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ABSTRACT AimThe aim of the current study is to conduct a comprehensive phylogenetic analysis of the genusArbaciato elucidate the evolution and phylogenetic relationships among all extant species and reevaluate the presence of geographic structure within species that have wide, fragmented distributions. LocationSpecimens ofArbaciawere collected from 34 localities spanning the Atlantic and Pacific Oceans, and the Mediterranean Sea. MethodsWe obtained sequences from three mitochondrial markers (COI, 16S and the control region and adjacent tRNAs) and two nuclear markers (28S and 18S; the latter ultimately excluded from the final analyses). Phylogenetic trees were constructed using maximum likelihood and Bayesian inference approaches. A time‐calibrated phylogenetic tree was inferred using a relaxed Bayesian molecular clock and three fossil calibration points. ResultsOur analysis supports the monophyly of the genusArbacia, including the speciesArbacia nigra(previously assigned to the monotypic genusTetrapygus). The new phylogenetic topology suggests an alternative biogeographic scenario of initial divergence between Atlantic and Pacific subclades occurring approximately 9 million years ago. The dispersal and subsequent diversification of the Pacific subclade to the southeast Pacific coincides with the onset of glacial and interglacial cycles in Patagonia. In the Atlantic subclade, the split betweenA. punctulataandA. lixulaoccurred 3.01–6.30 (median 3.74 million years ago), possibly associated with the strengthening of the Gulf Stream current connecting the western and eastern Atlantic. Our study also reveals significant genetic and phylogeographic structures within both Atlantic species, indicating ongoing differentiation processes between populations. Main ConclusionOur study provides valuable insights into the evolutionary history and biogeography of the genusArbaciaand highlights the complex interplay between historical climate changes and oceanic currents in shaping the distribution and diversification of echinoids in the Atlantic and Pacific Oceans. 

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. 

Abstract Time‐scaled phylogenies underpin the interrogation of evolutionary processes across deep timescales, as well as attempts to link these to Earth's history. By inferring the placement of fossils and using their ages as temporal constraints, tip dating under the fossilized birth–death (FBD) process provides a coherent prior on divergence times. At the same time, it also links topological and temporal accuracy, as incorrectly placed fossil terminals should misinform divergence times. This could pose serious issues for obtaining accurate node ages, yet the interaction between topological and temporal error has not been thoroughly explored. We simulate phylogenies and associated morphological datasets using methodologies that incorporate evolution under selection, and are benchmarked against empirical datasets. We find that datasets of 300 characters and realistic levels of missing data generally succeed in inferring the correct placement of fossils on a constrained extant backbone topology, and that true node ages are usually contained within Bayesian posterior distributions. While increased fossil sampling improves the accuracy of inferred ages, topological and temporal errors do not seem to be linked: analyses in which fossils resolve less accurately do not exhibit elevated errors in node age estimates. At the same time, inferred divergence times are biased, probably due to a mismatch between the FBD prior and the shape of our simulated trees. While these results are encouraging, suggesting that even fossils with uncertain affinities can provide useful temporal information, they also emphasize that palaeontological information cannot overturn discrepancies between model priors and the true diversification history. 

Eurypterids—Palaeozoic marine and freshwater arthropods commonly known as sea scorpions—repeatedly evolved to remarkable sizes (over 0.5 m in length) and colonized continental aquatic habitats multiple times. We compiled data on the majority of eurypterid species and explored several previously proposed explanations for the evolution of giant size in the group, including the potential role of habitat, sea surface temperature and dissolved sea surface oxygen levels, using a phylogenetic comparative approach with a new tip-dated tree. There is no compelling evidence that the evolution of giant size was driven by temperature or oxygen levels, nor that it was coupled with the invasion of continental aquatic environments, latitude or local faunal diversity. Eurypterid body size evolution is best characterized by rapid bursts of change that occurred independently of habitat or environmental conditions. Intrinsic factors played a major role in determining the convergent origin of gigantism in eurypterids. 

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.