D. Enard

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

This study uses phylogenomic data to analyze the branching order of Paenungulata, finding strong evidence for a polytomy with limited gene support for any specific resolution.

Positive selection analyses identify a single WWE domain residue that shapes ZAP into a super restriction factor

This study identifies a single residue in ZAP's WWE domain that enhances its antiviral activity against alphaviruses by improving viral translation inhibition.

Pervasive relaxed selection on spermatogenesis genes coincident with the evolution of polygyny in gorillas

This study identifies genes under relaxed purifying selection in gorillas linked to male reproductive function, showing their association with human male infertility.

Quantifying Adaptive Evolution of the Human Immune Cell Landscape

The paper quantifies adaptive evolution in human immune cell types and states, finding elevated adaptation rates in specific cell types and early immune responses.

An efficient and robust ABC approach to infer the rate and strength of adaptation

The paper introduces ABC-MK, an efficient ABC method to infer adaptation rates and strengths, finding stronger positive selection in RNA-VIPs than DNA-VIPs in humans.

Stability evolution as a major mechanism of human protein adaptation in response to viruses

The paper investigates stability evolution as a mechanism for virus-driven adaptation in human proteins, finding stability changes are more common in virus-interacting proteins than previously thought.

Adaptive duplication and functional diversification of Protein kinase R contribute to the uniqueness of bat-virus interactions

This study shows that bat PKR genes have evolved through duplication and functional diversification, enabling unique antiviral defenses against DNA and RNA viruses.

Mixture Density Regression reveals frequent recent adaptation in the human genome

This paper introduces Mixture Density Regressions (MDRs) to analyze recent adaptation in the human genome and finds that positive selection is relatively common, with several genomic factors associated with adaptation.

Decreased adaptation at human disease genes as a possible consequence of interference between advantageous and deleterious variants

The paper compares selective sweeps between disease and non-disease genes across populations, finding disease genes have fewer sweeps, likely due to interference from deleterious variants.

An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia

The paper uses evolutionary analysis of human genomes to identify ancient viral selection events involving coronavirus-interacting genes in East Asian populations over 20,000 years ago.

Exceptional diversity and selection pressure on SARS-CoV and SARS-CoV-2 host receptor in bats compared to other mammals

The paper examines selection pressure on ACE2 in bats and other mammals, finding stronger positive selection in bats and highlighting potential susceptible species for SARS-CoV and SARS-CoV-2.

Ancient RNA virus epidemics through the lens of recent adaptation in human genomes

The paper identifies genomic footprints of ancient RNA virus epidemics in human populations over the past 50,000 years, showing RNA viruses drove many adaptive events across diverse populations.

Viruses rule over adaptation in conserved human proteins

The paper shows that virus-interacting proteins, even when conserved across species, experience high adaptive evolution, with viruses driving over 75% of adaptation in the most conserved human proteins.

Exploiting selection at linked sites to infer the rate and strength of adaptation

The paper develops a method to estimate adaptation rate and strength using genomic data, finding most human protein adaptation is weakly beneficial, but virus-interacting proteins show stronger and more frequent adaptation.

Pervasive adaptation in Plasmodium-interacting proteins in mammals

This study identifies 410 Plasmodium-interacting proteins in mammals, showing they experience significantly more positive selection than other proteins, linked to immune interactions and pathogen pressure.