A5082054411- Evolution and Paleontology Studies
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Language and cultural evolution
- Model Reduction and Neural Networks
- Neural Networks and Applications
- Evolutionary Game Theory and Cooperation
- Chromosomal and Genetic Variations
- Structural Health Monitoring Techniques
- Linguistics and Cultural Studies
- Animal Behavior and Reproduction
- Paleontology and Evolutionary Biology
- Wildlife Ecology and Conservation
- Linguistics and language evolution
- Authorship Attribution and Profiling
- Amphibian and Reptile Biology
- Plant and animal studies
- Linguistic Variation and Morphology
- Microbial Community Ecology and Physiology
- Species Distribution and Climate Change
- Bat Biology and Ecology Studies
- Bioinformatics and Genomic Networks
- Ichthyology and Marine Biology
- Fish biology, ecology, and behavior
- Electromagnetic Simulation and Numerical Methods
University of Reading
2014-2023
Rice University
1998-2016
University of Glasgow
2010
Aberystwyth University
2008
University of Auckland
2008
Santa Fe Institute
2008
Henley College
2006
University of Michigan–Ann Arbor
2003
Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from distribution traits observed in contemporary organisms. Because phylogenies are normally inferences data, it is desirable account for uncertainty estimates tree and its branch lengths when making about or other comparative parameters. Here we present general Bayesian approach testing hypotheses across statistically justified samples phylogenies, focusing on specific issue reconstructing states....
We describe a Bayesian method for investigating correlated evolution of discrete binary traits on phylogenetic trees. The fits continuous‐time Markov model to pair traits, seeking the best fitting models that their joint phylogeny. employ methodology reversible‐jump (RJ) chain Monte Carlo search among large number possible models, some which conform independent two others evolution. RJ visits these in proportion posterior probabilities, thereby directly estimating support hypothesis In...
We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites the alignment evolve qualitatively distinct ways, but does not require prior knowledge of these patterns partitioning call this qualitative variability pattern evolution across "pattern-heterogeneity" to distinguish it both homogenous process and one characterized principally by differences rates...
BackgroundConcerted evolution is normally used to describe parallel changes at different sites in a genome, but it also observed languages where specific phoneme the same other many words lexicon—a phenomenon known as regular sound change. We develop general statistical model that can detect concerted aligned sequence data and apply study Turkic language family.ResultsLinguistic evolution, unlike genetic substitutional process, dominated by events of evolutionary Our identified more than 70...
Significance Humans are uniquely capable of using cultural innovations to occupy a range environments, raising the intriguing question whether historical human migrations have followed familiar habitats or moved relatively independently them. Beginning ∼5,000 y ago, savannah-dwelling populations Bantu-speaking peoples swept out West Central Africa, eventually occupying vast geographical area. We show that this expansion avoided unfamiliar rainforest by following savannah corridors emerged...
Phylogenetic comparative methods are increasingly used to give new insights into the dynamics of trait evolution in deep time. For continuous traits core these is a suite models that attempt capture evolutionary patterns by extending Brownian constant variance model. However, properties often poorly understood, which can lead misinterpretation results. Here we focus on one - Ornstein Uhlenbeck (OU) We show OU model frequently incorrectly favoured over simpler when using Likelihood ratio...
A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the of speciation. We found that approximately 22% substitutional changes DNA level can be attributed to evolution, and remainder accumulates from background gradual divergence. Punctuational effects occur more than twice rate plants fungi animals, but proportion total divergence attributable change does not vary among these groups. cause departures a...
Linguists speculate that human languages often evolve in rapid or punctuational bursts, sometimes associated with their emergence from other languages, but this phenomenon has never been demonstrated. We used vocabulary data three of the world's major language groups—Bantu, Indo-European, and Austronesian—to show 10 to 33% overall differences among these arose bursts change language-splitting events. Our findings identify a general tendency for increased rates linguistic evolution fledgling...
The search for ever deeper relationships among the World’s languages is bedeviled by fact that most words evolve too rapidly to preserve evidence of their ancestry beyond 5,000 9,000 y. On other hand, quantitative modeling indicates some “ultraconserved” exist might be used find deep linguistic time barrier. Here we use a statistical model, which takes into account frequency with are in common everyday speech, predict existence set such highly conserved seven language families Eurasia...
There are approximately 7000 languages spoken in the world today. This diversity reflects legacy of thousands years cultural evolution. How far back we can trace this history depends largely on rate at which different components language evolve. Rates lexical evolution widely thought to impose an upper limit 6000–10 000 reliably identifying relationships. In contrast, it has been argued that certain structural elements much more stable. Just as biologists use highly conserved genes uncover...
Communal signalling—wherein males and females collaborate to produce joint visual or acoustic displays—is perhaps the most complex least understood form of communication in social animals. Although many communal signals appear mediate competitive interactions within between coalitions individuals, previous studies have highlighted a confusing array environmental factors that may explain evolution these displays, we still lack global synthesis needed understand why are distributed so unevenly...
The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach allows the rate of evolution vary across phylogeny, we find long-term directional bias toward increasing in mammals. This pattern holds separately 10 11 orders which sufficient data are available and arises from tendency accelerated rates produce increases, but not decreases, size. On branch-by-branch basis, increases have more than...
There is disagreement about the routes taken by populations speaking Bantu languages as they expanded to cover much of sub-Saharan Africa. Here, we build phylogenetic trees and map them onto geographical space in order assess likely pathway expansion test between dispersal scenarios. The results clearly support a scenario which groups first moved south through rainforest from homeland somewhere near Nigeria-Cameroon border. Emerging on side rainforest, one branch west. Another towards Great...
Despite important recent progress in our understanding of brain evolution, controversy remains regarding the evolutionary forces that have driven its enormous diversification size. Here, we report passerine birds, migratory species tend to brains are substantially smaller (relative body size) than those resident species, confirming and generalizing previous studies. Phylogenetic reconstructions based on Bayesian Markov chain methods suggest an scenario which some large brained tropical...
Summary It is widely recognized that macroecological patterns are not independent of the evolution lineages involved in generating these patterns. While many researchers have begun to evaluate effect ancestor–descendant relationships on observed using phylogenetic comparative method, most studies only utilize cross‐sectional method ‘remove history’, without considering option evaluating its removing it. Currently, use this explicitly three fundamental evolutionary assumptions method: (i)...
Rates of phenotypic evolution vary widely in nature and these rates may often reflect the intensity natural selection. Here we outline an approach for detecting exceptional shifts rate across phylogenies. We introduce a simple new branch-specific metric ∆V/∆B that divides observed change along branch into two components: (1) attributable to background (∆B), (2) departures from (∆V). Where amount expected derived variation morphological doubles explained by (∆V/∆B > 2), identify this as...
Members of the order Rhizobiales include those capable nitrogen fixation in nodules as well pathogens animals and plants. This lifestyle diversity has important implications for agricultural medical research. Leveraging large-scale genomic data, we infer that originated a free-living ancestor ∼1,500 million years ago (Mya) later emergence host-associated lifestyles broadly coincided with rise their eukaryotic hosts. In particular, first nodulating lineage arose from either Azorhizobium or...
A puzzle of language is how speakers come to use the same words for particular meanings, given that there are often many competing alternatives (e.g., “sofa,” “couch,” “settee”), and seldom a necessary connection between word its meaning. The well-known process random drift—roughly corresponding in this context “say what you hear”—can cause frequencies alternative fluctuate over time, it even possible one replace all others, without any form selection being involved. However, drift alone an...
Abstract Macroevolution posed difficulties for Darwin and later theorists because species’ phenotypes frequently change abruptly, or experience long periods of stasis, both counter to the theory incremental gradualism. We introduce a statistical model that accommodates this uneven evolutionary landscape by estimating two kinds historical change: directional changes shift mean phenotype along branches phylogenetic tree, evolvability alter clade’s ability explore its trait-space. In mammals,...
The node-density effect is an artifact of phylogeny reconstruction that can cause branch lengths to be underestimated in areas the tree with fewer taxa. Webster, Payne, and Pagel (2003, Science 301:478) introduced a statistical procedure (the "delta" test) detect this artifact, here we report results computer simulations examine test's performance. In sample 50,000 random data sets, find delta test detects 94.4% cases which it present. When not present (n = 10,000 simulated sets) showed type...