Abstract Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these grow increasingly complex, users often encounter significant challenges with summarizing, visualizing communicating their key results. We present RevGadgets , an R package creating publication‐quality figures from results large variety analyses performed in RevBayes (and other software packages). demonstrate how to use through set vignettes that cover...

The birth-death model is commonly used to infer speciation and extinction rates by fitting the phylogenetic trees with exclusively extant taxa. Recently, it was demonstrated that are not identifiable if allowed vary freely over time. group of models have same likelihood called a congruence class, there no statistical evidence favor one other. This issue has led researchers question what patterns can reliably be inferred from phylogenies only taxa whether time-variable should fitted at all....

Models based on the Ornstein-Uhlenbeck process have become standard for comparative study of adaptation. Cooper et al. (2016) cast doubt this practice by claiming statistical problems with fitting models to data. Specifically, they claim that tests Brownian motion may too high Type I error rates and such are exacerbated measurement error. In note, we argue these results little relevance estimation adaptation three reasons. First, point out did not consider detection distinct optima (e.g....

Increased brain size in humans and other primates is hypothesized to confer cognitive benefits but brings costs associated with growing maintaining energetically expensive neural tissue. Previous studies have argued that changes either diet or levels of sociality led shifts size, results were equivocal. Here we test these hypotheses using phylogenetic comparative methods designed jointly account for estimate the effects adaptation phylogeny. Using largest current sample primate body sizes...

Abstract The origin of sensory structures provides an excellent framework for studying how constraints and selective pressures affect the evolution complex features. mammalian middle ear from jaw hinge non-mammalian synapsids offers a deep-time perspective on but is limited by poor understanding early synapsid hearing. This work tests hypothesis that size reflected lamina angular bone in followed strict, negative allometric trend may be expected sound receiver. Allometry first investigated...

Abstract The huge antlers of the extinct Irish elk have invited evolutionary speculation since Darwin. In 1970s, Stephen Jay Gould presented first extensive data on antler size in and combined these with comparative from other deer to test hypothesis that gigantic were outcome a positive allometry constrained large-bodied proportionally even larger antlers. He concluded had as predicted for its interpreted this within his emerging framework developmental constraints an explanatory factor...

Abstract Diversification rates inferred from phylogenies are not identifiable if the allowed to vary freely over time. There infinitely many combinations of speciation and extinction rate functions that have exact same likelihood score for a given phylogeny, building congruence class. The specific shape characteristics such classes yet been studied. Whether within class share common features is also known. Prior hypotheses typically render diversification identifiable, but results then...

Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these may coincide with key evolutionary events such as the development novel morphological characters, acquisition adaptive traits, polyploidization or other structural genomic changes, dispersal to new habitat and subsequent increase environmental niche space. However, while multiple methods now exist estimate identify using phylogenetic topologies, appropriate use...

Documented occurrences of fossil taxa are the empirical foundation for understanding large-scale biodiversity changes and evolutionary dynamics in deep time. The record contains vast amounts understudied taxa. Yet compilation huge volumes data remains a labour-intensive impediment to more complete Earth's history. Even so, many occurrence records species genera these can be uncovered palaeontological literature. Here, we extract observations fossils their inferred ages from unstructured text...

Abstract The increasing availability of 3D-imaging technology provides new opportunities for measuring morphology. Photogrammetry enables easy 3D-data acquisition compared to conventional methods and here we assess its accuracy the size deer antlers, a complex morphological structure. Using proprietary photogrammetry software, generated 3D images antlers 92 individuals from 29 species cervids that vary widely in antler shape used these measure volume. By repeating process, found relative...

Abstract Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, communicating their key results. We present RevGadgets , an R package creating publication-quality figures from results large variety analyses performed in RevBayes (and other software packages). demonstrate how to use through set vignettes that cover...

Abstract Identifying along which lineages shifts in diversification rates occur is a central goal of comparative phylogenetics; these may coincide with key evolutionary events such as the development novel morphological characters, acquisition adaptive traits, polyploidization or other structural genomic changes, dispersal to new habitat and subsequent increase environmental niche space. However, while multiple methods now exist estimate identify using phylogenetic topologies, appropriate...

We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. compare these results with combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and Global Facility (GBIF). Using DB TMO separately combination, we present latitudinal richness curves using standard estimators (Chao2 Jackknife) range-through approaches. Our quantitatively document a bimodal...

Summary 1. Diversification rates inferred from phylogenies are not identifiable. There infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building congruence class. The specific shape characteristics such classes yet been studied. Whether within class share common features is also known. 2. Instead striving to make diversification identifiable, we can embrace their inherent non-identifiable nature. We use...