A Total-Evidence Dated Phylogeny of Echinoids and the Evolution of Body Size across Adaptive Landscape

Abstract

12Several unique properties of echinoids (sea urchins) make them useful for exploring 13 macroevolutionary dynamics, including their remarkable fossil record that can be incorporated 14 into explicit phylogenetic hypotheses. However, this potential cannot be exploited without a 15 robust resolution of the echinoid tree of life. We revisit the phylogeny of crown group 16 Echinoidea using both the largest phylogenomic dataset compiled for the clade, as well as a 17 large-scale morphological matrix with a dense fossil sampling. We also gather a new 18 compendium of both tip and node age constraints, allowing us to combine phylogenomic, 19 morphological and stratigraphic data using a total-evidence dating approach. For this, we 20 develop a novel method for subsampling phylogenomic datasets that selects loci with high 21 phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our approach 22 restructure much of the higher-level phylogeny of echinoids, and demonstrates that combining 23 different data sources increases topological accuracy. We are able to resolve multiple alleged 24 conflicts between molecular and morphological datasets, such as the position of Echinothurioida 25 and Echinoneoida, as well as unravelling the relationships between sand dollars and their closest 26 relatives. We then use this topology to trace the evolutionary history of echinoid body size 27 through more than 270 million years, revealing a complex pattern of convergent evolution to 28 stable peaks in macroevolutionary adaptive landscape. Our efforts show how combining 29 phylogenomic and paleontological evidence offers new ways of exploring evolutionary forces 30 operating across deep timescales.31 32

Sequence Diversity, Locus Structure, and Evolutionary History of the SpTransformer Genes in the Sea Urchin Genome

“…To date, Trf genes have been identified in six sea urchin species ( 65 , 80 – 82 ), all of which are members of the Camarodonta order of euechinoids ( 83 ). Of these species, Lytechinus [LCA ~60 MYA ( 84 )] and Heliocidaris [LCA ~75 MYA ( 84 )] are not members of the Strongylocentrotid family ( 85 ) and therefore were appropriate choices as outgroups. The initial phylogenetic analysis of exon 2 from 138 SpTrf genes including those from the two genomic loci described here resulted in a polytomic tree structure that was an outcome of the large gaps required for optimal alignments ( Supplementary Figure S16 ).…”

Endless forms most stupid, icky, and small: The preponderance of noncharismatic invertebrates as integral to a biologically sound view of life

“…It would likely surprise most people that the seemingly destructive, “antiprogress” force of extinction has been instrumental in shaping our modern fauna. For example, all living sea urchins and sand dollars (Echinodermata: Echinoidea) are descended from a few taxa that just happened to make it through the biggest mass extinction known, the End‐Permian (252 Ma) (Erwin, 1994, 2006; Koch & Thompson, 2020). We will never know whether these surviving species were actually better adapted than all the others; random chance is just as likely (Erwin, 2006).…”

DataSheet_1.pdf

“…To date, Trf genes have been identified in six sea urchin species (65,(80)(81)(82), all of which are members of the Camarodonta order of euechinoids (83). Of these species, Lytechinus [LCA ~60 MYA (84)] and Heliocidaris [LCA ~75 MYA (84)] are not members of the Strongylocentrotid family (85) and therefore were appropriate choices as outgroups. The initial phylogenetic analysis of exon 2 from 138 SpTrf genes including those from the two genomic loci described here resulted in a polytomic tree structure that was an outcome of the large gaps required for optimal alignments (Supplementary Figure S16).…”