G. A. Bazykin

Mutational signatures in wild type Escherichia coli strains reveal dominance of DNA polymerase errors

The paper analyzes mutational signatures in E. coli strains to show DNA polymerase errors, not DNA repair disruptions, drive mutation accumulation in both natural and lab settings.

Memory persistence and differentiation into antibody-secreting cells accompanied by positive selection in longitudinal BCR repertoires

The paper analyzes longitudinal BCR repertoires to show clonal persistence and differentiation into ASCs with positive selection and affinity maturation.

Complex fitness landscape shapes variation in a hyperpolymorphic species

The paper analyzes genetic variation in Schizophyllum commune, finding that nonsynonymous site linkage disequilibrium suggests positive epistasis and balancing selection.

Phylogenetic inference of changes in amino acid propensities with single-position resolution

This paper develops a method to detect changes in amino acid fitness across lineages using phylogenetic and sequence data, validated on HIV-1 and influenza A proteins.

Pairs of compensatory frameshifting mutations contribute to evolution of protein-coding sequences in vertebrates and insects

The paper identifies pairs of compensatory frameshifting mutations in vertebrates and insects, showing they generate novel protein sequences and contribute to evolutionary diversity.

Population genomics of two closely related anhydrobiotic midges reveals differences in adaptation to extreme desiccation

This study compares the population genomics of two anhydrobiotic midges, revealing differences in the genetic architecture and adaptation of the PIMT gene family to desiccation.

Adaptive evolution at mRNA editing sites in soft-bodied cephalopods

The paper shows that mRNA editing sites in cephalopods are shaped by adaptive evolution through substitutions that mimic the edited nucleotides, indicating a role for RNA editing in molecular adaptation.

Senescence and entrenchment in evolution of amino acid sites

The paper distinguishes between entrenchment and senescence in amino acid site evolution, showing entrenchment dominates in negatively selected sites while senescence occurs in positively selected sites.

Rapid accumulation of mutations in growing mycelia of a hypervariable fungus Schizophyllum commune

The paper measures mutation accumulation in Schizophyllum commune mycelium, finding a high mutation rate per meter of growth compared to other species.

SELVa: Simulator of Evolution with Landscape Variation

SELVa simulates evolutionary substitution processes under changing fitness landscapes across a phylogeny of lineages.

Recombination in a natural population of the bdelloid rotifer Adineta vaga

This study analyzes the genome of Adineta vaga to show that recombination occurs despite the absence of meiosis, suggesting a mechanism for genetic exchange in asexual populations.

Genetics of adaptation of the ascomycetous fungus Podospora anserina to submerged cultivation

This study investigates genetic changes in Podospora anserina during adaptation to submerged cultivation, identifying 125 SNVs and 23 indels across eight populations, with evidence of positive selection on genes related to growth and development.

Architecture of parallel adaptation to freshwater in multiple populations of threespine stickleback

The paper examines parallel adaptation to freshwater in threespine stickleback populations, finding that divergence islands (DIs) are clustered and some are universal across populations.

Error-prone bypass of DNA lesions during lagging strand replication is a common source of germline and cancer mutations

The paper identifies error-prone bypass of DNA lesions on the lagging strand as a major source of human germline and cancer mutations, supported by mutational asymmetry analysis and experimental validation.

Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans

The paper analyzes loss-of-function allele prevalence across 32 metazoan species and finds no correlation with lifetime fecundity or other life-history traits.

Bursts of amino acid replacements in protein evolution

The paper detects bursts of rapid amino acid substitutions in proteins across two species groups, attributing them to positive selection rather than neutral processes.

Pathogenic Amino Acid Variants In Mitochondrial Proteins More Frequently Arise In Lineages Closely Related To Human Than In Distant Lineages

The paper shows that pathogenic amino acid variants in human mitochondrial proteins are more common in closely related species than distant ones, suggesting these variants are more tolerated in humans.