The phylogenomics of evolving virus virulence

JL Geoghegan, EC Holmes - Nature Reviews Genetics, 2018 - nature.com
How virulence evolves after a virus jumps to a new host species is central to disease
emergence. Our current understanding of virulence evolution is based on insights drawn …

Evolution in the light of fitness landscape theory

I Fragata, A Blanckaert, MAD Louro, DA Liberles… - Trends in ecology & …, 2019 - cell.com
By formalizing the relationship between genotype or phenotype and fitness, fitness
landscapes harbor information on molecular and evolutionary constraints. The shape of the …

Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics

G Avecilla, JN Chuong, F Li, G Sherlock… - PLoS …, 2022 - journals.plos.org
The rate of adaptive evolution depends on the rate at which beneficial mutations are
introduced into a population and the fitness effects of those mutations. The rate of beneficial …

Next-generation cophylogeny: unravelling eco-evolutionary processes

I Blasco-Costa, A Hayward, R Poulin… - Trends in Ecology & …, 2021 - cell.com
A fundamental question in evolutionary biology is how microevolutionary processes
translate into species diversification. Cophylogeny provides an appropriate framework to …

Towards an integrative view of virus phenotypes

JP DeLong, MA Al-Sammak, ZT Al-Ameeli… - Nature Reviews …, 2022 - nature.com
Understanding how phenotypes emerge from genotypes is a foundational goal in biology.
As challenging as this task is when considering cellular life, it is further complicated in the …

Measuring coevolutionary dynamics in species-rich communities

AR Hall, B Ashby, J Bascompte, KC King - Trends in Ecology & Evolution, 2020 - cell.com
Identifying different types of coevolutionary dynamics is important for understanding
biodiversity and infectious disease. Past work has often focused on pairs of interacting …

Functional comparison of MERS-coronavirus lineages reveals increased replicative fitness of the recombinant lineage 5

S Schroeder, C Mache, H Kleine-Weber… - Nature …, 2021 - nature.com
Middle East respiratory syndrome coronavirus (MERS-CoV) is enzootic in dromedary
camels across the Middle East and Africa. Virus-induced pneumonia in humans results from …

Construction and characterization of synthetic bacterial community for experimental ecology and evolution

J Cairns, R Jokela, J Hultman, M Tamminen… - Frontiers in …, 2018 - frontiersin.org
Experimental microbial ecology and evolution have yielded foundational insights into
ecological and evolutionary processes using simple microcosm setups and phenotypic …

Novel genomic approaches to study antagonistic coevolution between hosts and parasites

H Märkle, S John, A Cornille, PD Fields… - Molecular …, 2021 - Wiley Online Library
Host‐parasite coevolution is ubiquitous, sha** genetic and phenotypic diversity and the
evolutionary trajectory of interacting species. With the advances of high throughput …