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Data and code from: Simple a posteriori insertion of fossil tips in molecular phylogenies can improve inferences of continuous trait evolution

DeHaan, Lindsey1; Slater, Graham2; Friedman, Matt1

Published Sep 22, 2026 on Dryad. https://doi.org/10.5061/dryad.d51c5b0j6

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Sep 22, 2026 version files 1.05 GB

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Abstract

Integrating neontological and paleontological information improves inferences about the tempo and mode of phenotypic evolution over long timescales. Such investigations require a total-evidence phylogeny and a matching phenotypic dataset for both extant and extinct species. However, outside a few exemplar clades, morphological matrices establishing formal phylogenetic placements of fossils within molecular phylogenies are often lacking, limiting the inclusion of fossil data in macroevolutionary inferences. Informal fossil placements are commonly inferred through morphological assessment (e.g., as is often the case for node-age calibrations), but determining branch length durations is less straightforward. Using simulations, we compared four methods of a posteriori fossil insertion on models of continuous trait evolution. We find that arbitrarily assigning branch lengths to fossil taxa or analytically estimating them using continuous trait data had minor impacts on phenotypic inferences relative to true branch lengths. However, use of minimum fossil branch lengths biased model selection toward an Ornstein-Uhlenbeck process and inflated rate estimates. Applying these methods to a comparative dataset of carangarian fishes revealed an early burst pattern of trait evolution that goes undetected in extant-only analyses. We demonstrate that a posteriori insertion of fossils, even with designated rather than inferred branch lengths, shifts inferences about the tempo and mode of phenotypic evolution relative to those based only on extant taxa.