldwell & Pierce (2020) .…”

Revising dating estimates and the antiquity of eusociality in termites using the fossilized birth–death process

“…Because of the well‐identified limitations of node‐dating analyses, tip‐dating analyses are becoming popular (Parham et al ., 2012; Ronquist et al ., 2012a; Heath et al ., 2014; Matzke & Wright, 2016; Simões et al ., 2020). They are, however, not devoid of their own limitations, which has occasionally triggered some doubts in their resulting age estimates, which might have seemed unreasonably old (e.g.…”

“…Arcila & Tyler, 2017). Several reasons have been suggested from the lack of an FBD process, to inaccurate topologies and inadequate models of evolution (Arcila & Tyler, 2017; Luo et al ., 2020; Simões et al ., 2020). Here, tip‐dating analyses all provide older estimates than node‐dating analyses.…”

“…estimated mean of branch rate variance) so that ages estimated from those analyses should be interpreted with caution. A recent study on sphenodontian reptiles came to the same conclusion regarding the negative impact of sampling for ancestors in dating estimates relying only on morphological datasets (Simões et al ., 2020).…”