DOI: 10.5061/dryad.brv15dv9t
title: Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

description: Echinoids are key components of modern marine ecosystems. Despite a
 remarkable fossil record, the emergence of their crown group is documented
 by few specimens of unclear affinities, rendering their early history
 uncertain. The origin of sand dollars, one of its most distinctive clades,
 is also unclear due to an unstable phylogenetic context. We employ
 eighteen novel genomes and transcriptomes to build a phylogenomic dataset
 with a near-complete sampling of major lineages. With it, we revise the
 phylogeny and divergence times of echinoids, and place their history
 within the broader context of echinoderm evolution. We also introduce the
 concept of a chronospace—a multidimensional representation of node
 ages—and use it to explore methodological decisions involved in time
 calibrating phylogenies. We find the choice of clock model to have the
 strongest impact on divergence times, while the use of site-heterogeneous
 models and alternative node prior distributions showing minimal effects.
 The choice of loci has an intermediate impact, affecting mostly deep
 Paleozoic nodes, for which clock-like genes recover dates more congruent
 with fossil evidence. Our results reveal that crown group echinoids
 originated in the Permian and diversified rapidly in the Triassic, despite
 the relative lack of fossil evidence for this early diversification. We
 also clarify the relationships between sand dollars and their close
 relatives and confidently date their origins to the Cretaceous, implying
 ghost ranges spanning approximately 50 million years, a remarkable
 discrepancy with their rich fossil record.
description: Transciptomic reads were trimmed with Trimommatic v. 0.36,
 followed by further sanitation steps using the Agalma 2.0 phylogenomic
 workflow and de novo assembly with Trinity 2.5.1. Assembled transcriptomes
 were cleaned from non-metazoan contaminants using alien_index v. 3.0, and
 from cross-contaminants product of multiplexed sequencing using
 CroCo. Adapters were removed from genomic reads using
 BBDuk, followed by quality and length-based trimming using UrQt 1.0.18.
 Assembly was performed with MEGAHIT v. 1.1.2. Draft genomes were masked
 using RepeatMasker v. 4.1.0 before obtaining gene predictions
 with AUGUSTUS 3.2.3. For this last step, a custom set of universal
 single-copy orthologs obtained from the latest
 <em>Strongylocentrotus purpuratus</em> genome assembly (Spur
 v. 5.0) was employed as the training dataset. Citations
 and further methodological details can be found in Mongiardino Koch et
 al (2021) - Phylogenomic analyses of echinoid diversification prompt a
 re-evaluation of their fossil
 record. bioRxiv 2021.07.19.453013; doi: https://doi.org/10.1101/2021.07.19.453013.
description: This repository contains three folders: A)
 Assemblies.zip including all transcriptomic and genomic assemblies
 associated with Mongiardino Koch et al (2021). Transciptomic datasets are
 marked with a 'T', gene predictions from genomic datasets with a
 'G'. B) Chronospaces.zip including all time
 calibrated posterior distributions of topologies obtained.
 C) Phylogenomic_datasets.zip including supermatrices and
 partition files. R code to build and plot chronospaces
 using the topologies found in B) is also included.