Testing character-evolution models in phylogenetic paleobiology: a case study with Cambrian echinoderms

Abstract

Macroevolutionary inference has historically been treated as a two-step process, involving the inference of a phylogenetic tree, and then inference of a macroevolutionary model using that tree. Newer models, such as the fossilized birth-death model, blend the two steps. These methods make more complete use of fossils than the previous generation of Bayesian phylogenetic models. They also involve many more parameters than prior models, including parameters about which empiricists may have little intuition. In this paper, we set forth a framework for fitting complex, hierarchical models.We ultimately fit and use a joint tree and diversification model to estimate a dated phylogeny of the Cincta (Echinodermata), a morphologically distinct group of Cambrian echinoderms that lack the five-fold radial symmetry characteristic of extant members of the phylum. Although the phylogeny of cinctans remains poorly supported in places, we show how models of character change and diversification contribute to understanding patterns of phylogenetic relatedness and testing macroevolutionary hypotheses. Finally our new analysis raises interesting questions about how incorporating age information is expected to affect a phylogeny, and provides a framework for future systematic and macroevolutionary studies of cinctan echinoderms.

Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity

“…Our models also assume that morphological data subsets (defined by the number of states) evolve at different relative rates, and that rate variation within data subsets follows a gamma distribution. Models that accommodate variation in the rate and process of evolution using biologically meaningful data partitions (for example, partitioning between feeding and non-feeding characters, as in Wright et al 2020, or between reproductive and vegetative characters, etc.) provide another opportunity to improve model realism.…”

“…Discrepancies between the clock and non-clock analyses (see Fig. S77), and between node-based and TED analyses, provide a strong example of the potential for temporal data to alter our inferences of phylogenetic relationships (Drummond et al 2006; Gavryushkina et al 2017; Lee and Yates 2018; Wright et al 2020). TED analyses, by co-estimating the position of the fossils and the divergence times of the tree, allow for both the morphological characteristics and the temporal data associated with the fossils (their ages) to influence their position in the phylogeny.…”

“…e ., that they were drawn from separate mixture models). This model differs from previous work where each time slice was allowed to have an independent rate parameter (rather than being drawn from a mixture model), but used a small number of time slices (see Zhang et al 2016; Wright et al 2020). Our approach balances model complexity (the number of rate parameters) and the temporal resolution over which rates vary (the number of time slices).…”

Phylogenetic Comparative Methods: A User's Guide for Paleontologists

“…Until recently, there have been largely separate analytical frameworks for phylogenetic inference (inferring relationships between taxonomic units using morphological or molecular character data) and phylogenetic comparative methods (testing hypotheses about evolution while treating the relationships as known). In this paper we only discuss the latter, but other articles in this volume focus on a unified methodological framework that integrates the two (Warnock and Wright 2020;Wright et al 2020). Many other types of information, such as biogeographic data (Matzke and Wright 2016;Landis 2017), can be used in this modelling framework, and as new models are developed the scope of questions that can be addressed will increase.…”

Morphological and phylogeographic evidence for budding speciation: an example in hominins

“…These approaches aim to reconstruct ancestor-descendant (AD) sequences of fossil taxa through the stratigraphic record using a unified model of lineage diversification and stratigraphic preservation (Gavryushkina et al 2014, Zhang et al 2016). These approaches have been increasingly leveraged to address empirical patterns in the fossil record (Wright et al 2020), yielding results that authors have interpreted to highlight the ubiquity of budding speciation as a dominant process in the diversification of new taxa (Bapst and Hopkins 2017). Nevertheless, few investigations have directly examined morphological support for mode.…”