A5015120030- Evolution and Paleontology Studies
- Genetic diversity and population structure
- Plant and animal studies
- Species Distribution and Climate Change
- Amphibian and Reptile Biology
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Ecology and Vegetation Dynamics Studies
- Animal Behavior and Reproduction
- Genetics, Bioinformatics, and Biomedical Research
- Wildlife Ecology and Conservation
- Evolutionary Game Theory and Cooperation
- Insect and Arachnid Ecology and Behavior
- Morphological variations and asymmetry
- Animal Ecology and Behavior Studies
- Fish Ecology and Management Studies
- Fish biology, ecology, and behavior
- Biomedical Text Mining and Ontologies
- Data Visualization and Analytics
- Adhesion, Friction, and Surface Interactions
- Marine animal studies overview
- Evolutionary Algorithms and Applications
- Ichthyology and Marine Biology
- Parasite Biology and Host Interactions
- Ecosystem dynamics and resilience
University of Idaho
2016-2025
Swiss Federal Institute of Aquatic Science and Technology
2016-2019
Smithsonian Institution
2014-2017
National Museum of Natural History
2014-2017
University of California, Los Angeles
2014-2017
University of Connecticut
2014-2017
University of Cincinnati
2012-2017
Yale University
2017
Duke University
2017
Universidad Nacional Autónoma de México
2017
Abstract Summary: GEIGER is a new software package, written in the R language, to describe evolutionary radiations. can carry out simulations, parameter estimation and statistical hypothesis testing. Additionally, GEIGER's simulation algorithms be used analyze power of comparative approaches. Availability: This open source entirely language freely available through Comprehensive Archive Network (CRAN) at http://cran.r-project.org/. Contact: lukeh@uidaho.edu
Abstract Summary: Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches either computationally infeasible or inappropriate this size. To address both these problems, we present geiger v2.0 , a complete overhaul popular R package . We reimplemented more efficient algorithms developed several new accomodating heterogeneous models...
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences numerous lines from a single ancestral type. However, identifying radiations has proven difficult due to lack broad-scale comparative datasets. Here, we use phylogenetic data on body size and shape in animal clades test key model radiation, which initially rapid morphological evolution is followed by relative stasis. We compared the fit this both...
The uneven distribution of species richness is a fundamental and unexplained pattern vertebrate biodiversity. Although in groups like mammals, birds, or teleost fishes often attributed to accelerated cladogenesis, we lack quantitative conceptual framework for identifying comparing the exceptional changes tempo evolutionary history. We develop MEDUSA, stepwise approach based upon Akaike information criterion detecting multiple shifts birth death rates on an incompletely resolved phylogeny....
A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement "phylogenetic signal" data sets composed observations collected from species related by a tree. Phylogenetic signal is measure statistical dependence among species' trait values due to their relationships. Although pattern (statistical dependence), there nonetheless widespread propensity literature attribute this aspects evolutionary process or rate. This may be due,...
Identification of general properties evolutionary radiations has been hindered by the lack a statistical and phylogenetic approach applicable across diverse taxa. We present comparative analytical framework for examining patterns diversification morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different evolution. Taxa whose occurred disproportionately early in their history partition more among, rather than within, subclades. This inverse...
Summary Our growing understanding of the plant tree life provides a novel opportunity to uncover major drivers angiosperm diversity. Using time‐calibrated phylogeny, we characterized hot and cold spots lineage diversification across by modeling evolutionary using stepwise AIC (MEDUSA). We also tested whole‐genome duplication ( WGD ) radiation lag‐time model, which postulates that increases in tend lag behind established events. Diversification rates have been incredibly heterogeneous...
Our understanding of macroevolutionary patterns adaptive evolution has greatly increased with the advent large-scale phylogenetic comparative methods. Widely used Ornstein–Uhlenbeck (OU) models can describe an process divergence and selection. However, inference dynamics landscapes from data is complicated by interpretational difficulties, lack identifiability among parameter values common requirement that hypotheses must be assigned a priori. Here, we develop reversible-jump Bayesian method...
Comparative biologists often attempt to draw inferences about tempo and mode in evolution by comparing the fit of evolutionary models phylogenetic comparative data consisting a molecular phylogeny with branch lengths trait measurements from extant taxa. These kinds approaches ignore historical evidence for pattern process contained fossil record. In this article, we show through simulation that incorporation information dramatically improves our ability distinguish among quantitative using...
Abstract Background One of the main explanations for stunning diversity teleost fishes (~29,000 species, nearly half all vertebrates) is that a fish-specific whole-genome duplication event (FSGD) in ancestor to teleosts triggered their subsequent radiation. However, one critical assumption this hypothesis, diversification rates increased soon after acquisition duplicated genome, has never been tested. Results Here we show three major rate shifts within ray-finned occurred at base radiation,...
Evolutionary biologists since Darwin have been fascinated by differences in the rate of trait‐evolutionary change across lineages. Despite this continued interest, we still lack methods for identifying shifts evolutionary rates on growing tree life while accommodating uncertainty process. Here introduce a Bayesian approach complex patterns evolution continuous traits. The method (auteur) uses reversible‐jump Markov chain Monte Carlo sampling to more fully characterize complexity trait...
Abstract Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, concept has provoked strong and differing opinions concerning its definition nature among researchers studying wide diversity systems. Here, we take broad view what constitutes an adaptive radiation, seek to find commonalities disparate examples, ranging from plants invertebrate vertebrate animals, remote islands lakes continents, better understand processes shared across...
Understanding the rate at which new species form is a key question in studying evolution of life on earth. Here we review our current understanding speciation rates, focusing studies based fossil record, phylogenies, and mathematical models. We find that rates estimated from these different can be dramatically different: some quickly often, while others much less frequently. suggest instead being contradictory, differences across scales reconciled by common model. Under "ephemeral model",...
We argue that biotas at scales from local communities to entire continents are nearly always open new species and their diversities far any ecological limits. show the fossil, phylogenetic, morphological evidence has been used suggest processes set limits diversity in evolutionary time is weak inconsistent. At same time, biological invasions, experiments, analyses strongly supports openness of species. urge biologists recognize ecology largely moved beyond simple notions equilibrium a...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack community-wide, consensus-based, human- machine-interpretable language for describing phenotypes genomic environmental contexts is perhaps most pressing scientific bottleneck integration across many key fields in biology, including genomics, systems development, medicine, evolution, ecology, systematics. Here we survey phenomics...
A review of the field phylogenetic comparative methods.
Convergent evolution has played an important role in the development of ecological niche concept. We investigated patterns convergent and divergent Caribbean Anolis lizards. These lizards diversified independently on each islands Greater Antilles, producing same set habitat specialists island. Using a phylogenetic comparative framework, we examined morphological convergence five functionally distinct sets characters: body size, shape, head lamella number, sexual size dimorphism. find...
Natural selection arising from resource competition and environmental heterogeneity can drive adaptive radiation. Ecological opportunity facilitates this process, resulting in rapid divergence of ecological traits many celebrated radiations. In other cases, sexual is thought to fuel mating signals ahead divergence. Comparing rates between naturally sexually selected offer insights into processes underlying species radiations, but date such comparisons have been largely qualitative. Here, we...