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1. 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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2. 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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3. Phylogenomic dating and Bayesian biogeography illuminate an antitropical pattern for eucerine bees

   https://doi.org/10.1111/jbi.14359  

   Freitas, Felipe_V; Branstetter, Michael_G; Casali, Daniel_M; Aguiar, Antonio_J_C; Griswold, Terry; Almeida, Eduardo_A_B (April 2022, Journal of Biogeography)

   Abstract AimAn antitropical pattern is characterized by the occurrence of closely related taxa south and north of the tropics but absent or uncommonly represented closer to the equator, in contrast to most taxa, which tend to have their highest diversity in the tropical regions. We investigate the antitropical distribution of eucerine bees with the aim of contributing to the characterization and understanding of this pattern. LocationAll continents except Antarctica and Australia. TaxonEucerine bees (Hymenoptera: Apidae: Eucerinae). MethodsWe carried out phylogenomic dating under two different clock models and used multiple strategies to vary matrix composition, evaluating the overlapping of divergence times estimated across models using Bhattacharyya coefficients. Lastly, we reconstructed the biogeographic history of eucerine bees using a Bayesian implementation of the DEC model. ResultsEucerinae is estimated to have started diversifying during the Palaeocene, with all its tribes originating during the Palaeocene/Eocene transition in southern South America. At least two range expansions happened into North America before the full closure of the Isthmus of Panama. We show that divergence between closely related groups with disjunct distributions would have happened in periods when the climate favoured the expansion of open habitats and became isolated when the forests were re‐established. Main conclusionsWe describe the early diversification of eucerine bees, revealing an intimate association with southern South America. Events of range evolution of Eucerinae were likely affected by periods of global cooling and aridification, and palaeoclimatic and vegetational conditions probably have been more relevant to the formation of the antitropical distribution of Eucerinae than the consolidation of the Isthmus of Panama connecting the Americas. We also demonstrate that most uncertainty in divergence time estimation is not due to the amount of molecular data being used, but more likely other factors like fossil calibrations and violations of clock models. 

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4. Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights

   https://doi.org/10.1002/ajb2.1695  

   Lee, Aaron_K; Gilman, Ian_S; Srivastav, Mansa; Lerner, Ariel_D; Donoghue, Michael_J; Clement, Wendy_L (July 2021, American Journal of Botany)

   PremisePhylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement ofHeptacodiumandZabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb‐Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times. MethodsSampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off‐target reads, and 10 fossils were used to calibrate dated trees. ResultsVarying numbers of targeted loci and off‐target plastomes were recovered from most taxa. Nuclear and plastid data confidently placeHeptacodiumwith Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement ofZabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm‐wide dating analyses, but many major splitting events date to the Eocene. ConclusionsThe Angiosperms353 probe set facilitated the assembly of a large, single‐copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades. 

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5. Putting the F into FBD analysis: tree constraints or morphological data?

   https://doi.org/10.1111/pala.12679  

   Barido‐Sottani, Joëlle; Pohle, Alexander; De_Baets, Kenneth; Murdock, Duncan; Warnock, Rachel_C_M (November 2023, Palaeontology)

   Abstract The fossilized birth–death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils are directly integrated into the tree, leading to a statistically coherent prior on divergence times. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. We use simulations to evaluate two different approaches to handling fossil placement in FBD analyses: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or using total‐evidence analyses, which use a morphological data matrix in addition to the molecular alignment. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. We see similar patterns in datasets which include rate variation, however, relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non‐time calibrated inference. Overall, we show that both fossil placement approaches are reliable even when including uncertainty. Our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process. 

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