Pollen sterols are associated with phylogenetics and environment but not with pollinators

Phytosterols are primary plant metabolites that have fundamental structural and regulatory functions. They are also essential nutrients for phytophagous insects, including pollinators, that cannot synthesize sterols. Despite the well-described composition and diversity in vegetative plant tissues, few studies have examined phytosterol diversity in pollen. We quantified 25 pollen phytosterols in 122 plant species (105 genera, 51 families) to determine their composition and diversity across plant taxa. We searched literature and databases for plant phylogeny, environmental conditions, and pollinator guilds of the species to examine the relationships with pollen sterols. 24-methylenecholesterol, sitosterol and isofucosterol were the most common and abundant pollen sterols. We found phylogenetic clustering of twelve individual sterols, total sterol content and sterol diversity, and of sterol groupings that reflect their underlying biosynthesis pathway (24 carbon alkylation, ring B desaturation). Plants originating in tropical-like climates (higher mean annual temperature, lower temperature seasonality, higher precipitation in wettest quarter) were more likely to record higher pollen sterol content. However, pollen sterol composition and content showed no clear relationship with pollinator guilds. Our study is the first to show that pollen sterol diversity is phylogenetically clustered and that pollen sterol content may adapt to environmental conditions

Ericaceae phylogenies

Molecular phylogenies of Ericaceae. Dated maximum clade credibility (MCC) tree as inferred using BEAST. Based on rbcL and matK sequence data from GenBank and dated with 18 fossil calibrations and divergence time estimates. Different formats and taxon-subsamples as used in analyses (details see README)

The Formation of Diversity - The Role of Environment and Biogeography in Dung Beetle Species Richness, and the Adequacy of Current Diversification Models

Model based approaches to study the driving factors behind diversification have become increasingly popular, but in the recent years, various weaknesses of these models have received increased attention. One way to ensure those issues do not affect one’s inferences, is to test a model’s adequacy as a way to judge its suitability to describe the data in an absolute sense. Here, I implement a simple adequacy test for diversification models in the R package BoskR, using metrics for tree shape. I demonstrate the method’s ability to distinguish trees simulated under different models, and then use it to test the adequacy of a range of birth-death diversification models for a large set of empirical phylogenies. I find that while most models are adequate to describe a majority of the empirical trees, a few trees cannot be described by any of those models. Furthermore, the best fitting of a set of models may not always be adequate, highlighting the practical use of incorporating model adequacy tests in the standard procedures for diversification studies.For the empirical parts of my dissertation, I investigate the diversification and biogeography of dung beetles. It has been hypothesized that their origin and distribution are either the result of Gondwanan vicariance, or out-of-Africa dispersal. Furthermore, dung beetle diversification is thought to have been affected by mammals – particularly large herds of herbivores inhabiting the vast grasslands after the Miocene – and potentially also by non-avian dinosaurs, if dinosaur dung-adapted beetles were affected by the K-Pg extinction of their dung producers. Crucial to answering these questions is to know whether dung beetles are of Mesozoic or Cenozoic origin. Thus, I construct a large dated phylogeny, and use model-based inference to estimate their ancestral area, and the influence of range evolution and diversity of dung producers on their diversification rates. My results suggest that dung beetles originated in Gondwana during the Mesozoic, but it remains unclear to which extent range evolution affected diversification. While adaptation to dinosaur dung and subsequent co-extinction are plausible, the available data cannot support a radiation with the rise of grasslands and herds of herbivores

MonoPhy: a simple R package to find and visualize monophyly issues

Background. The monophyly of taxa is an important attribute of a phylogenetic tree. A lack of it may hint at shortcomings of either the tree or the current taxonomy, or can indicate cases of incomplete lineage sorting or horizontal gene transfer. Whichever is the reason, a lack of monophyly can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species. Results. The R package MonoPhy allows assessment and exploration of monophyly of taxa in a phylogeny. It can assess the monophyly of genera using the phylogeny only, and with an additional input file any other desired higher order taxa or unranked groups can be checked as well. Conclusion. Summary tables, easily subsettable results and several visualization options allow quick and convenient exploration of monophyly issues, thus making MonoPhy a valuable tool for any researcher working with phylogenies

Data from: On the complexity of triggering evolutionary radiations

Recent developments in phylogenetic methods have made it possible to reconstruct evolutionary radiations from extant taxa, but identifying the triggers of radiations is still problematic. Here, we propose a conceptual framework to explore the role of variables that may impact radiations. We classify the variables into extrinsic conditions vs intrinsic traits, whether they provide background conditions, trigger the radiation, or modulate the radiation. We used three clades representing angiosperm phylogenetic and structural diversity (Ericaceae, Fagales and Poales) as test groups. We located radiation events, selected variables potentially associated with diversification, and inferred the temporal sequences of evolution. We found 13 shifts in diversification regimes in the three clades. We classified the associated variables, and determined whether they originated before the relevant radiation (backgrounds), originated simultaneously with the radiations (triggers), or evolved later (modulators). By applying this conceptual framework, we establish that radiations require both extrinsic conditions and intrinsic traits, but that the sequence of these is not important. We also show that diversification drivers can be detected by being more variable within a radiation than conserved traits that only allow occupation of a new habitat. This framework facilitates exploration of the causative factors of evolutionary radiations

Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) [version 1; peer review: 2 approved, 1 approved with reservations]

Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of evolution. Modern statistical methods involve not just the estimation of a tree, but also solutions to more complex models involving fossil record information and other data sources. Markov Chain Monte Carlo (MCMC) is a leading method for approximating the posterior distribution of parameters in a mathematical model. It is deployed in all Bayesian phylogenetic tree estimation software. While many researchers use MCMC in phylogenetic analyses, interpreting results and diagnosing problems with MCMC remain vexing issues to many biologists. In this manuscript, we will offer an overview of how MCMC is used in Bayesian phylogenetic inference, with a particular emphasis on complex hierarchical models, such as the fossilized birth-death (FBD) model. We will discuss strategies to diagnose common MCMC problems and troubleshoot difficult analyses, in particular convergence issues. We will show how the study design, the choice of models and priors, but also technical features of the inference tools themselves can all be adjusted to obtain the best results. Finally, we will also discuss the unique challenges created by the incorporation of fossil information in phylogenetic inference, and present tips to address them

Plant scent and plant–insect interactions—Review and outlook from a macroevolutionary perspective

Funding Information: We thank two anonymous reviewers for their helpful comments on the earlier version of this paper. O.S. was supported on NSF‐DEB‐1940868 and NSF‐DEB‐2045842. B.N.S. was supported by the Bioinformatics and Computational Biology Program at the University of Idaho in partnership with IBEST (the Institute for Bioinformatics and Evolutionary Studies). M.P.B. acknowledges the International Postdoc Grant from the Swedish Research Council (2020‐06422). Y.Y. was supported by the Hainan Provincial Natural Science Foundation of China (2019RC137). R.R. acknowledges Conacyt (Mexico) grant (2019‐000003‐01EXTF‐00226) and the German Academic Exchange Service (DAAD) (57504644). P.Z. acknowledges the Swiss National Science Foundation (SNSF) Spark grant (CRSK‐3_196506). P.Z. and R.R. acknowledge the SNSF Prima grant (PR00P3_193237), and RESPONSE scheme funded by the European Union′s Horizon 2020 research and innovation program under the Marie Sklodowska‐Curie grant agreement No. 847585. Funding Information: We thank two anonymous reviewers for their helpful comments on the earlier version of this paper. O.S. was supported on NSF-DEB-1940868 and NSF-DEB-2045842. B.N.S. was supported by the Bioinformatics and Computational Biology Program at the University of Idaho in partnership with IBEST (the Institute for Bioinformatics and Evolutionary Studies). M.P.B. acknowledges the International Postdoc Grant from the Swedish Research Council (2020-06422). Y.Y. was supported by the Hainan Provincial Natural Science Foundation of China (2019RC137). R.R. acknowledges Conacyt (Mexico) grant (2019-000003-01EXTF-00226) and the German Academic Exchange Service (DAAD) (57504644). P.Z. acknowledges the Swiss National Science Foundation (SNSF) Spark grant (CRSK-3_196506). P.Z. and R.R. acknowledge the SNSF Prima grant (PR00P3_193237), and RESPONSE scheme funded by the European Union′s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 847585. Publisher Copyright: © 2022 Institute of Botany, Chinese Academy of Sciences.The astonishing diversity of plants and insects and their entangled interactions are cornerstones in terrestrial ecosystems. Co-occurring with species diversity is the diversity of plant secondary metabolites (PSMs). So far, their estimated number is more than 200 000 compounds, which are not directly involved in plant growth and development but play important roles in helping plants handle their environment including the mediation of plant–insect interactions. Here, we use plant volatile organic compounds (VOCs), a key olfactory communication channel that mediates plant–insect interactions, as a showcase of PSMs. In spite of the cumulative knowledge of the functional, ecological, and microevolutionary roles of VOCs, we still lack a macroevolutionary understanding of how they evolved with plant–insect interactions and contributed to species diversity throughout the long coevolutionary history of plants and insects. We first review the literature to summarize the current state-of-the-art research on this topic. We then present various relevant types of phylogenetic methods suitable to answer macroevolutionary questions on plant VOCs and suggest future directions for employing phylogenetic approaches in studying plant VOCs and plant–insect interactions. Overall, we found that current studies in this field are still very limited in their macroevolutionary perspective. Nevertheless, with the fast-growing development of metabolome analysis techniques and phylogenetic methods, it is becoming increasingly feasible to integrate the advances of these two areas. We highlight promising approaches to generate new testable hypotheses and gain a mechanistic understanding of the macroevolutionary roles of chemical communication in plant–insect interactions.Peer reviewe

Maximum Clade Credibility Tree of Poales

Maximum Clade Credibility Tree of Poale

Maximum Clade Credibility Tree of Fagales

Maximum Clade Credibility Tree of Fagale