Now showing items 1-19 of 19

    • The Balance Between Mutators and Nonmutators in Asexual Populations 

      Desai, Michael M; Fisher, Daniel S. (Genetics Society of America, 2011)
      Mutator alleles, which elevate an individual’s mutation rate from 10 to 10,000-fold, have been found at high frequencies in many natural and ex- perimental populations. Mutators are continually produced from nonmu- tators, ...
    • The competition between simple and complex evolutionary trajectories in asexual populations 

      Ochs, Ian E; Desai, Michael M (BioMed Central, 2015)
      Background: On rugged fitness landscapes where sign epistasis is common, adaptation can often involve either individually beneficial “uphill” mutations or more complex mutational trajectories involving fitness valleys or ...
    • Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations 

      Frenkel, Evgeni; McDonald, Michael J; Van Dyken, J. David; Kosheleva, Katya; Lang, Gregory I.; Desai, Michael Manish (Proceedings of the National Academy of Sciences, 2015)
      Identifying the mechanisms that create and maintain biodiversity is a central challenge in biology. Stable diversification of microbial populations often requires the evolution of differences in resource utilization. ...
    • Distortions in Genealogies due to Purifying Selection 

      Nicolaisen, Lauren Elisabeth (2014-06-06)
      As deleterious variants continually arise in a population, they tend to be purged via purifying selection, leading to distortions in the shapes of genealogies relative to neutral expectations. In recent years, a mounting ...
    • The Dynamics of Genetic Draft in Rapidly Adapting Populations 

      Kosheleva, Katya; Desai, Michael Manish (Genetics Society of America, 2013)
      The accumulation of beneficial mutations on competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations ...
    • Epistasis and Pleiotropy in Evolving Populations 

      Jerison, Elizabeth (2016-07-25)
      In the era of high-throughput genome sequencing, it has become possible to measure the genetic changes that drive evolution. These direct observations enable us to test both qualitative and quantitative hypotheses about ...
    • Fate of a mutation in a fluctuating environment 

      Cvijovic, Ivana; Good, Benjamin Harmar; Jerison, Elizabeth; Desai, Michael Manish (Proceedings of the National Academy of Sciences, 2015)
      Natural environments are never truly constant, but the evolutionary implications of temporally varying selection pressures remain poorly understood. Here we investigate how the fate of a new mutation in a fluctuating ...
    • The Fates of Mutant Lineages and the Distribution of Fitness Effects of Beneficial Mutations in Laboratory Budding Yeast Populations 

      Frenkel, Evgeni; Good, Benjamin Harmar; Desai, Michael Manish (Genetics Society of America, 2014)
      The outcomes of evolution are determined by which mutations occur and fix. In rapidly adapting microbial populations, this process is particularly hard to predict because lineages with different beneficial mutations often ...
    • Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics 

      Perron, Gabriel; Whyte, Lyle; Turnbaugh, Peter; Hanage, William P.; Dantas, Gautam; Desai, Michael M (Public Library of Science, 2013-07-02)
      Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms ...
    • Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations 

      Desai, Michael Manish; Walczak, Aleksandra M.; Fisher, Daniel S. (Genetics Society of America, 2013)
      Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft ...
    • Genetic Diversity in the Interference Selection Limit 

      Good, Benjamin H.; Walczak, Aleksandra M.; Neher, Richard A.; Desai, Michael M. (Public Library of Science, 2014)
      Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical ...
    • Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations 

      Lang, Gregory I.; Botstein, David; Desai, Michael M (Genetics Society of America, 2011)
      The fate of a newly arising beneficial mutation depends on many factors, such as the population size and the availability and fitness effects of other mutations that accumulate in the population. It has proven difficult ...
    • A genomic and evolutionary approach reveals non-genetic drug resistance in malaria 

      Herman, Jonathan D; Rice, Daniel P; Ribacke, Ulf; Silterra, Jacob; Deik, Amy A; Moss, Eli L; Broadbent, Kate M; Neafsey, Daniel E; Desai, Michael M; Clish, Clary B; Mazitschek, Ralph; Wirth, Dyann F (BioMed Central, 2014)
      Background: Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis ...
    • Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes 

      Baym, Michael; Kryazhimskiy, Sergey; Lieberman, Tami D.; Chung, Hattie; Desai, Michael M.; Kishony, Roy (Public Library of Science, 2015)
      Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. ...
    • Molecular Evolution in Rapidly Evolving Populations 

      Good, Benjamin Harmar (2016-05-17)
      Advances in DNA sequencing are creating new opportunities for studying the process of evolution. These measurements can be particularly useful for rapidly evolving microbial organisms, whose small size and fast generation ...
    • Pervasive Genetic Hitchhiking and Clonal Interference in 40 Evolving Yeast Populations 

      Lang, Gregory I.; Rice, Daniel P.; Hickman, Mark J.; Sodergren, Erica; Weinstock, George M.; Botstein, David; Desai, Michael M. (2013)
      The dynamics of adaptation determines which mutations fix in a population, and hence how reproducible evolution will be. This is central to understanding the spectra of mutations recovered in evolution of antibiotic ...
    • Sex Speeds Adaptation by Altering the Dynamics of Molecular Evolution 

      McDonald, Michael J.; Rice, Daniel P.; Desai, Michael M. (2016)
      Sex and recombination are pervasive throughout nature despite their substantial costs1. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology2,3. One longstanding hypothesis ...
    • The Structure of Allelic Diversity in the Presence of Purifying Selection 

      Desai, Michael M; Nicolaisen, Lauren Elisabeth; Walczak, Aleksandra M.; Plotkin, Joshua B. (Elsevier, 2012)
      In the absence of selection, the structure of equilibrium allelic diversity is described by the elegant sampling formula of Ewens. This formula has helped shape our expectations of empirical patterns of molecular variation. ...
    • The Structure of Genealogies in the Presence of Purifying Selection: a "Fitness-Class Coalescent" 

      Walczak, Aleksandra M.; Nicolaisen, Lauren Elisabeth; Plotkin, Joshua B.; Desai, Michael M (Genetics Society of America, 2012)
      Compared to a neutral model, purifying selection distorts the structure of genealogies and hence alters the patterns of sampled genetic variation. Although these distortions may be common in nature, our understanding of ...