Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

OA MacLean, S Lytras, S Weaver, JB Singer… - PLoS …, 2021 - journals.plos.org
Virus host shifts are generally associated with novel adaptations to exploit the cells of the
new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus …

Phylogenetic comparative methods and the evolution of multivariate phenotypes

DC Adams, ML Collyer - Annual Review of Ecology, Evolution …, 2019 - annualreviews.org
Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for
multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in …

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things)

LJ Revell - PeerJ, 2024 - peerj.com
Phylogenetic comparative methods comprise the general endeavor of using an estimated
phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution …

Data integration in Bayesian phylogenetics

GW Hassler, AF Magee, Z Zhang… - Annual review of …, 2023 - annualreviews.org
Researchers studying the evolution of viral pathogens and other organisms increasingly
encounter and use large and complex data sets from multiple different sources. Statistical …

Signatures of echolocation and dietary ecology in the adaptive evolution of skull shape in bats

JH Arbour, AA Curtis, SE Santana - Nature communications, 2019 - nature.com
Morphological diversity may arise rapidly as a result of adaptation to novel ecological
opportunities, but early bursts of trait evolution are rarely observed. Rather, models of …

Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data

C Blair, C Ané - Systematic Biology, 2020 - academic.oup.com
Genomic data have had a profound impact on nearly every biological discipline. In
systematics and phylogenetics, the thousands of loci that are now being sequenced can be …

A cautionary note on “A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies”

M Grabowski, J Pienaar, KL Voje… - Systematic …, 2023 - academic.oup.com
Abstract Models based on the Ornstein–Uhlenbeck process have become standard for the
comparative study of adaptation. have cast doubt on this practice by claiming statistical …

A penalized likelihood framework for high-dimensional phylogenetic comparative methods and an application to new-world monkeys brain evolution

J Clavel, L Aristide, H Morlon - Systematic Biology, 2019 - academic.oup.com
Working with high-dimensional phylogenetic comparative data sets is challenging because
likelihood-based multivariate methods suffer from low statistical performances as the …

Phylogenetic comparative methods on phylogenetic networks with reticulations

P Bastide, C Solís-Lemus, R Kriebel… - Systematic …, 2018 - academic.oup.com
The goal of phylogenetic comparative methods (PCMs) is to study the distribution of
quantitative traits among related species. The observed traits are often seen as the result of …

Evolution of cortical geometry and its link to function, behaviour and ecology

E Schwartz, KH Nenning, K Heuer, N Jeffery… - Nature …, 2023 - nature.com
Studies in comparative neuroanatomy and of the fossil record demonstrate the influence of
socio-ecological niches on the morphology of the cerebral cortex, but have led to oftentimes …