Major transformations in brain size and proportions, such as the enlargement of the brain during the evolution of birds, are accompanied by profound modifications to the skull roof. However, the hypothesis of concerted evolution of shape between brain and skull roof over major phylogenetic transitions, and in particular of an ontogenetic relationship between specific regions of the brain and the skull roof, has never been formally tested. We performed 3D morphometric analyses to examine the deep history of brain and skull-roof morphology in Reptilia, focusing on changes during the well-documented transition from early reptiles through archosauromorphs, including nonavian dinosaurs, to birds. Non-avialan taxa cluster tightly together in morphospace, whereas Archaeopteryx and crown birds occupy a separate region. There is a one-to-one correspondence between the forebrain and frontal bone and the midbrain and parietal bone. Furthermore, the position of the forebrain-midbrain boundary correlates significantly with the position of the frontoparietal suture across the phylogenetic breadth of Reptilia and during the ontogeny of individual taxa. Conservation of position and identity in the skull roof is apparent, and there is no support for previous hypotheses that the avian parietal is a transformed postparietal. The correlation and apparent developmental link between regions of the brain and bony skull elements are likely to be ancestral to Tetrapoda and may be fundamental to all of Osteichthyes, coeval with the origin of the dermatocranium.

Phylogenomic and paleontological data constitute complementary resources for unravelling 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 synthetizing 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 dataset 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 datasets 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.

BackgroundEchinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved.ResultsWe performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results.ConclusionsOur investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1300-4) contains supplementary material, which is available to authorized users.

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different datasets. Here, I calculate multiple gene properties for a range of phylogenomic datasets spanning animal, fungal and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared to alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties, and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.

Further methodological particularsSamples were taken from the collections of R.R. Gaines (n = 184), the Oxford University Museum of Natural History (n = 11), and the Yale Peabody Museum of Natural History (n = 18).Matrix material was selected randomly from that immediately surrounding (i.e., within a few centimeters) the fossil (in the case of museum specimens), or from the same bed as fossiliferous material (in the case of specimens in the collection of R.R. Gaines). Samples from which BST fossils are considered absent were selected from localities where significant collection efforts have revealed no soft-bodied fossils in these particular horizons. Although absence of recovered BST fossils does not provide absolute evidence of their absence from these horizons, we compared these samples to many others in our dataset in which soft bodied fossils are conspicuous and abundant. Material was hand-ground to approximately 10 m grain size with a porcelain pestle and mortar. Enough matrix material was ground to adequately cover single silicon crystal substrates 27 mm in diameter.All X-ray diffraction (XRD) peak positions were adjusted to correct for slight variations in sample height displacement error using positions of quartz reflections as internal standards. Analysis of the 060 region identified other peaks in the range 1.520-1.530 Å, but their abundance was positively correlated with that of calcite obtained from the bulk analysis, consistent with the identification of variable quantities of this mineral through bulk analysis (Kendall's τ = 0.6344, P < 10 -16 ). Additional confirmation of clay mineral species was obtained through analysis of oriented < 2 m clay separates. Such separates were analyzed from 22 samples representing the entire suite of clay minerals observed, in order to ensure consistency in clay mineral identification with the 060 powder analysis. The mineral identifications were consistent between the two methods. Statistical methodologyAbundance of all clay minerals showed a highly skewed zero-inflated distribution, resulting in a departure from multivariate normality, and most pairs of clay minerals proved to be significantly correlated (Fig. DR2). We therefore transformed the dataset to a matrix of pair-wise Euclidean distances between observations, and we used principal coordinate analysis (PCoA) to visualize the variability. Differences in clay mineral composition between samples with BST fossils and those with only fossil mineralized skeletons were tested using PERMANOVA (permutational multivariate analysis of variance, Anderson, 2001). Differences in the multivariate spread of both groups were tested using permutational analysis of multivariate dispersion, hereafter PERMDISP (Anderson, 2006). Both analyses were implemented using the package vegan (Oksanen et al., 2016), and significance was evaluated by performing 10 5 permutations.We performed a multiple logistic regression to investigate how different clay minerals affected the probability of samples containing BST fossils. This regress...

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.

Neriidae are a small family of acalyptratae flies, mostly distributed in the tropics. Very little is known about their biology, and the evolutionary relationships among species have never been evaluated. We perform the first comprehensive phylogenetic analysis of the family, including 48 species from all biogeographic regions inhabited, as well as five species of Micropezidae and one Cypselosomatidae as outgroups. We build a morphological data matrix of 194 characters, including 72 continuous characters. We first explore ways to deal with the issue of scaling continuous characters, including rescaling ranges to unity and using implied weighting. We find that both strategies result in very different phylogenetic hypotheses, and that implied weighting reduces the problem of scaling, but only partially. Furthermore, using implied weighting after rescaling characters improves the congruence between partitions and results in higher values of group support. With respect to the Neriidae, we confirm the monophyly of the family and of most its genera, although we do not obtain any of the currently accepted suprageneric groups. We propose to restrict the Eoneria and Nerius groups exclusively to the Neotropical fauna, and synonymize Glyphidops subgenus Oncopsia Enderlein with Glyphidops subgenus Glyphidops Enderlein, eliminating the subgeneric divisions. This revised phylogeny presents a striking biogeographic consistency, and shows that previous main divisions of the family were based on events of convergence.

Brittle stars (Phylum Echinodermata, Class Ophiuroidea) have evolved rapid locomotion employing muscle and skeletal elements within their (usually) five arms to apply forces in a manner analogous to that of vertebrates. Inferring the inner workings of the arm has been difficult as the skeleton is internal and many of the ossicles are sub‐millimeter in size. Advances in 3D visualization and technology have made the study of movement in ophiuroids possible. We developed six virtual 3D skeletal models to demonstrate the potential range of motion of the main arm ossicles, known as vertebrae, and six virtual 3D skeletal models of non‐vertebral ossicles. These models revealed the joint center and relative position of the arm ossicles during near‐maximal range of motion. The models also provide a platform for the comparative evaluation of functional capabilities between disparate ophiuroid arm morphologies. We made observations on specimens of Ophioderma brevispina and Ophiothrix angulata. As these two taxa exemplify two major morphological categories of ophiuroid vertebrae, they provide a basis for an initial assessment of the functional consequences of these disparate vertebral morphologies. These models suggest potential differences in the structure of the intervertebral articulations in these two species, implying disparities in arm flexion mechanics. We also evaluated the differences in the range of motion between segments in the proximal and distal halves of the arm length in a specimen of O. brevispina, and found that the morphology of vertebrae in the distal portion of the arm allows for higher mobility than in the proximal portion. Our models of non‐vertebral ossicles show that they rotate further in the direction of movement than the vertebrae themselves in order to accommodate arm flexion. These findings raise doubts over previous hypotheses regarding the functional consequences of ophiuroid arm disparity. Our study demonstrates the value of integrating experimental data and visualization of articulated structures when making functional interpretations instead of relying on observations of vertebral or segmental morphology alone. This methodological framework can be applied to other ophiuroid taxa to enable comparative functional analyses. It will also facilitate biomechanical analyses of other invertebrate groups to illuminate how appendage or locomotor function evolved.