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1. Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies

   https://doi.org/10.1093/bioinformatics/btab307  

   Tao, Qiqing ; Barba-Montoya, Jose ; Kumar, Sudhir ( July 2021 , Bioinformatics)

   Abstract Motivation Precise time calibrations needed to estimate ages of species divergence are not always available due to fossil records' incompleteness. Consequently, clock calibrations available for Bayesian dating analyses can be few and diffused, i.e. phylogenies are calibration-poor, impeding reliable inference of the timetree of life. We examined the role of speciation birth–death (BD) tree prior on Bayesian node age estimates in calibration-poor phylogenies and tested the usefulness of an informative, data-driven tree prior to enhancing the accuracy and precision of estimated times. Results We present a simple method to estimate parameters of the BD tree prior from the molecular phylogeny for use in Bayesian dating analyses. The use of a data-driven birth–death (ddBD) tree prior leads to improvement in Bayesian node age estimates for calibration-poor phylogenies. We show that the ddBD tree prior, along with only a few well-constrained calibrations, can produce excellent node ages and credibility intervals, whereas the use of an uninformative, uniform (flat) tree prior may require more calibrations. Relaxed clock dating with ddBD tree prior also produced better results than a flat tree prior when using diffused node calibrations. We also suggest using ddBD tree priors to improve the detection of outliers and influential calibrationsmore »in cross-validation analyses. These results have practical applications because the ddBD tree prior reduces the number of well-constrained calibrations necessary to obtain reliable node age estimates. This would help address key impediments in building the grand timetree of life, revealing the process of speciation and elucidating the dynamics of biological diversification. Availability and implementation An R module for computing the ddBD tree prior, simulated datasets and empirical datasets are available at https://github.com/cathyqqtao/ddBD-tree-prior.« less
2. Freeze tolerance influenced forest cover and hydrology during the Pennsylvanian

   https://doi.org/10.1073/pnas.2025227118  

   Matthaeus, William J. ; Macarewich, Sophia I. ; Richey, Jon D. ; Wilson, Jonathan P. ; McElwain, Jennifer C. ; Montañez, Isabel P. ; DiMichele, William A. ; Hren, Michael T. ; Poulsen, Christopher J. ; White, Joseph D. ( October 2021 , Proceedings of the National Academy of Sciences)

   The distribution of forest cover alters Earth surface mass and energy exchange and is controlled by physiology, which determines plant environmental limits. Ancient plant physiology, therefore, likely affected vegetation-climate feedbacks. We combine climate modeling and ecosystem-process modeling to simulate arboreal vegetation in the late Paleozoic ice age. Using GENESIS V3 global climate model simulations, varyingpCO₂,pO₂, and ice extent for the Pennsylvanian, and fossil-derived leaf C:N, maximum stomatal conductance, and specific conductivity for several major Carboniferous plant groups, we simulated global ecosystem processes at a 2° resolution withPaleo-BGC. Based on leaf water constraints, Pangaea could have supported widespread arboreal plant growth and forest cover. However, these models do not account for the impacts of freezing on plants. According to our interpretation, freezing would have affected plants in 59% of unglaciated land during peak glacial periods and 73% during interglacials, when more high-latitude land was unglaciated. Comparing forest cover, minimum temperatures, and paleo-locations of Pennsylvanian-aged plant fossils from the Paleobiology Database supports restriction of forest extent due to freezing. Many genera were limited to unglaciated land where temperatures remained above −4 °C. Freeze-intolerance of Pennsylvanian arboreal vegetation had the potential to alter surface runoff, silicate weathering, CO₂levels, and climate forcing. As amore »bounding case, we assume total plant mortality at −4 °C and estimate that contracting forest cover increased net global surface runoff by up to 6.1%. Repeated freezing likely influenced freeze- and drought-tolerance evolution in lineages like the coniferophytes, which became increasingly dominant in the Permian and early Mesozoic.

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3. Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

   https://doi.org/10.1186/s12862-021-01935-1  

   Chen, De ; Hosner, Peter A. ; Dittmann, Donna L. ; O’Neill, John P. ; Birks, Sharon M. ; Braun, Edward L. ; Kimball, Rebecca T. ( November 2021 , BMC Ecology and Evolution)

   Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results.

   In this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different “gene shopping” schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select amore »subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree.

   We provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.

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4. 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)

   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 nullmore »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.« less
5. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants

   https://doi.org/10.1093/gbe/evab042  

   Geng, Yuan ; Cai, Chao ; McAdam, Scott A.M ; Banks, Jo Ann ; Wisecaver, Jennifer H ; Zhou, Yun ( March 2021 , Genome Biology and Evolution)

   Gaut, Brandon (Ed.)

   Abstract As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, wemore »uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.« less