Population and evolutionary dynamics of recombining genes and alleles in bacteria

PROJECT SUMMARY/ABSTRACT
Species are conventionally defined as groups of individuals that breed with each other and produce
fertile offspring, but not with those of other species (according to Ernst Mayr's Biological Species Concept).
However, it is difficult to apply this eukaryotic definition of species to microbes because, even if they reproduce
clonally, DNA may be acquired between strains and between species. Genetic recombination allows a
bacterial cell to acquire novel traits through incorporation of DNA fragments from other organisms into its own
genome. Recombination influences a myriad of evolutionary and population processes, including levels of
standing diversity, niche expansion, spread of resistance and virulence determinants, and rapid adaptive
changes in response to new or fluctuating environmental conditions. These processes are fundamental to
questions critical to society and public health, such as whether an emerging disease is caused by a new
species or variants of existing ones, what factors make a strain resistant or transmissible, and how a pathogen
will respond to clinical interventions and host immune system. It is often assumed that all strains recombine at
a uniform frequency and randomly across the entire species. However, recent work from the PI's lab show that
recombination rates of strains of the same species vary along a continuum spanning several orders of
magnitude, with a unique pattern of exchange for different strains and lineages. The causes and
consequences of within-species variation in recombination is poorly understood, and therefore we still lack a
coherent model for genome evolution that incorporates this variation. Filling in this gap in our knowledge of
recombination has important ramifications for understanding species formation in microbes and the
mechanisms that keep them separate once they begin to diverge. The goal of our proposed research is to
elucidate how variation in recombination rates between strains impact population structure, genome evolution
and speciation in microbes. Using a combination of comparative population genomics, laboratory experiments
and mathematical modeling, we will answer the following questions: (1) To what extent does the probability of
recombination influenced by the genetic distance and ecology of the parental strains? (2) How do different
modes and genetic units of recombination vary across a species? (3) What are the evolutionary consequences
of variable recombination rates in genome structure and divergence? Output from this research will help
address the fundamental question in microbiology of whether species exist and if so, what processes keep
them separate and distinct. The proposed research will also be a significant step forward to developing an
evolution-based taxonomical framework and species boundaries for microbes. The results of the studies
proposed in this application are expected to lead to other opportunities for fruitful cross-disciplinary research at
the boundary of evolutionary biology, microbial genetics, computational biology and epidemiology.

Grant Number: 5R35GM142924-05
NIH Institute/Center: NIH
Principal Investigator: Cheryl Marie Andam