The origins and prehistory of domestic sheep (Ovis aries) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Ge...

Obelisks are widespread RNA-based agents found in diverse environmental and human-associated microbiomes. These apparently unbranched and circular RNAs represent a previously uncharacterized class of ...

During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints co...

Nature - Repurposing of a gill gene regulatory program for outer ear evolution

Genomic pathogen sequencing during the COVID-19 pandemic highlighted the critical role of surveillance in understanding the persistence of SARS-CoV-2 in the human population despite high levels of protective immunity and the effect of the changing circulating variants on public health, advising policymakers and informing vaccine design. With nearly 20 million SARS-CoV-2 genomes currently available in the GISAID database, the sequencing effort since 2020 has surpassed those of other viruses, followed by less than half a million influenza virus genomes (GISAID) and less than 50,000 HIV-1 genomes (GenBank) all collected over several decades. The almost real-time resolution of circulating SARS-CoV-2 variants allowed scientists to readily detect and characterize genome changes corresponding to the virus’s functional and antigenic evolution in humans and anthroponosis events to other animals. This phenotypic change was apparent from the outset of the pandemic, with genomic surveillance revealing the first “functional” substitution, D614G (1, 2), and first significant antigenic substitution, N439K (3), both changes in the virus’s Spike entry glycoprotein. In addition to such point mutations creating variants with altered phenotypic properties, the global sequencing effort uncovered several mechanisms this new human virus used to maintain its circulation in the population: recurring indel mutations generating new variants, e.g., deletion H69/V70 (4); independent occurrence of the same amino acid substitutions at the same site in different variants (convergence) (5, 6); the emergence of variants of concern associated with multiple beneficial mutations through saltation-like evolution linked to chronic infections (7, 8); and bringing novel sets of mutations together in one variant (recombination) (9, 10), which can have a combinatory beneficial effect for the virus (positive epistasis) (11).

This work presents a framework for estimating cell division numbers using DNA replication-associated polyguanine tract mutations, with applications for understanding tumor natural histories and origin...

Abstract. The development of accurate bioinformatic software tools is crucial for the effective analysis of complex biological data. This study examines th

SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.

A comprehensive meta-analysis of global terrestrial and marine genetic diversity covering more than three decades of research demonstrates rapid loss of genetic diversity and identifies conservation i...

Mass poultry vaccination affects H5 avian influenza virus transmission and evolution, revealing complex host-virus dynamics.

This Review discusses the various molecular mechanisms underlying the generation of new genes and highlights their important functions and phenotypes with an emphasis on the evolutionary forces underl...

Scientific Data - Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes

Directed protein evolution is central to biomedical applications but faces challenges such as experimental complexity, inefficient multiproperty optimization, and local maxima traps. Although in silic...

Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analy...

Large-scale experimental analysis of Human Domainome 1, a library containing more than 500,000 missense mutation variants across more than 500 human protein domains, reveals that 60% of pathogenic mis...

RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...

The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetic...