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This week in Molecular Biology and Evolution

Throughout the evolution of life on earth, bits of genetic material are routinely swapped among different species of bacteria to give them a competitive advantage. But rarely do such gene transfers happen between bacteria and higher organisms.

Now, Prof. Nikolas Nikolaidis, et. al., report on a rare case where plant genes called expansins, which are responsible for loosening or weakening protective cell wall, were transferred from plants to bacteria, fungi and amoeba that are known plant pathogens or live nearby in the soil.

"Our study reveals a rare phenomenon in molecular evolution where plant genes have been transferred to simpler organisms like fungi and bacteria," said Nikolaidis. "The protein products of these genes are weakening the plant cell wall allowing plants to grow. In the case of bacteria and fungi, these proteins are related with the ability of these species to colonize plant roots and their virulence as plant pathogens. Our study suggests that by using proteins acquired from their hosts bacteria and fungi have found new adaptive ways to utilize their hosts resources and maybe become more advanced pathogens."

The research team found two independent instances of such horizontal gene transfers that occurred from plants to bacteria and fungi. These events were followed by gene swapping amongst bacteria and fungi to refine their evolutionary fitness. The authors also looked at the details of the gene swapping at the molecular level, and found fused DNA segments that point to a similar gene function, binding to plant and bacteria cell walls.

The evolution of these non-plant expansins represents a unique case in which bacteria and fungi have found innovative and adaptive ways to interact with and infect plants. This evolutionary paradigm suggests that, despite their low frequency, such rare events have contributed significantly in the evolution of prokaryotic and eukaryotic species.

Can evolutionary tools reliably tell us about dengue virus' past outbreaks?

The mosquito-borne virus dengue is most prevalent in Southeastern Asia, with four common strains or "serotypes" of the virus infecting up to 10 percent of children in Vietnam annually. Dengue virus is a major challenge for evolutionary biologists because of its complex ecology and rapidly changing disease dynamics. But can evolutionary models become a reliable tool for epidemiologists studying infectious disease?

Coming up with a model to relate dengue's genealogical history, or phylodynamics, with the epidemiology, of the disease is challenging because of its complexity: seasonal infection rates, changes in mosquito population sizes, the different viral strains, urban versus rural populations densities, and the widespread movement of peoplewhere viruses can usurp geographic boundaries, are all contributing factors.

Now, David Rasmussen, et. al., have looked at dengue virus serotype 1 (DENV-1) in southern Vietnam, the most dominant strain of the virus found in southern Vietnam, for which a large number of sequence samples (237) are available along with reliable data on dengue hospitalizations. They incorporated some of these additional ecological complexities to tweak different evolutionary or "phylodynamic" models and were able to reconstruct dengue's past dynamics from genealogies that are consistent with the observed hospitalization data and also lead to new insights into the factors shaping viral family histories.

Their best-fit models accounted for population variation in urban vs. rural areas or the population dynamics of mosquitos, matching the hospital reported cases. This gave new insights for the researchers to create new and improved models that are more reliable and accurate for the complex dynamics of infectious disease.

Running hot and cold on the trail to measuring adaptation in fruit flies

How does species adaptation occur at the genomic level? With the ability to rapidly sequence whole genomes at low cost, next-generation sequencing has ushered in a new era of excitement in experimental evolutionary biology. The ability to manipulate model organisms and sequence whole genomes to pinpoint which genes are responsible for adaptation within a given population---dubbed "evolve and resequence"---now aims to fill in the gaps.

Authors Christian Schltterer et. al., used an experimental genetic workhorse, the fruit fly Drosophila melanogaster, and subjected a population to two different environments, one hot and one cold, and asked if they could quantify the genetic response in each. Wild flies were collected and expanded to a population of 1,000, grown in the hot and cold environments for at least 15 generations, and then subjected to whole genome sequencing.

Identifying a large number of variants involved in the adaptive response (called candidates), the authors provide convincing evidence that their candidates include loci with functions specific to either the hot or cold environment. Nevertheless, they also deduced that the number of candidate loci was greatly overestimated due to a lack of independence among them that was previously unrecognized. The authors outline how this problem, which severely limits the ability to reliably fine-map such sites, could be ameliorated by modifications to the design of such studies.


Contact: Joe Caspermeyer
Molecular Biology and Evolution (Oxford University Press)

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