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February 24, 2011

This week's picks

Responses to the Assurance game in monkeys, apes, and humans using equivalent procedures "...only a subset of humans achieved these efficient outcomes, and pairs of both other species did so as well"

The origin and dynamic evolution of chemical information transfer
"chemicals are emitted, which can unintentionally provide information (cues) and... act as direct precursors for the evolution of intentional communication (signals)."
"In most cases, the excrements are cues, but the behavioural modulations... constitute signals helping to draw receivers' attention to the cues "
"males prefer flower bouquets to the sexual pheromone of local females, presumably because [the orchid] exploits pre-existing sensory biases of their pollinators"

Classic Selective Sweeps Were Rare in Recent Human Evolution
"amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations"

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
"the Thaumarchaea (including Nitrosopumilis maritimus in our analysis) forms an independent group distinct from the Crenarchaea or Euryarchaea"

Footprints pull origin and diversification of dinosaur stem lineage deep into Early Triassic "...a few million years after the Permian/Triassic mass extinction (252.3 Ma)"

Optimal antiviral treatment strategies and the effects of resistance
"contrary to previous results, it is always optimal to treat at the maximum rate provided that this treatment occurs at the right time. "

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions
"transparent Daphnia hosts and fluorescently-labelled spores of the bacterium"

February 18, 2011

Free downloads of applied evolution papers...

...from the Applied Evolution Summit (Heron Island, 2010) are available, temporarily, from Evolutionary Applications.

I've already discussed part of my paper, "Past evolutionary tradeoffs represent opportunities for crop genetic improvement and increased human lifespan".

I also made minor contributions to two overview papers:
Evolutionary principles and their practical application
and Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems.

Check out these and other exciting papers and download the ones you want, before they go behind a pay-wall. Some of these would be great for participatory seminars.
turtle.JPG

February 16, 2011

Sleep as a survival strategy

This week's paper, Bacterial persistence and bet hedging in Sinorhizobium meliloti, was just published in Communicative and Integrative Biology. It's a brief but important follow-up to a paper in Current Biology, which I've already discussed.

Bacterial persisters are a serious medical problem. An infection that appears to have been cured by antibiotics sometimes "springs back to life." Evolutionary biologists have focused on cases where the renewed infection is caused by an antibiotic-resistant mutant, a classic example of evolution by human-imposed selection. Sometimes, however, the resurgent bacteria are still susceptible to the original antibiotic, yet bounce back after one or more treatments. What gives?

Many antibiotics only kill bacteria that are actively growing. So, if a few cells go dormant, these persisters may survive until the antibiotic breaks down, even if they aren't otherwise resistant.

Will Ratcliff recently reported that Sinorhizobium meliloti bacteria, best known as the nitrogen-fixing, root-nodule symbiont of alfalfa, can also make dormant cells. When S. meliloti cells divide, under starvation conditions, the elder daughter inherits most of the accumulated wealth (energy-rich polyhydroxybutyrate or PHB) and the younger daughter goes off to seek her fortune. You can see this unequal allocation of PHB in the Nile-red-stained image of a dividing cell, below right.PHB.jpg
This apparent bet-hedging strategy is much more organized and more common than the random, one-in-a-thousand process that seems typical of human pathogens. A rhizobial population that starts with the usual normal distribution of PHB (above left) divides, initially, into one with roughly equal numbers of persisters and growers (above center).

Our original paper showed that about 70% of the high-PHB S. meliloti persisters are still alive after 528 days without food. So the well-known ability of rhizobia to survive in soil for months or years between legume hosts may not depend on their ability to out-compete other soil bacteria for limited food supplies.

But how relevant is this work with rhizobia, which benefit their legume hosts by providing them with nitrogen, to the antibiotic-resistant bacterial persisters that cause disease? In this new paper, Will Ratcliff showed that...

AntibioticPersisters.jpg
...the rhizobial persisters are resistant to the antibiotic, ampicillin. He generated mixtures of high-PHB persisters and low-PHB growers in two different ways, either by growing them differently or using centrifugation to separate high- and low-PHB cells (all of the same genotype). Either way, ampicillin killed more cells in mixtures that were mostly low-PHB growers than in mixtures that were mostly high-PHB persisters, as shown above.

Will also followed up on the apparently lower protein synthesis in the persisters, as seen in the earlier figure as less green-fluorescent protein (GFP) fluorescence in the high-PHB persister daughter cell. He showed that the eldest daughter ("old-pole") cells had consistently less GFP fluorescence, consistent with the lower protein synthesis expected in dormant or semidormant cells.

We are continuing work on this system, exploring the conditions under which persisters may, by consuming fewer resources, free resources for their clonemates nearby. S. meliloti is directly important as the main nitrogen source for alfalfa, which occupies more land than most other crops. But we also hope that insights from this work may lead to more-effective control of infections caused by other bacterial persisters.

This work is being supported by National Science Foundation grant NSF/DEB-0918897.

February 10, 2011

Evolution of cooperation, disease, relatives, birds...

Some recent papers that look interesting:

The evolution of host protection by vertically transmitted parasites

Cooperation among non-relatives evolves by state-dependent generalized reciprocity

Before senescence: the evolutionary demography of ontogenesis

Costs of memory: lessons from 'mini' brains

Land inheritance establishes sibling competition for marriage and reproduction in rural Ethiopia

Major global radiation of corvoid birds originated in the proto-Papuan archipelago

Within and transgenerational immune priming in an insect to a DNA virus

Multiple strategies in structured populations

Long-term isolation of a highly mobile seabird on the Galapagos

February 4, 2011

This week's picks

Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness

Modularity of gene-regulatory networks revealed in sea-star development

Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants
The microbial chemicals fungus-growing ants use to control pests can also kill their crop. I'm not surprised.

Not just another genome
Daphnia may be a valuable model system for studying ecology and evolution

Directed Evolution of a Protein Container
Evolution trumps design again.

Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae

H-index and Erdos number

There must be some mistake here. Professor Smith, of PhD comics has out-performed me by a factor of 3 (papers in Science or Nature) to 17 (PhDs graduated), by every criterion except the H-index of citation impact, where I hold a slight lead, 23 to 19. In other words, 23 of my papers have been cited 23 or more times, so far. And my lead seems to be increasing.
cites.jpg

I don't think my H-index is unusually high, so maybe Smith's is unusually low. Perhaps, if he treated his students better, they'd write better papers together?

Also, where's his Erdos number, the degrees-of-separation formula that inspired this XKCD cartoon? Mine is 5, via T.R. Sinclair, R.H. Rand, H.D. Block, and P.C. Rosenbloom. The first two links are via papers in nonmathematical journals, though. I'd be more interested in my W.D. Hamilton number, anyway. Incidentally, Hamilton's H-index is only 15, so maybe it's not such a reliable measure of scientific impact after all. Other approaches to citation analysis have been developed, including "eigenfactors."

February 1, 2011

Want more evolution articles?

This months Carnival of Evolution is up at Denim and Tweed.