D. A. Petrov

Parameterizing Pantherinae: de novo mutation rate estimates from Panthera and Neofelis pedigrees

The paper estimates de novo mutation rates in Panthera and Neofelis species using pedigrees, finding rates between 0.5 and 1.4e-08 per generation per base pair.

Combinatorial in vivo genome editing identifies widespread epistasis during lung tumorigenesis

The paper uses in vivo genome editing to study genetic interactions in lung cancer, finding widespread negative epistasis among tumor suppressor genes.

Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities

This study shows how initial population size and resource competition shape gut microbial community coalescence, with dose-dependent effects persisting even after many generations.

Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking

The paper tracks adaptive genetic changes in Drosophila melanogaster under fluctuating selection pressures, revealing rapid, parallel genomic responses and predictable selection targets over time.

Oncogenic context shapes the fitness landscape of tumor suppression

The paper models tumor suppression fitness landscapes across four oncogenic contexts and finds context-specific tumor suppressor effects.

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

The paper presents 183 new genome assemblies for 179 drosophilid species using single-fly long-read sequencing, improving phylogenomic coverage and enabling a well-resolved multi-locus phylogeny.

Strong environmental memory revealed by experimental evolution in static and fluctuating environments

The paper tracks yeast lineages in static and fluctuating environments, finding fitness deviations and environmental memory effects due to prior conditions.

Unraveling the Genomic Diversity and Admixture History of Captive Tigers in the United States

This study analyzes the genomic diversity and admixture history of captive tigers in the U.S., finding admixture from all six wild tiger subspecies and developing a reference panel for conservation.

Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma

This study characterizes the fitness landscapes of tumor suppressor genes in oncogene-negative lung adenocarcinoma, finding that multiple mutations can drive tumor growth with minimal constraints on mutational order.

A multiplexed in vivo approach to identify driver genes in small cell lung cancer

The paper develops a multiplexed in vivo approach to identify driver genes in SCLC using CRISPR/Cas9 and lentiviral barcoding, finding TSC1 as a robust tumor suppressor.

Combinatorial tumor suppressor inactivation efficiently initiates lung adenocarcinoma with therapeutic vulnerabilities

This study identifies RAS/PI3K pathway activation as a common driver in oncogene-negative lung adenocarcinomas and shows these tumors are vulnerable to targeted therapy.

Direct observation of adaptive tracking on ecological timescales in Drosophila

The paper tracks phenotypic and genomic adaptation in Drosophila over ten generations, showing rapid and dynamic responses to environmental change.

Highly contiguous assemblies of 101 drosophilid genomes

The paper presents high-quality genome assemblies for 101 drosophilid lines using Oxford Nanopore sequencing, achieving high contig N50 and BUSCO completeness.

The cis-regulatory effects of modern human-specific variants

The paper investigates the regulatory effects of modern human-specific variants using a massively parallel reporter assay in three cell types, finding 1,791 active sequences and 407 driving differential expression.

Shifts in antimalarial drug policy since 2006 have rapidly selected P. falciparum resistance alleles in Angola

This study examines changes in P. falciparum drug resistance alleles in Angola after a shift to artemisinin combination therapy, finding declining CQ resistance but rising resistance to ACT partner drugs and SP.

Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

The paper reanalyzes Drosophila melanogaster population genomic data to confirm that recent and strong sweeps are likely soft sweeps, despite criticism of the original findings.

Genetic Adaptation in New York City Rats

The paper investigates genetic adaptation in New York City rats by analyzing whole-genome sequences to identify signatures of selection related to urban living.

Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

This study shows microbiome manipulation drives rapid genomic adaptation in Drosophila melanogaster by altering allele frequencies across the genome.

Evolutionary dynamics in structured populations under strong population genetic forces

This study uses modeling to show how migration and selection interact to create non-monotonic FST patterns in adapting populations and estimates high migration rates in a Simian-HIV population.

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.

The clarifying role of time series data in the population genetics of HIV

This paper uses time series data to show that soft sweeps drove early HIV treatment failure, contrasting with harder sweeps associated with better drugs.

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

This study identifies transposable element-induced mutations in Drosophila that influence stress response, behavior, and development through genetic analysis of population frequencies and functional effects.

Rapid seasonal evolution in innate immunity of wild Drosophila melanogaster

The paper investigates rapid seasonal evolution in innate immunity of Drosophila melanogaster by analyzing immune responses and genetic variation across populations.

High resolution spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host

This study tracks SHIV evolution in macaques to show drug resistance spreads rapidly across compartments but does not equilibrate, with the gut showing faster turnover and less wild-type virus retention.

Segregation lift: A general mechanism for the maintenance of polygenic variation under seasonally fluctuating selection.

The paper introduces a mechanism called segregation lift that explains how polygenic variation can be maintained under seasonally fluctuating selection by considering dominance and epistasis in multi-locus models.