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1. Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity

   https://doi.org/10.1093/sysbio/syab020  

   May, Michael R ; Contreras, Dori L ; Sundue, Michael A ; Nagalingum, Nathalie S ; Looy, Cindy V ; Rothfels, Carl J ( March 2021 , Systematic Biology)

   Folk, Ryan (Ed.)

   Abstract Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ${\sim}$2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth–death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.] 

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2. Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity.

   May, M.R. ; Contreras, D.L. ; Sundue, M.A. ; Nagalingum, N.S. ; Looy, C.V. ; Rothfels, C.J. ( March 2021 , Systematic biology)

   Ryan Folk (Ed.)

   Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ∼2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth–death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.] 

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3. Phylogenetic analysis of the Archaeocidaridae and Palaeozoic Miocidaridae (Echinodermata, Echinoidea) and the origin of crown group echinoids

   https://doi.org/10.1002/spp2.1280  

   Thompson, Jeffrey R. ; Mirantsev, Georgy V. ; Petsios, Elizabeth ; Bottjer, David J. ; Smith, ed., Andrew ( September 2019 , Papers in Palaeontology)

   The archaeocidarids comprise the most derived stem group echinoids and have long been regarded as closely related to the crown group. The fossil record of echinoids in the Palaeozoic is, however, poor, so details surrounding the initial divergence of crown group echinoids are not well constrained. In order to better understand the phylogenetic relationships of the most derived stem group and most basal crown group echinoids, a phylogenetic analysis was undertaken of the Archaeocidaridae, including the generaNortonechinus,Devonocidaris,Lepidocidaris,PolytaxicidarisandArchaeocidarisand the Palaeozoic miocidarid cidaroids from the genusEotiaris. We found thatArchaeocidarisappears to be paraphyletic with respect to crown group echinoids. Furthermore, we mapped character evolution along our phylogeny and found that the diversification of archaeocidarids and miocidarids may be linked to large‐scale macroecological changes taking place in the late Palaeozoic, including increasing predation pressure and echinoid encrustation by epibionts. We compared the stratigraphical distribution of archaeocidarid and miocidarid occurrences to our resulting phylogenies, and found that the fit of our cladograms to the stratigraphic record of archaeocidarid occurrences is worse than other echinoid groups, supporting the idea that the imbricate plated archaeocidarids have a poor fossil record. In the course of carrying out these analyses, we also felt it necessary to describe a new species ofArchaeocidaris,Archaeocidaris ivanovisp. nov. We also provide novel descriptions and interpretations forDevonocidaris primaevus,Archaeocidaris brownwoodensis,Archaeocidaris aphelesand revise the synonymy ofArchaeocidaris legrandensisand ?Eotiaris meurevillensis, which may be a crown group echinoid.

    

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4. Life history of an archaic placental mammal, Pantolambda bathmodon (Placentalia, Pantodonta)

   Funston, Gregory F. ; dePolo, Paige E. ; Shelley, Sarah L. ; Wible, John R. ; Williamson, Thomas E. ; Brusatte, Stephen L. ( May 2021 , Vertebrate anatomy morphology palaeontology)

   null (Ed.)

   The rise of mammals after the extinction of the dinosaurs remains one of the most enigmatic intervals in the evolution of mammals. A relatively sparse Paleocene fossil record and confusing interrelationships between taxa means that little is known of the evolution, ecology, and biology of these animals. As a result, the life history of these organisms is completely unstudied, despite likely playing a key role in the ability of these clades to rapidly proliferate and increase in body size in recovering ecosystems. However, intensive collection efforts in the San Juan Basin of New Mexico in the last decade have drastically improved the record of many Paleocene mammals, and offer the first opportunity to address questions about the life history of these animals. Here, we present preliminary results of an in-depth paleohistological analysis of Pantolambda bathmodon, an early, possibly gregarious pantodont, using an ontogenetic series of individuals. Pantodonts were bizarre, herbivorous eutherians of unknown phylogenetic affinity, and were among the first mammal lineages to reach large body sizes in the Paleocene. In examining both dental and skeletal records of growth from the same individuals, including a juvenile still bearing deciduous teeth, our study is among the most comprehensive paleohistological analyses of any fossil mammal. This intensive approach allows for unprecedented insights into the life history of this species. Neonatal lines in the teeth indicate that the deciduous premolars and the first upper molar were erupted prior to birth, similar to precocious, nidifugous mammals today. Daily incremental lines in the enamel and dentine suggest rapid crown formation times (~45–70 days) and a gestation period of at least 15 weeks. A stress line in the postcranial bones, recording an anomalous decrease in growth towards the end of this individual’s life, may represent the weaning event. In the absence of geochemical evidence, it is unclear which of two stress lines in the teeth corresponds to this event, but these lines occur roughly one and two months after birth, respectively. The weanling perished approximately 2.5 months after birth, weighing about 17 kg. An adult individual exhibiting severe wear on the dentition allows us to estimate maximum longevity in Pantolambda bathmodon at about 7 years. In comparison with life history data on living mammals from the PanTheria dataset, Pantolambda bathmodon had a gestation length and weaning duration below average for a placental of its adult body size (42 kg), but within the range of known variation. However, its lifespan was exceptionally short, falling outside the bounds of comparable living mammals. Together, these lines of evidence suggest a relatively rapid pace of life in Pantolambda bathmodon, despite its relatively large body size. Ongoing sampling of more individuals and geochemical analyses should allow for estimation of time to sexual maturity and help to confirm the identity of the weaning line, completing our picture of the life history of this pioneering species. 

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5. A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

   https://doi.org/10.1098/rspb.2019.1502  

   Friedman, Matt ; Feilich, Kara L. ; Beckett, Hermione T. ; Alfaro, Michael E. ; Faircloth, Brant C. ; Černý, David ; Miya, Masaki ; Near, Thomas J. ; Harrington, Richard C. ( September 2019 , Proceedings of the Royal Society B: Biological Sciences)

   null (Ed.)

   The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of ‘core’ Stromateoidei, and a clade comprising ‘Gempylidae’ and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae + Tetragonurus ). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene–Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes. 

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