Search for: All records

Abstract Time-calibrated phylogenetic trees are a tremendously powerful tool for studying evolutionary, ecological, and epidemiological phenomena. Such trees are predominantly inferred in a Bayesian framework, with the phylogeny itself treated as a parameter with a prior distribution (a “tree prior”). However, we show that the tree “parameter” consists, in part, of data, in the form of taxon samples. Treating the tree as a parameter fails to account for these data and compromises our ability to compare among models using standard techniques (e.g., marginal likelihoods estimated using path-sampling and stepping-stone sampling algorithms). Since accuracy of the inferred phylogeny strongly depends on how well the tree prior approximates the true diversification process that gave rise to the tree, the inability to accurately compare competing tree priors has broad implications for applications based on time-calibrated trees. We outline potential remedies to this problem, and provide guidance for researchers interested in assessing the fit of tree models. [Bayes factors; Bayesian model comparison; birth-death models; divergence-time estimation; lineage diversification] 

Abstract We undertook a molecular phylogenetic revision of hayscented ferns (Dennstaedtiaceae: Dennstaedtioideae) using four plastid markers. Our sampling represents ca. 40% of the extant diversity and includes the type species for each of the relevant segregate genera. We coded 18 discrete morphological characters which we used to find diagnosable clades. We show that Dennstaedtia is polyphyletic, with the majority of species forming three morphologically distinct clades, but its type ( D. flaccida ) is nested within Microlepia . As such, we support the conservation of Dennstaedtia with a new type, D. dissecta . Following our results, we develop a classification of four genera: Dennstaedtia , Microlepia , Mucura (gen. nov.) and Sitobolium . Beyond the inclusion of D. flaccida , we propose to maintain Microlepia with its current circumscription. Except for a single adventive species in the Neotropics, Microlepia is a Paleotropical genus of about 60 species diagnosed by their distinctive perispore ornamentation of rodlets, and by petioles that lack epipetiolar buds. Mucura is a Neotropical genus of two species that differ from all other Dennstaedtiaceae by the combination of dichotomously branching rhizomes, petioles that lack epipetiolar buds, marginal sori with both abaxial and adaxial indusia, and trilete spores with a unique perispore ornamentation. As defined here, Dennstaedtia is a pantropical genus of about 55 species recognized by having unbranched rhizomes, petioles bearing epipetiolar buds, and by often bearing proliferous buds upon the leaves. Sitobolium is a small clade of ca. five species distinguished by their relatively small leaves that have elongate catenate hairs. These hairs often bear a capitate non‐glandular terminal cell. In support of our classification, we provide a key to the eleven genera of Dennstaedtiaceae, and for the four genera of Dennstaedtioideae we provide morphological and geographic synopses, a list of constituent species, and necessary new combinations. 

Abstract PremisePteridophytes—vascular land plants that disperse by spores—are a powerful system for studying plant evolution, particularly with respect to the impact of abiotic factors on evolutionary trajectories through deep time. However, our ability to use pteridophytes to investigate such questions—or to capitalize on the ecological and conservation‐related applications of the group—has been impaired by the relative isolation of the neo‐ and paleobotanical research communities and by the absence of large‐scale biodiversity data sources. MethodsHere we present the Pteridophyte Collections Consortium (PCC), an interdisciplinary community uniting neo‐ and paleobotanists, and the associated PteridoPortal, a publicly accessible online portal that serves over three million pteridophyte records, including herbarium specimens, paleontological museum specimens, and iNaturalist observations. We demonstrate the utility of the PteridoPortal through discussion of three example PteridoPortal‐enabled research projects. ResultsThe data within the PteridoPortal are global in scope and are queryable in a flexible manner. The PteridoPortal contains a taxonomic thesaurus (a digital version of a Linnaean classification) that includes both extant and extinct pteridophytes in a common phylogenetic framework. The PteridoPortal allows applications such as greatly accelerated classic floristics, entirely new “next‐generation” floristic approaches, and the study of environmentally mediated evolution of functional morphology across deep time. DiscussionThe PCC and PteridoPortal provide a comprehensive resource enabling novel research into plant evolution, ecology, and conservation across deep time, facilitating rapid floristic analyses and other biodiversity‐related investigations, and providing new opportunities for education and community engagement. 

Abstract Organisms such as allopolyploids and F1 hybrids contain multiple distinct subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference and other analyses since it is not apparent which gene copies from different loci are from the same subgenome and thus share an evolutionary history.Here we introduce homologizer, a flexible Bayesian approach that uses a phylogenetic framework to infer the phasing of gene copies across loci into their respective subgenomes.Through the use of simulation tests, we demonstrate that homologizer is robust to a wide range of factors, such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data, by analysing a multilocus dataset consisting of nine diploids and 19 tetraploids from the fern family Cystopteridaceae.Finally, we describe how homologizer may potentially be used beyond its core phasing functionality to identify non‐homologous sequences, such as hidden paralogs or contaminants. 

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.] 

Green plants (Viridiplantae) include around 450,000–500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.