Genome dynamics during experimental evolution

JE Barrick, RE Lenski - Nature Reviews Genetics, 2013 - nature.com
Evolutionary changes in organismal traits may occur either gradually or suddenly. However,
until recently, there has been little direct information about how phenotypic changes are …

Life is physics: evolution as a collective phenomenon far from equilibrium

N Goldenfeld, C Woese - Annu. Rev. Condens. Matter Phys., 2011 - annualreviews.org
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it
is widely treated as a subset of population genetics, and thus its scope is artificially limited …

Polyploidy can drive rapid adaptation in yeast

AM Selmecki, YE Maruvka, PA Richmond, M Guillet… - Nature, 2015 - nature.com
Polyploidy is observed across the tree of life, yet its influence on evolution remains
incompletely understood,,,. Polyploidy, usually whole-genome duplication, is proposed to …

Genomic analysis of a key innovation in an experimental Escherichia coli population

ZD Blount, JE Barrick, CJ Davidson, RE Lenski - Nature, 2012 - nature.com
Evolutionary novelties have been important in the history of life, but their origins are usually
difficult to examine in detail. We previously described the evolution of a novel trait, aerobic …

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

F Farzadfard, TK Lu - Science, 2014 - science.org
Introduction The conversion of transient information into long-lasting responses is a common
aspect of many biological processes and is crucial for the design of sophisticated synthetic …

Rapid generation of potent antibodies by autonomous hypermutation in yeast

A Wellner, C McMahon, MSA Gilman… - Nature chemical …, 2021 - nature.com
The predominant approach for antibody generation remains animal immunization, which
can yield exceptionally selective and potent antibody clones owing to the powerful …

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

TD Lieberman, KB Flett, I Yelin, TR Martin… - Nature …, 2014 - nature.com
Advances in sequencing technologies have enabled the identification of mutations acquired
by bacterial pathogens during infection,,,,,,,,,. However, it remains unclear whether adaptive …

Second-Order Selection for Evolvability in a Large Escherichia coli Population

RJ Woods, JE Barrick, TF Cooper, U Shrestha… - Science, 2011 - science.org
In theory, competition between asexual lineages can lead to second-order selection for
greater evolutionary potential. To test this hypothesis, we revived a frozen population of …

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

BH Good, IM Rouzine, DJ Balick… - Proceedings of the …, 2012 - National Acad Sciences
When large asexual populations adapt, competition between simultaneously segregating
mutations slows the rate of adaptation and restricts the set of mutations that eventually fix …

Genetic variation and the fate of beneficial mutations in asexual populations

GI Lang, D Botstein, MM Desai - Genetics, 2011 - academic.oup.com
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 …