Bacterial Recombination in vivo Didelot, Xavier; Falush, Daniel
Horizontal Gene Transfer in the Evolution of Pathogenesis,
06/2008
Book Chapter
INTRODUCTIONIn eukaryotes, the great majority of genetic recombination takes place during the complex and highly organized process of meiotic division, a part of sexual reproduction. As a consequence ...there are a number of constraints on patterns of variability in the recombination process. Recombination takes place only between organisms that are similar enough for their offspring to be viable, and therefore it is generally limited in the novelty it can introduce. Within species, the most common cause of reproductive isolation is geographical separation. In most higher animals and plants, the number of crossovers per chromosome is predictably a number between 1 and 5 in both sexes. Even where individuals differ in the amount of recombination that they initiate, for example because of the absence of crossing over in male Drosophila, the existence of a common mating pool will tend to homogenize the population with respect to the amount of genetic exchange that has occurred in the ancestry of each individual. In summary, while the mating process is elegant, eukaryotic recombination is typically quite predictable with minimal differences in genetic patterns between individuals in the same species.In bacteria, there are no such rules. Recombination is never obligate and occurs by three distinct mechanisms; transformation, transduction, and conjugation, each of which in their nature can vary enormously between lineages.
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often ...not able to make full use of this complex information. We present a Bayesian method for inferring the phylogenetic relationship among related organisms found within metagenomic samples. Our approach exploits variation in the frequency of taxa among samples to simultaneously infer each lineage haplotype, the phylogenetic tree connecting them, and their frequency within each sample. Applications of the algorithm to simulated data show that our method can recover a substantial fraction of the phylogenetic structure even in the presence of strong mixing among samples. We provide examples of the method applied to data from green sulfur bacteria recovered from an Antarctic lake, plastids from mixed Plasmodium falciparum infections, and virulent Neisseria meningitidis samples.
We investigated global patterns of variation in 157 whole genome sequences of Vibrio parahaemolyticus, a free-living and seafood associated marine bacterium. Pandemic clones, responsible for recent ...outbreaks of gastroenteritis in humans have spread globally. However, there are oceanic gene pools, one located in the oceans surrounding Asia and another in the Mexican Gulf. Frequent recombination means that most isolates have acquired the genetic profile of their current location. We investigated the genetic structure in the Asian gene pool by calculating the effective population size in two different ways. Under standard neutral models, the two estimates should give similar answers but we found a thirty fold difference. We propose that this discrepancy is caused by the subdivision of the species into a hundred or more ecotypes which are maintained stably in the population. To investigate the genetic factors involved, we used 51 unrelated isolates to conduct a genome-wide scan for epistatically interacting loci. We found a single example of strong epistasis between distant genome regions. A majority of strains had a type VI secretion system associated with bacterial killing. The remaining strains had genes associated with biofilm formation and regulated by c-di-GMP signaling. All strains had one or other of the two systems and none of isolate had complete complements of both systems, although several strains had remnants. Further top-down analysis of patterns of linkage disequilibrium within frequently recombining species will allow a detailed understanding of how selection acts to structure the pattern of variation within natural bacterial populations.
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