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January 29, 2013

A citation a day keeps ideas in play

I'm always amazed how badly out-of-date many of my colleagues' publication lists are. Spend a few minutes setting up a Google Scholar page, and you'll always be up-to-date with publications and citations. Here's mine.

My first evolution-themed paper, proposing host sanctions as an explanation for the evolutionary persistence of legume-rhizobia cooperation, was published in 2000.

January 25, 2013

What's for dinner?

This week's picks all have something to do with food.

Tree climbing and human evolution "aspects of the hominin ankle associated with bipedalism remain compatible with vertical climbing [to collect fruit or honey]"

Earliest evidence for cheese making in the sixth millennium bc in northern Europe" "compelling evidence for the vessels having being used to separate fat-rich milk curds from the lactose-containing whey... in the manufacture of reduced-lactose milk products among lactose-intolerant prehistoric farming communities"

Anatomical enablers and the evolution of C4 photosynthesis in grasses
"when environmental changes promoted C4 evolution, suitable anatomy was present only in members of the PACMAD clade [which doesn't include rice] explaining the clustering of C4 origins in this lineage"

Macropredatory ichthyosaur from the Middle Triassic and the origin of modern trophic networks "recovery from Earth's most severe extinction event at the Permian-Triassic boundary... may have occurred faster [in oceans than on land]"

Sustainable bioenergy production from marginal lands in the US Midwest" "successional herbaceous vegetation, once well established, has a direct GHG emissions mitigation capacity that rivals that of purpose-grown crops "

Extracellular transmission of a DNA mycovirus and its use as a natural fungicide
"Our findings may prompt a reconsideration of the generalization that mycoviruses lack an extracellular phase in their life cycles and stimulate the search for other DNA mycoviruses with potential use as natural fungicides. "

January 18, 2013

Modular mice, experimental evolution, Bayesian enzymes, environmental extinction

Here are some papers that look interesting this week:

Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice
"In burrows built by first-generation backcross mice, entrance-tunnel length and the presence of an escape tunnel can be uncoupled... a classic 'extended phenotype' can evolve through multiple genetic changes each affecting distinct behaviour modules"

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections
"We developed a biofilm model enabling long-term selection for daily adherence to and dispersal from a plastic bead in a test tube... experimental evolution may illuminate the ecology and selective dynamics of chronic infections and improve treatment strategies."

Navigating the protein fitness landscape with Gaussian processes
"sequence design algorithms motivated by Bayesian decision theory.... allowed us to engineer active P450 enzymes that are more thermostable than any previously made"

Evolution: A history of give and take
"deep-sea sediment cores show that environmental change correlates closely with extinction but not with speciation"

January 11, 2013

Predictability, multiple fitness peaks, fungus-growing ants, pesticide resistance...

Predictability of evolution depends nonmonotonically on population size
"evolutionary predictability based on an experimentally measured eight-locus fitness landscape for the filamentous fungus Aspergillus niger.... entropies display an initial decrease and a subsequent increase with population size N"

Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild "We measured the adaptive landscape in a nascent adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas, and found multiple coexisting high-fitness regions driven by increased competition at high densities"

Laccase detoxification mediates the nutritional alliance between leaf-cutting ants and fungus-garden symbionts "laccase activity is highest where new leaf material enters the fungus garden [in ant feces], but where fungal mycelium is too sparse"

A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae "selection for the ability to mount a broad response to the diverse defense chemistry of plants predisposes the evolution of pesticide resistance in generalists"

See my Darwinian Agriculture Blog for links to videos of two of my talks.

January 4, 2013

This week's picks

Prosocial preferences do not explain human cooperation in public-goods games "an increased awareness of how cooperation benefits others leads to a reduction, rather than an increase, in the level of cooperation"

Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production "male sterility under short-day conditions and male fertility under long-day conditions"

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load "an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates"

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV) "Bayesian birth-death skyline plot, which explicitly estimates the rate of transmission, recovery, and sampling and thus allows inference of the effective reproductive number directly from genetic data."

Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution "decapitated animals display a clear photoavoidance response"

Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria "microbial chemosynthesis is also surprisingly pervasive throughout the dark oceans, serving as a significant CO2 sink even at sites far removed from vents"

Chytrid fungus Batrachochytrium dendrobatidis has nonamphibian hosts and releases chemicals that cause pathology in the absence of infection "B. dendrobatidis prevalence in crayfish was up to 29%, and that crayfish presence in Colorado wetlands was a positive predictor of B. dendrobatidis infections in cooccurring amphibians"