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Estimates of diversification rates at the tips of a phylogeny provide a flexible approach for correlation analyses with multiple traits and to map diversification rates in space while also avoiding the uncertainty of deep time rate reconstructions. Available methods for tip rate estimation make different assumptions, and thus their accuracy usually depends on the characteristics of the underlying...
Many clades that span the marine–freshwater boundary are disproportionately more diverse in the younger, shorter lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification...
The state‐dependent speciation and extinction (SSE) models have recently been criticized due to their high rates of “false positive” results. Many researchers have advocated avoiding SSE models in favor of other “nonparametric” or “semiparametric” approaches. The hidden Markov modeling (HMM) approach provides a partial solution to the issues of model adequacy detected with SSE models. The inclusion...
Most species have evolved adaptations to reduce the chances of predation. In many cases, adaptations to coexist with one predator generate tradeoffs in the ability to live with other predators. Consequently, the ability to live with one predator may limit the geographic distributions of species, such that adaptive evolution to coexist with novel predators may facilitate range shifts. In a case study...
Integration influences patterns of trait evolution, but the relationship between these patterns and the degree of trait integration is not well understood. To explore this further, we study a specialized pollination mechanism in conifers whose traits are linked through function but not development. This mechanism depends on interactions among three characters: pollen that is buoyant, ovules that face...
Hundreds of studies have been dedicated to estimating speciation and extinction from phylogenies of extant species. Although it has long been known that estimates of extinction rates using trees of extant organisms are often uncertain, an influential paper by Rabosky (2010) suggested that when birth rates vary continuously across the tree, estimates of the extinction fraction (i.e., extinction rate/speciation...
One of the most striking biodiversity patterns is the uneven distribution of marine species richness, with species diversity in the Indo‐Australian Archipelago (IAA) exceeding all other areas. However, the IAA formed fairly recently, and marine biodiversity hotspots have shifted across nearly half the globe since the Paleogene. Understanding how lineages have responded to shifting biodiversity hotspots...
With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long‐standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative...
Comparative methods used to study patterns of evolutionary change in a continuous trait on a phylogeny range from Brownian motion processes to models where the trait is assumed to evolve according to an Ornstein–Uhlenbeck (OU) process. Although these models have proved useful in a variety of contexts, they still do not cover all the scenarios biologists want to examine. For models based on the OU...
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