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Abstract Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time‐scaling phylogenetic trees have dramatically grown in complexity, and depend today upon numerous methodological choices. Arriving at objective justifications for all of these is difficult and time‐consuming. Thus, divergence times are routinely inferred under only one or a handful of parametric conditions, often times chosen arbitrarily. Progress towards building robust biological timescales necessitates the development of better methods to visualize and quantify the sensitivity of results to these decisions.Here, we present an R package that assists in this endeavour through the use of chronospaces, that is, graphical representations summarizing variation in the node ages contained in time‐calibrated trees. We further test this approach by estimating divergence times for three empirical datasets—spanning widely differing evolutionary timeframes—using the software PhyloBayes.Our results reveal large differences in the impact of many common methodological decisions, with the choice of clock (uncorrelated vs autocorrelated) and loci having strong effects on inferred ages. Other decisions have comparatively minor consequences, including the use of the computationally intensive site‐heterogeneous model CAT‐GTR, whose effect might only be discernible for exceedingly old divergences (e.g. the deepest eukaryote nodes).The packagechronospaceimplements a range of graphical and analytical tools that assist in the exploration of sensitivity and the prioritization of computational resources in the inference of divergence times. 

Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest oceanic trenches. Their reduced skeletons and limited number of phylogenetically informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with 13 novel transcriptomes. Using a highly curated dataset of 1100 orthologues, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favour one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories. 

Abstract Evidence from the earliest-known crinoids (Tremadocian, Early Ordovician), called protocrinoids, is used to hypothesize initial steps by which elements of the calyx evolved. Protocrinoid calyces are composed of extraxial primary and surrounding secondary plates (both of which have epispires along their sutures) that are unlike those of more crownward fossil and extant crinoids in which equivalent calycinal plating is strongly organized. These reductions inspired several schemes by which to name the plates in these calyces. However, the primary-secondary systems seen in protocrinoids first appeared among Cambrian stem radial echinoderms, with primaries representing centers around which secondaries were sequentially added during ontogeny. Therefore, the protocrinoid calyx represents an intermediate condition between earliest echinoderms and crownward crinoids. Position and ontogeny indicate certain primaries remained as loss of secondaries occurred, resulting in abutting of primaries into the conjoined alternating circlets characteristic of crinoids. This transformative event included suppression of secondary plating and modification or, more commonly, elimination of respiratory structures. These data indicate subradial calyx plate terminology does not correspond with most common usage, but rather, supports an alternative redefinition of these traditional expressions. Extension and adoral growth of fixed rays during calyx ontogeny preceded conjoined primaries in earliest crinoids. Restriction with modification or elimination of calyx respiratory structures also accompanied this modification. Phylogenetic analyses strongly support crinoid origination from early pentaradiate echinoderms, separate from blastozoans. Accordingly, all Tremadocian crinoids express a distinctive aggregate of plesiomorphic and apomorphic commonalities; all branch early within the crinoid clade, separate from traditional subclass-level clades. Nevertheless, each taxon within this assemblage expresses at least one diagnostic apomorphy of camerate, cladid, or disparid clades. 

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 18 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 show 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.