Quantifying evolutionary dynamics of the basic genome of E. coli

Purushottam Dixit, Tin Yau Pang, F. William Studier, Sergei Maslov
(Submitted on 11 May 2014)

The ~4-Mbp basic genome shared by 32 independent isolates of E. coli representing considerable population diversity has been approximated by whole-genome multiple-alignment and computational filtering designed to remove mobile elements and highly variable regions. Single nucleotide polymorphisms (SNPs) in the 496 basic-genome pairs are identified and clonally inherited stretches are distinguished from those acquired by horizontal transfer (HT) by sharp discontinuities in SNP density. The six least diverged genome-pairs each have only one or two HT stretches, each occupying 42-115-kbp of basic genome and containing at least one gene cluster known to confer selective advantage. At higher divergences, the typical mosaic pattern of interspersed clonal and HT stretches across the entire basic genome are observed, including likely fragmented integrations across a restriction barrier. A simple model suggests that individual HT events are of the order of 10-kbp and are the chief contributor to genome divergence, bringing in almost 12 times more SNPs than point mutations. As a result of continuing horizontal transfer of such large segments, 400 out of the 496 strain-pairs beyond genomic divergence of share virtually no genomic material with their common ancestor. We conclude that the active and continuing horizontal transfer of moderately large genomic fragments is likely to be mediated primarily by a co evolving population of phages that distribute random genome fragments throughout the population by generalized transduction, allowing efficient adaptation to environmental changes.

Background selection as baseline for nucleotide variation across the Drosophila genome
Josep M Comeron

The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages.

Tandem duplications and the limits of natural selection in Drosophila yakuba and Drosophila simulans
Rebekah L Rogers, Julie M Cridland, Ling Shao, Tina T Hu, Peter Andolfatto, Kevin R Thornton
Subjects: Populations and Evolution (q-bio.PE)

Tandem duplications are an essential source of genetic novelty, and their prevalence in natural populations is expected to influence the trajectory of adaptive walks. Here, we describe evolutionary impacts of recently-derived, segregating tandem duplications in Drosophila yakuba and Drosophila simulans. We observe an excess of duplicated genes involved in defense against pathogens, chorion development, cuticular peptides, and lipases or endopeptidases associated with the accessory glands, as well as insecticide metabolism, suggesting that duplications function in Red Queen dynamics and rapid evolution. We observe evidence of widespread selection on the D. simulans X, suggesting adaptation through duplication is common on the X. Though we find many high frequency variants, duplicates display an excess of low frequency variants consistent with largely detrimental impacts, limiting the variation that can effectively facilitate adaptation. Although we observe hundreds of gene duplications, we show that segregating variation is insufficient to provide duplicate copies of the entire genome, and the number of duplications in the population spans 13.4% of major chromosome arms in D. yakuba and 9.7% in D. simulans. Whole gene duplication rates are low at $1.1 \times 10^{-9}$ in D. yakuba and $6.1 \times 10^{-9}$ in D. simulans, suggesting long wait times for new mutations. Hence, if adaptive processes are dependent on individual duplications, evolution will be severely limited by mutation. Hence, parallel recruitment of the same duplicated gene in different species will be rare and standing variation will define evolutionary outcomes, in spite of convergence across rapidly evolving phenotypes.