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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 package chronospace implements 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 FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We present the mitochondrial genome of the deep-sea, epibenthic, irregular echinoid Echinocrepis rostrata, representing the first sequenced mitogenome of the order Holasteroida. The length of the complete E. rostrata mitochondrial genome is 15,716 base pairs, and its GC content is 34.87%. It contains 13 protein-coding genes, two rRNA genes, and 22 tRNA genes, whose order is identical to that of all other available echinoid mitogenomes. Phylogenetic analysis of available mitochondrial genomes, based on all coding loci, places E. rostrata as the sister group to spatangoids (heart urchins). [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Recently, the genetic basis and developmental mechanisms underlying the process of melanization have become progressively elucidated, allowing us to study the evolutionary processes that govern the huge variability of pigmentation observed in nature. However, environmental factors contributing to such variability have received little attention, even though they might have profound ecological consequences. Here we describe a method for analyzing the wing melanization patterns of drosophilids in both qualitative and quantitative ways. We test this method on wings of Drosophila buzzatii Patterson & Wheeler individuals, reared in control and alkaloid-enriched mediums. The alkaloids were extracted from the secondary host of these flies, Echinopsis terscheckii (Parm. ex Pfeiff.) Friedrich & Rowley, and their effect on wing pigmentation is analyzed, bearing in mind the adverse effects that these compounds have on the development of D. buzzatii. Alkaloid-reared flies were shown to attain a higher degree of wing melanization, accompanied with differences in the spatial distribution of the pigment. Modifications at both metabolic and gene regulatory levels are proposed to explain the changes that chemical stressful conditions are shown to induce in this character. We propose the utilization of this procedure in studies of environmental dependence of pigmentation. [ABSTRACT FROM AUTHOR]

We present the mitochondrial genome of the deep-sea, epibenthic, irregular echinoid Echinocrepis rostrata , representing the first sequenced mitogenome of the order Holasteroida. The length of the complete E. rostrata mitochondrial genome is 15,716 base pairs, and its GC content is 34.87%. It contains 13 protein-coding genes, two rRNA genes, and 22 tRNA genes, whose order is identical to that of all other available echinoid mitogenomes. Phylogenetic analysis of available mitochondrial genomes, based on all coding loci, places E. rostrata as the sister group to spatangoids (heart urchins)., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

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.

Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth-death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.

Phylogenomic and paleontological data constitute complementary resources for unraveling 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 synthesizing 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 data set 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 data sets 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. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.]., (© The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)