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Summary The effects of single chromosome number change—dysploidy – mediating diversification remain poorly understood. Dysploidy modifies recombination rates, linkage, or reproductive isolation, especially for one‐fifth of all eukaryote lineages with holocentric chromosomes. Dysploidy effects on diversification have not been estimated because modeling chromosome numbers linked to diversification with heterogeneity along phylogenies is quantitatively challenging.We propose a new state‐dependent diversification model of chromosome evolution that links diversification rates to dysploidy rates considering heterogeneity and differentiates between anagenetic and cladogenetic changes. We apply this model toCarex(Cyperaceae), a cosmopolitan flowering plant clade with holocentric chromosomes.We recover two distinct modes of chromosomal evolution and speciation inCarex. In one diversification mode, dysploidy occurs frequently and drives faster diversification rates. In the other mode, dysploidy is rare, and diversification is driven by hidden, unmeasured factors. When we use a model that excludes hidden states, we mistakenly infer a strong, uniformly positive effect of dysploidy on diversification, showing that standard models may lead to confident but incorrect conclusions about diversification.This study demonstrates that dysploidy can have a significant role in speciation in a large plant clade despite the presence of other unmeasured factors that simultaneously affect diversification. 

Abstract The spectacular variation in species forms and richness across space and time can be explored using sophisticated and powerful tools recently developed by evolutionary modellers. In this contribution, we ask if the classic ‘Simpsonian’ view of tachytelic (fast), horotelic (standard) and bradytelic (slow) diversification rates can be distinguished with currently available tools and data. A neglected topic here is the role that the uncertainty of diversification rate estimates plays, where the lack of in‐depth uncertainty measures could hinder our ability to confidently suggest differences in speciation or extinction rates in any given comparison.We propose quantifying the relative uncertainty of diversification estimates, to better compare diversification tempo across phylogenies of different sizes and ages. We present three case studies, using the most popular models for diversification rate estimation, with or without fossils, to investigate claims of bradytely or tachytely. Using summary statistics and linear models, we ask if point estimates of diversification rates are comparable across clades. More specifically, we fit a linear model to understand which phylogenetic tree properties (including size and age) may affect the uncertainty of diversification estimates.We found the ‘Goldilocks of uncertainty’: Phylogenies that are young with insufficient tips or that are old increase the uncertainty of diversification estimates. The choice of diversification modelling approach is independent of the pattern of diversification rates decaying exponentially with clade age.In practice, we still cannot confidently compare diversification rates or their variation, due to uncertainties stemming from clade age, sample size and biased sampling. We emphasize the need for researchers to focus on estimating and presenting uncertainty in their estimates. Such uncertainty estimates are currently absent from many publications, limiting our ability to compare the tempo of diversifications across the tree of life. We conclude by proposing solutions and guidelines to encourage new studies for measure uncertainty. 

Abstract Geological events such as mountain uplift affect how, when, and where species diversify, but measuring those effects is a longstanding challenge. Andean orogeny impacted the evolution of regional biota by creating barriers to gene flow, opening new habitats, and changing local climate. B⁢o⁢m⁢a⁢r⁢e⁢a (Alstroemeriaceae) are tropical plants with (often) small, isolated ranges; in total, B⁢o⁢m⁢a⁢r⁢e⁢a species occur from central Mexico to central Chile. This genus appears to have evolved rapidly and quite recently, and rapid radiations are often challenging to resolve with traditional phylogenetic inference. In this study, we apply phylogenomics—with hundreds of loci, gene-tree-based data curation, and a multispecies-coalescent approach—to infer the phylogeny of B⁢o⁢m⁢a⁢r⁢e⁢a. We use this phylogeny to untangle the potential drivers of diversification and biogeographic history. In particular, we test if Andean orogeny contributed to the diversification of B⁢o⁢m⁢a⁢r⁢e⁢a. We find that B⁢o⁢m⁢a⁢r⁢e⁢a originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of mountain uplift. Furthermore, Andean lineages diversified faster than non-Andean relatives. B⁢o⁢m⁢a⁢r⁢e⁢a thus demonstrates that—at least in some cases—geological change rather than environmental stability has driven high species diversity in a tropical biodiversity hotspot. These results also demonstrate the utility (and danger) of genome-scale data for making macroevolutionary inferences. 

Abstract A long-standing hypothesis in evolutionary biology is that the evolution of resource specialization can lead to an evolutionary dead end, where specialists have low diversification rates and limited ability to evolve into generalists. In recent years, advances in comparative methods investigating trait-based differences associated with diversification have enabled more robust tests of this idea and have found mixed support. We test the evolutionary dead end hypothesis by estimating net diversification rate differences associated with nest-type specialization among 3224 species of passerine birds. In particular, we test whether the adoption of hole-nesting, a nest-type specialization that decreases predation, results in reduced diversification rates relative to nesting outside of holes. Further, we examine whether evolutionary transitions to the specialist hole-nesting state have been more frequent than transitions out of hole-nesting. Using diversification models that accounted for background rate heterogeneity and different extinction rate scenarios, we found that hole-nesting specialization was not associated with diversification rate differences. Furthermore, contrary to the assumption that specialists rarely evolve into generalists, we found that transitions out of hole-nesting occur more frequently than transitions into hole-nesting. These results suggest that interspecific competition may limit adoption of hole-nesting, but that such competition does not result in limited diversification of hole-nesters. In conjunction with other recent studies using robust comparative methods, our results add to growing evidence that evolutionary dead ends are not a typical outcome of resource specialization. [Cavity nesting; diversification; hidden-state models; passerines; resource specialization.] 

Files and code for "Simpson's bradytely or tachytely? The importance of quantifying rate uncertainty". Felsenstein review for Methods in Ecology and Evolution. 2024. Authors: Rosana Zenil-Ferguson (University of Kentucky) and Lee Hsiang Liow (University of Oslo). 

A long-standing hypothesis in evolutionary biology is that the evolution of resource specialization can lead to an evolutionary dead end, where specialists have low diversification rates and limited ability to evolve into generalists. In recent years, advances in comparative methods investigating trait-based differences associated with diversification have enabled more robust tests of this idea and have found mixed support. We test the evolutionary dead end hypothesis by estimating net diversification rate differences associated with nest site specialization among 3,224 species of passerine birds. In particular, we test whether the adoption of hole-nesting, a nest site specialization that decreases predation, results in reduced diversification rates relative to nesting outside of holes. Further, we examine whether evolutionary transitions to the specialist hole-nesting state have been more frequent than transitions out of hole-nesting. Using diversification models that accounted for background rate heterogeneity and different extinction rate scenarios, we found that hole-nesting specialization was not associated with diversification rate differences. Furthermore, contrary to the assumption that specialists rarely evolve into generalists, we found that transitions out of hole-nesting occur more frequently than transitions into hole-nesting. These results suggest that interspecific competition may limit adoption of hole-nesting, but that such competition does not result in limited diversification of hole-nesters. In conjunction with other recent studies using robust comparative methods, our results add to growing evidence that evolutionary dead ends are not a typical outcome of resource specialization.