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1. Grassland restoration characteristics influence phylogenetic and taxonomic structure of plant communities and suggest assembly mechanisms

   https://doi.org/10.1111/1365-2745.13250  

   Barber, Nicholas A.; Farrell, Anna K.; Blackburn, Ryan C.; Bauer, Jonathan T.; Groves, Anna M.; Brudvig, Lars A.; Jones, Holly P.; Gibson, ed., David (August 2019, Journal of Ecology)

   Abstract Phylogenetic and species‐based taxonomic descriptions of community structure may provide complementary information about the mechanisms driving community assembly across different environments. Environmental filtering may have similar effects on taxonomic and phylogenetic diversity under the assumption of niche conservatism, whereas competitive exclusion could produce contrasting patterns in these diversity metrics. In grassland restorations, these diversity patterns might then reveal potential assembly mechanisms underlying the impacts of restoration and management conditions on community structure.We compared plant community structure (alpha diversity, composition, and within‐site beta diversity) from both phylogenetic and taxonomic perspectives. Using surveys from 120 tallgrass prairie restorations in four regions of the Midwestern United States, we examined the effects of four potential drivers or environmental gradients: precipitation in the first year of restoration, seed mix richness, time since last prescribed fire, and restoration age, and included soil conditions as a covariate.First‐year precipitation influenced taxonomic community structure, but had weak effects on phylogenetic diversity and composition. Similarly, greater seed mix richness increased taxonomic diversity but did not influence phylogenetic diversity. Taxonomic, but not phylogenetic, diversity generally was lower in older restorations and those with a longer time since the last prescribed fire. These drivers consistently explained more variation in taxonomic than phylogenetic diversity and composition, perhaps in part because species turnover was largely among related species, producing weak impacts on phylogenetic community measures.An impact of precipitation on taxonomic but not phylogenetic diversity suggests that there may not be large differences in drought tolerance among clades that would cause phylogenetic patterns to arise from this environmental filter. Declining taxonomic diversity but not phylogenetic diversity is consistent with competitive exclusion as an assembly mechanism when competition is strongest between related species.Synthesis. This research shows how studying taxonomic and phylogenetic diversity of ecosystem restorations can inform plant community ecology and help natural resource managers better predict the outcomes of restoration actions and management. 

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2. Non‐linear phylogenetic regression using regularised kernels

   https://doi.org/10.1111/2041-210X.14385  

   Rosas‐Puchuri, Ulises; Santaquiteria, Aintzane; Khanmohammadi, Sina; Solís‐Lemus, Claudia; Betancur‐R, Ricardo (August 2024, Methods in Ecology and Evolution)

   Abstract Phylogenetic regression is a type of generalised least squares (GLS) method that incorporates a modelled covariance matrix based on the evolutionary relationships between species (i.e. phylogenetic relationships). While this method has found widespread use in hypothesis testing via phylogenetic comparative methods, such as phylogenetic ANOVA, its ability to account for non‐linear relationships has received little attention.To address this, here we implement a phylogenetic Kernel Ridge Regression (phyloKRR) method that utilises GLS in a high‐dimensional feature space, employing linear combinations of phylogenetically weighted data to account for non‐linearity. We analysed two biological datasets using the Radial Basis Function and linear kernel function. The first dataset contained morphometric data, while the second dataset comprised discrete trait data and diversification rates as response variable. Hyperparameter tuning of the model was achieved through cross‐validation rounds in the training set.In the tested biological datasets, phyloKRR reduced the error rate (as measured by RMSE) by around 20% compared to linear‐based regression when data did not exhibit linear relationships. In simulated datasets, the error rate decreased almost exponentially with the level of non‐linearity.These results show that introducing kernels into phylogenetic regression analysis presents a novel and promising tool for complementing phylogenetic comparative methods. We have integrated this method into Python package named phyloKRR, which is freely available at:https://github.com/ulises‐rosas/phylokrr. 

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3. Cretaceous pollen cone with three‐dimensional preservation sheds light on the morphological evolution of cycads in deep time

   https://doi.org/10.1111/nph.18852  

   Elgorriaga, Andres; Atkinson, Brian A. (March 2023, New Phytologist)

   Summary The Cycadales are an ancient and charismatic group of seed plants. However, their morphological evolution in deep time is poorly understood. While molecular divergence time analyses estimate a Cretaceous origin for most major living cycad clades, much of the extant diversity is inferred to be a result of Neogene diversifications. This leads to long branches throughout the cycadalean phylogeny that, with few exceptions, have yet to be rectified by unequivocal fossil cycads.We report a permineralized pollen cone from the Campanian Holz Shale located in Silverado Canyon, CA, USA (c.80 million yr ago). This fossil was studied via serial sectioning, SEM, 3D reconstruction and phylogenetic analyses.Microsporophyll and pollen morphology indicate this cone is assignable toSkyttegaardia, a recently described genus based on disarticulated lignitized microsporophylls from the Early Cretaceous of Denmark. Data from this new species, including a simple cone architecture, anatomical details and vasculature organization, indicate cycadalean affinities forSkyttegaardia. Phylogenetic analyses support this assignment and recoverSkyttegaardiaas crown‐group Cycadales, nested within Zamiaceae.Our findings support a Cretaceous diversification for crown‐group Zamiaceae, which included the evolution of morphological divergent extinct taxa with unique traits that have yet to be widely identified in the fossil record. 

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4. Woody encroachment affects multiple dimensions of ant diversity in a neotropical savanna

   https://doi.org/10.1111/icad.12633  

   Neves, K.; Santos, B.; Schultz, T.; Gotzek, D.; Abreu, R. C. R.; Durigan, G.; Vasconcelos, H. L. (February 2023, Insect Conservation and Diversity)

   Abstract Although savanna woody encroachment has become a global phenomenon, relatively little is known about its effects on multiple dimensions and levels of savanna biodiversity.Using a combination of field surveys, a species‐level phylogeny, and functional metrics drawn from a morphological dataset, we evaluated how the progressive increase in tree cover in a fire‐suppressed savanna landscape affects the taxonomic, functional, and phylogenetic diversity of neotropical ant communities, at both the alpha and beta levels. Ants were sampled along an extensive tree cover gradient, ranging from open savannas to forests established in former savanna areas.Variation in tree cover had a significant influence on all facets of diversity at the beta level, whereas at the alpha level tree cover variation affected the taxonomic and functional but not the phylogenetic diversity of the ant communities.In general, ant community responses to variation in tree cover were largely non‐linear as differences in taxonomic alpha diversity and in the taxonomic, functional, and phylogenetic composition of the sampled communities were often much stronger at the savanna/forest transition than at any other part of the gradient. This indicates that savanna ant communities switch rapidly to an alternative state once the savanna turns into forest.Ant communities in the newly formed forest areas lacked many of the species typical of the savanna habitats, suggesting that the maintenance of a fire suppression policy is likely to result in a decrease in ant diversity and in the homogenisation of the ant fauna at the landscape scale. 

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5. SiPhyNetwork : An R package for simulating phylogenetic networks

   https://doi.org/10.1111/2041-210X.14116  

   Justison, Joshua A.; Solis‐Lemus, Claudia; Heath, Tracy A. (May 2023, Methods in Ecology and Evolution)

   Abstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators for macroevolution are limited in the ways they model gene flow.We presentSiPhyNetwork, an R package for simulating phylogenetic networks under a birth–death‐hybridization process.Our package unifies the existing birth–death‐hybridization models while also extending the toolkit for modelling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression.Specifically, we model different reticulate events by allowing events to either add, remove or keep constant the number of lineages. Additionally, we allow reticulation events to be trait dependent, creating the ability to model the expanse of isolating mechanisms that prevent gene flow. This tool makes it possible for researchers to model many of the complex biological factors associated with gene flow in a phylogenetic context. 

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