Daniel B. Weissman
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Transition of <i>Staphylococcus aureus</i> tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years Open
Mobile genetic elements (MGEs), including plasmids, phages and genome islands, are major sources of bacterial genetic diversity. The small plasmid pT181 confers tetracycline resistance in bacterial pathogen Staphylococcus aureus via an eff…
Genetic drift acts strongly on within-host influenza virus populations during acute infection but does not act alone Open
The evolutionary dynamics of seasonal influenza A viruses (IAVs) have been well characterized at the population level, with antigenic drift known to be a major force in driving strain turnover. The evolution of IAV populations at the withi…
View article: Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria
Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria Open
When multiple beneficial alleles at multiple loci are present in a population but not linked together in any one individual, there is no general evolutionary result that determines whether recombination will speed up or slow down the emerg…
View article: The distribution of the time to the most recent pairwise genetic common ancestor of a set of sampled genomes
The distribution of the time to the most recent pairwise genetic common ancestor of a set of sampled genomes Open
In a sample of chromosomes from a recombining population, each pair of individuals will have different most recent common genetic ancestors at different loci. We consider the distribution of the time to the most recent of these most recent…
Evolutionary rescue by aneuploidy in tumors exposed to anticancer drugs Open
Evolutionary rescue occurs when a population, facing a sudden environmental change that would otherwise lead to extinction, adapts through beneficial mutations, allowing it to recover and persist. A prime example of evolutionary rescue is …
View article: Effects of recombination on multi-drug resistance evolution in <i>Plasmodium falciparum</i> malaria
Effects of recombination on multi-drug resistance evolution in <i>Plasmodium falciparum</i> malaria Open
When multiple beneficial alleles are present in a population but not linked together in any one individual, there is no general evolutionary result that determines whether recombination will speed up or slow down the emergence and evolutio…
Average nucleotide identity-based <i>Staphylococcus aureus</i> strain grouping allows identification of strain-specific genes in the pangenome Open
Staphylococcus aureus causes both hospital- and community-acquired infections in humans worldwide. Due to the high incidence of infection, S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding re…
Average Nucleotide Identity based <i>Staphylococcus aureus</i> strain grouping allows identification of strain-specific genes in the pangenome Open
Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding reso…
Population structure can reduce clonal interference when sexual reproduction and dispersal are synchronized Open
In populations with limited recombination, clonal interference among beneficial mutations limits the maximum rate of adaptation. Spatial structure slows the spread of beneficial alleles; in purely asexual populations, this increases the am…
View article: Fifty shades of greenbeard: robust evolution of altruism based on similarity of complex phenotypes
Fifty shades of greenbeard: robust evolution of altruism based on similarity of complex phenotypes Open
We study the evolution of altruistic behaviour under a model where individuals choose to cooperate by comparing a set of continuous phenotype tags. Individuals play a donation game and only donate to other individuals that are sufficiently…
Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes Open
Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large…
Modeling the evolution of recombination plasticity: A prospective review Open
Meiotic recombination is one of the main sources of genetic variation, a fundamental factor in the evolutionary adaptation of sexual eukaryotes. Yet, the role of variation in recombination rate and other recombination features remains unde…
Isolation by distance in populations with power-law dispersal Open
Limited dispersal of individuals between generations results in isolation by distance, in which individuals further apart in space tend to be less related. Classic models of isolation by distance assume that dispersal distances are drawn f…
View article: Corrigendum: Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
Corrigendum: Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern Open
Corrigendum on: Ghafari M, Liu Q, Dhillon A, Katzourakis A and Weissman DB (2022) Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern. Front. Virol. 2:942555. doi: 10.3389/fviro.2022.942555 In the publi…
Spatial structure alters the site frequency spectrum produced by hitchhiking Open
The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and sim…
View article: Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern Open
The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Despite unprecedented efforts to increase genomic surveillance, f…
Heterogeneity in viral populations increases the rate of deleterious mutation accumulation Open
RNA viruses have high mutation rates, with the majority of mutations being deleterious. We examine patterns of deleterious mutation accumulation over multiple rounds of viral replication, with a focus on how cellular coinfection and hetero…
Masks Do No More Than Prevent Transmission: Theory and Data Undermine the Variolation Hypothesis Open
Background Masking serves an important role in reducing the transmission of respiratory viruses, including SARS-CoV-2. During the COVID-19 pandemic, several perspective and review articles have also argued that masking reduces the risk of …
Spatial structure alters the site frequency spectrum produced by hitchhiking Open
The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and sim…
View article: 50 shades of greenbeard: Robust evolution of altruism based on similarity of complex phenotypes
50 shades of greenbeard: Robust evolution of altruism based on similarity of complex phenotypes Open
We study the evolution of altruistic behavior under a model where individuals choose to cooperate by comparing a set of continuous phenotype tags. Individuals play a donation game and only donate to other individuals that are sufficiently …
View article: Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern Open
The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Despite unprecedented efforts to increase genomic surveillance, f…
SARS-CoV-2 evolution and immune escape in immunocompromised patients treated with exogenous antibodies Open
Background SARS-CoV-2 mutations conferring escape from neutralizing antibodies can arise in immunocompromised patients with prolonged infection, but the conditions that facilitate immune escape are still not fully understood. Methods We ch…
View article: Detecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes
Detecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes Open
Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large…
Heterogeneity in viral infections increases the rate of deleterious mutation accumulation Open
1 Abstract RNA viruses have high mutation rates, with the majority of mutations being deleterious. We examine patterns of deleterious mutation accumulation over multiple rounds of viral replication, with a focus on how cellular coinfection…
Fitness dependence preserves selection for recombination across diverse mixed mating systems Open
Meiotic recombination and the factors affecting its rate and fate in nature have inspired many theoretical studies in evolutionary biology. Classical theoretical models have inferred that non-zero recombination can be favoured under a rath…
Isolation by Distance in Populations with Power-law Dispersal Open
Limited dispersal of individuals between generations results in isolation by distance, in which individuals further apart in space tend to be less related. Classic models of isolation by distance assume that dispersal distances are drawn f…
Inferring Transmission Bottleneck Size from Viral Sequence Data Using a Novel Haplotype Reconstruction Method Open
Viral populations undergo a repeated cycle of within-host growth followed by transmission. Viral evolution is affected by each stage of this cycle. The number of viral particles transmitted from one host to another, known as the transmissi…