A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data

Abstract

Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic dataset for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two.

Exploring adaptive landscapes across deep time: A case study using echinoid body size

“…Body size is log 10 ‐scaled and shown relative to the value of the average optimum (4.08; see Table 2). Clade names follow the nomenclature of Kroh (2019) and Mongiardino Koch and Thompson (2020). The echinoids shown are members of each of the four adaptive regimes and are shown to scale.…”

“…2015; Puttick 2016; Schnitzler et al. 2017; Mongiardino Koch and Parry 2020; Mongiardino Koch and Thompson 2020; Mongiardino Koch et al. 2020).…”

“…The phylogenetic framework and taxonomic sampling derive from the recent total‐evidence dated phylogeny of Mongiardino Koch and Thompson (2020). This phylogeny contains 167 taxa representing 89% of echinoid families currently recognized in the World Echinoidea Database (Kroh and Mooi 2019).…”

“…Coupled with a robust phylogenomic backbone (Mongiardino Koch et al. 2018; Mongiardino Koch and Thompson 2020), the clade provides unparalleled opportunities for macroevolutionary research. In fact, several authors have used sea urchins to investigate evolutionary dynamics in deep time, including evidences of extinction selectivity (Smith and Jeffery 1998), dynamics of phenotypic disparity (Eble 2000), rates of morphological evolution (Hopkins and Smith 2015), and the origins of developmental innovations (Thompson et al.…”

Post-metamorphic skeletal growth in the sea urchin Paracentrotus lividus and implications for body plan evolution

“…b Simplified phylogenetic tree of crown group echinoids showing the transitions in sea urchin growth modes in regular and irregular echinoids, and their hypothesized molecular and cellular foundations. Tree is based on [ 43 ] and [ 47 ] …”