Journeys through discrete‐character morphospace: synthesizing phylogeny, tempo, and disparity

Abstract

Palaeontologists have long employed discrete categorical data to capture morphological variation in fossil species, using the resulting character–taxon matrices to measure evolutionary tempo, infer phylogenies and capture morphological disparity. However, to date these have been seen as separate approaches despite a common goal of understanding morphological evolution over deep time. Here I argue that there are clear advantages to considering these three lines of enquiry in a single space: the phylomorphospace. Conceptually these high‐dimensional spaces capture how a phylogenetic tree explores morphospace and allow us to consider important process questions around evolutionary rates, constraints, convergence and directional trends. Currently the literature contains fundamentally different approaches used to generate such spaces, with no direct comparison between them, despite the differing evolutionary histories they imply. Here I directly compare five different phylomorphospace approaches, three with direct literature equivalents and two that are novel. I use a single empirical case study of coelurosaurian theropod dinosaurs (152 taxa, 853 characters) to show that under many analyses the literature‐derived approaches tend to reflect introduced phylogenetic (rather than the intended morphological) signal. The two novel approaches, which produce limited ancestral state estimates prior to ordination, are able to minimize this phylogenetic signal and thus exhibit more realistic amounts of phylogenetic signal, rate heterogeneity, and convergent evolution.

Megaevolutionary dynamics in reptiles and the role of adaptive radiations in evolutionary innovation

“…We implemented MORD as our method of estimating pairwise taxon distances for the distance matrix D and the subsequent ordination matrix, made available through the Claddis R package 47 , implementing Cailliez’s correction for negative eigenvalues. Additionally, we increased our sample size by including internal nodes using ancestral state reconstructions through the recently developed pre-OASE1 method 63 . This procedure provides a much better approximation of the true morphospace when compared to methods to reconstruct ancestral nodes in most previous disparity studies using ancestral state reconstructions 63 .…”

“…Additionally, we increased our sample size by including internal nodes using ancestral state reconstructions through the recently developed pre-OASE1 method 63 . This procedure provides a much better approximation of the true morphospace when compared to methods to reconstruct ancestral nodes in most previous disparity studies using ancestral state reconstructions 63 .…”

Categorical versus geometric morphometric approaches to characterizing the evolution of morphological disparity in Osteostraci (Vertebrata, stem Gnathostomata)

“…We employed both preordination and postordination approaches to phylomorphospace construction, the relative merits of which were considered by Lloyd (). Postordination approaches are readily and therefore commonly applied, but ancestral values are forced to be within the range of sampled tip values and may lead to an underestimation of convergence.…”

“…Morphospaces and phylomorphospaces were constructed using the R packages phytools (Revell ) and ggplot2 (Wickham ). We followed two alternative approaches to creating phylomorphospaces based on post and preordination ancestral state estimation (OASE) (for a review, see Lloyd ). In the case of the preordination procedure, ancestral state reconstruction was achieved using stochastic character state mapping (Huelsenbeck et al .…”

Is Cyclocardia (Conrad) a wastebasket taxon? Exploring the phylogeny of the most diverse genus of the Carditidae (Archiheterodonta, Bivalvia)

“…(), and these data were used to perform a principal coordinate analysis (PCA). The estimation of ancestral state was introduced post‐ordination (post‐OASE approach according to Lloyd ). With these results, phylomorphospaces were generated (function: MorphospacePlot).…”