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June 14, 2013

Nursing Neanderthals, multisexual mutant mice, and the undead

Barium distributions in teeth reveal early-life dietary transitions in primates
"in a Middle Palaeolithic juvenile Neanderthal... exclusive breastfeeding for seven months, followed by seven months of supplementation.... [then] Ba levels in enamel returned to baseline prenatal levels, indicating an abrupt cessation of breastfeeding at 1.2 years of age"

Serotonin signaling in the brain of adult female mice is required for sexual preference
"male mutant mice lacking serotonin have lost sexual preference.... female mouse mutants lacking either central serotonergic neurons or serotonin... displayed increased female-female mounting"

Regeneration of Little Ice Age bryophytes emerging from a polar glacier with implications of totipotency in extreme environments "following 400 y of ice entombment... [bryophyte cells can ] dedifferentiate into a meristematic state (analogous to stem cells) and develop a new plant."

Quorum-sensing autoinducers resuscitate dormant Vibrio cholerae in environmental water samples
[I wonder if this would work with other "unculturable" microbes.]

March 8, 2013

Cooperation, inducible defense, cancer, and more

Here are some papers that look interesting this week.

Prairie Dogs Disperse When All Close Kin Have Disappeared "cooperation among kin is more important than competition among kin for young prairie dogs"

Variants at serotonin transporter and 2A receptor genes predict cooperative behavior differentially according to presence of punishment "Participants with a variant at the serotonin transporter gene contribute more, leading to group-level differences in cooperation, but this effect dissipates in the presence of punishment."

Plant mating system transitions drive the macroevolution of defense strategies
the repeated, unidirectional transition from ancestral self-incompatibility (obligate outcrossing) to self-compatibility (increased inbreeding) leads to the evolution of an inducible (vs. constitutive) strategy of plant resistance to herbivores."

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics "we reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later events during cancer progression"

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality"
"natural selection against optimal codons to achieve adaptive responses to environmental changes"

Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote "> 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally"

Recent land use change in the Western Corn Belt threatens grasslands and wetlands
"a recent doubling in commodity prices has created incentives for landowners to convert grassland to corn and soybean cropping... onto marginal lands characterized by high erosion risk and vulnerability to drought."

March 1, 2013

Copying in birds, dolphins, and viruses; evolution & environmental change; evolution of mutation rate

Learning and signal copying facilitate communication among bird species "where only two species regularly interact, one species' [alarm] calls incorporate the call of the other."

Vocal copying of individually distinctive signature whistles in bottlenose dolphins "Copying occurred almost exclusively between close associates such as mother-calf pairs and male alliances during separation... copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it... no evidence for the use of copying in aggression or deception."

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity "the only documented bacterial adaptive immune system is the CRISPR/Cas... a phage-encoded CRISPR/Cas system is used to counteract a phage inhibitory chromosomal island of the bacterial host. "

Evolutionary rescue from extinction is contingent on a lower rate of environmental change" "By assessing fitness of these engineered [E. coli] strains across a range of drug concentrations, we show that certain genotypes are evolutionarily inaccessible under rapid environmental change."

Fossil evidence for a hyperdiverse sclerophyll flora under a non-Mediterranean-type climate "sclerophyll hyperdiversity has developed in distinctly non-Mediterranean climates... likely a response to long-term climate stability."

A trade-off between oxidative stress resistance and DNA repair plays a role in the evolution of elevated mutation rates in bacteria "The dominant paradigm for the evolution of mutator alleles in bacterial populations is that they spread by indirect selection for linked beneficial mutations when bacteria are poorly adapted... [but] hydrogen peroxide, generates direct selection for an elevated mutation rate in the pathogenic bacterium Pseudomonas aeruginosa as a consequence of a trade-off between the fidelity of DNA repair and hydrogen peroxide resistance."


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"

September 14, 2012

This week: fossils, epidemics, cooperation, and aging

Arthropods in amber from the Triassic Period "arthropods some 100 Ma older than the earliest prior records in amber"

Unifying the spatial epidemiology and molecular evolution of emerging epidemics "spatial parameters of an emerging epidemic [can] be directly estimated from sampled pathogen genome sequences"

Evolution of cooperation and skew under imperfect information "full cooperation may not be achievable due to private information over individuals' outside options"

No third-party punishment in chimpanzees "Dominants retaliated when their own food was stolen, but they did not punish when the food of third-parties was stolen, even when the victim was related to them. "

Ageing: Mixed results for dieting monkeys
Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study "Our study suggests a separation between health effects, morbidity and mortality"

September 7, 2012

This week's picks

Stone tool production and utilization by bonobo-chimpanzees (Pan paniscus)
Just last week, we gave a kid a copy of "Monkey with a tool belt." No, this paper doesn't show that humans are descended from bonobos. DNA evidence shows that the bonobo-chimp split occurred after humans split from the common ancestor of all three.

Reproductive queue without overt conflict in the primitively eusocial wasp Ropalidia marginata "The dominance rank of an individual is not a significant predictor of its position in the succession hierarchy. "

Predatory Fish Select for Coordinated Collective Motion in Virtual Prey
"collective motion could evolve as a response to predation, without prey being able to detect and respond to predators"

Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis
"disease severity is predicted by the evolutionary dynamics of hepatitis C virus"

August 10, 2012

Fossils, convergent evolution, cooperation, and "groundwater footprints"

New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo "The new fossils confirm the presence of two contemporary species of early Homo, in addition to Homo erectus, in the early Pleistocene of eastern Africa."

A transitional snake from the Late Cretaceous period of North America "...snakes evolved from burrowing lizards. The skull is intermediate..."

Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase The same molecular change to a sodium pump, previously seen in Monarch butterflies, was found in four insect species (separated by 300 million years of evolution) feeding on plants making the same natural insecticides.

Heterogeneous networks do not promote cooperation when humans play a Prisoner's Dilemma "1,229 volunteers chosen among last year's high school students"

Water balance of global aquifers revealed by groundwater footprint" "80 per cent of aquifers have a groundwater footprint that is less than their area" but "the global groundwater footprint is currently about 3.5 times the actual area of aquifers", putting water supplies for 3.5 million people at risk. My book briefly compares the ecological footprints of conventional and organic farms.

August 3, 2012

Defense against malaria, cuckoos, mobile elements, and creationists

Fighting malaria with engineered symbiotic bacteria from vector mosquitoes
"symbiotic bacteria to deliver antimalaria effector molecules to the midgut lumen"

PLoS Biology: The Evolutionary Consequences of Blood-Stage Vaccination on the Rodent Malaria Plasmodium chabaudi
"recombinant blood stage malaria vaccines can drive the evolution of more virulent malaria parasites"

Cuckoos Combat Socially Transmitted Defenses of Reed Warbler Hosts with a Plumage Polymorphism
"social learning is specific to the cuckoo morph that neighbors mob"

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs
evolving defenses against active mobile elements

A complete insect from the Late Devonian period
400 million years ago? Like 400 million years (to three significant digits) before the Earth was created?

March 21, 2012

Cumulative culture and cooperation in humans and other primates

Two recent papers compare the problem-solving abilities of humans and other primates. Individual humans are smarter than individual chimps, of course. But our most-impressive intellectual feats depend on the accumulation of cultural knowledge over many generations. A blacksmith might make some of her own tools, but she didn't invent most of them, or smelt the iron from ore she mined herself. Computer programmers, in turn, depend on technology that built on the work of blacksmiths and many others.

I once read a story in which Earth was visited by aliens with vastly superior technology. Initially, humans assumed that the aliens must be much smarter than we are. It turned out that most of them were pretty stupid, easily duped by humans. It's just that their civilization was older, so they'd had time to invent spaceships and such, even with fewer geniuses than we have. How much of our technological superiority to nonhuman primates is due to superior individual problem-solving ability, and how much to cumulative culture?

"Identification of the Social and Cognitive Processes Underlying Human Cumulative Culture" was published in Science by L.G. Dean and others. They compared the ability of groups of 3-4 year-old human children, chimps with capuchin monkeys, in solving a "puzzle box", where retrieving the most-valued food reward depended on solving three successive levels of increasing difficulty. Only one chimp of 33 got to level 3, while many humans did. Why?

Humans copied others more than chimps or monkeys did. Chimps tended to copy the moves needed to get to the first level, but not beyond that, so it didn't help much to let them see a chimp that had been trained to reach level 3. All 23 clear cases of "teaching" (2/3 verbal and 1/3 via gestures) were by humans. Humans were more generous in other ways also: 47% shared food with others, while none of the chimps or monkeys did. Chimp mothers stole from their own offspring. In summary:

"The children responded to the apparatus as a social exercise, manipulating the box together, matching the actions of others, facilitating learning in others through verbal instruction and gesture, and engaging in repeated prosocial acts of spontaneous gifts of the rewards they themselves retrieved. In contrast, the chimpanzees and capuchins appeared to interact with the apparatus solely as a means to procure resources for themselves, in an entirely self-serving manner, largely independent of the performance of others, and exhibiting restricted learning that appeared primarily asocial in character."
Human adults may be different, however, with rich (or well-educated?) adults acting more like chimps. See last week's post.

The second paper also compares cooperation in humans and other primates. "Old World monkeys are more similar to humans than New World monkeys when playing a coordination game" was recently published by Sarah Brosnan and others in Proceedings of the Royal Society B. Pairs of humans, rhesus monkeys, and capuchin monkeys played the Assurance (or Stag Hunt) game, using computer joysticks to enter their moves. An individual choosing Hare gets a reward whatever the other player does. But if both choose Stag, they each get double the reward.

All of the human pairs talked, but only some talked about the game. Of those that did, all 22 pairs ended up playing mostly cooperatively -- but not 100%, even after seeing the potential benefit. Those who talked about other topics played mostly noncooperatively, forgoing the benefits of cooperation.

The two monkey species differed. For both species, if individuals could see the other's move, they learned to "cooperate" and got high rewards. (They could see each other, but did they realize they were playing with each other, rather than with the computer?) The capuchins played more randomly when they didn't know the other's move, whereas two pairs of rhesus monkeys quickly learned to trust their partner and cooperate (or, anyway, to play as if they did). Rhesus monkeys are native to Africa, rhesus monkeys to South America. So, as the authors put it:

"Old World primates outperformed New World primates,
rather than humans outperforming non-humans."
They speculate that, perhaps:
"...humans' abilities are built on a shared foundation that extends back at least as far as the split with Old World monkeys [which was longer ago than the split between apes and old-world monkeys, let alone the split between humans and other apes]."
An interesting hypothesis, but I would like to see data for more species.

October 28, 2011

Copy-protection strategies in birds

Brood parasites lay their eggs in the nests of other birds, typically of a different species. Why don't those birds recognize the foreign eggs and kick them out of the nest? The parasitic species have often evolved so that their eggs look much like those of their hosts. Can the host species evolve to recognize the intruders? This week's paper discusses two different evolutionary responses.

"How to evade a coevolving brood parasite: egg discrimination versus egg variability as host defences" was published by Claire Spottiswoode and Martin Stevens under Proceedings of the Royal Society's open-access option, so you can read the details for yourself here.

They compared three species of bird parasitized by different species of African finch. Individuals of one host species varied enormously in the appearance of their eggs, as shown below. The parasitic finches apparently don't match their eggs to the particular host individual, so their eggs would often be a poor match. But this host isn't as good at recognizing slightly different eggs, relative to a host that produces less-variable eggs. This difference between species is consistent with the hypothesis that the species with less-variable eggs was under stronger selection for ability to recognize subtle differences.
eggs.jpg
A statistician might point out that, however many birds they sampled of each species, any conclusions about correlations between species-level traits (egg variability among individuals and detection of visual differences) would need to be based on a larger number of species. But until someone comes up with a counter-example, I'll assume their conclusions are probably right, although not proven.

Speaking of correlations, the most-downloaded paper from that journal also deals with parasitism and intelligence. The authors of "Parasite prevalence and the worldwide distribution of cognitive ability" found that average IQ is lowest in countries with highest frequency of infectious disease. They argue that the metabolic cost of fighting disease leaves less energy for developing brains. Even if disease does affect brain development, I wonder whether energy is the key factor. They also suggest that increases in average IQ over decades may be due to reduced disease. Again, it seems like these two variables could interact in a variety of ways, especially if we are talking about national averages. Disease affects economies which affect prenatal care, nutrition, education, etc.?

August 12, 2011

This week's picks

Reciprocal Rewards Stabilize Cooperation in the Mycorrhizal Symbiosis Toby Kiers, who previously demonstrated host sanctions against cheating rhizobia, now shows that plants give less carbon to less-beneficial mycorrhizal fungi. I hope I can find time to discuss this paper in more detail soon.

Natural variation in Pristionchus pacificus dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones "strains may have evolved to induce dauer formation precociously in other strains in order to reduce the fitness of these strains"

Nest Inheritance Is the Missing Source of Direct Fitness in a Primitively Eusocial Insect

Polyandrous females benefit by producing sons that achieve high reproductive success in a competitive environment

Kin selection in den sharing develops under limited availability of tree hollows for a forest marsupial

Aging of the cerebral cortex differs between humans and chimpanzees "significant aging effects in humans were... individuals that were older than the maximum longevity of chimpanzees. Thus... brain structure shrinkage in human aging is evolutionarily novel and the result of an extended lifespan"

Bacterial persistence by RNA endonucleases

Host-parasite local adaptation after experimental coevolution of Caenorhabditis elegans and its microparasite Bacillus thuringiensis

Sperm chemotaxis, fluid shear, and the evolution of sexual reproduction

August 1, 2011

Are we doomed?

New Statesman asked a bunch of scientists this question. Bjørn Østman blogged that:

"it is likely that the human population will be decimated some time in the future, perhaps even as soon as within the next hundred years. A cataclysmic event caused by global climate change, perhaps? If anyone survives at all, I predict it will be in a number of smaller populations separated from each other geographically.... Assuming that the environmental changes caused by the global cataclysmic event are severe enough that the separated populations won't be able to interact (i.e., have sex) for long enough, the different populations will continue to diverge from each other, and speciation will eventually occur. 6-7, say, million years hence..."
I can't tell if this is supposed to be a joke, but I can't imagine humans surviving, yet staying isolated that long. And I can't imagine climate-change-related catastrophe reducing world population below a billion or so. To eliminate all but a few isolated populations would take a major extraterrestrial impact, global nuclear war, or maybe some disease.

I don't think humans are likely to go extinct within the next few thousand years. But is civilization doomed?

Can we define civilization as a continuum? At the high end:
* there is some form of collective decision-making that respects factual information and serves everyone's long-term interests, to the extent possible,
* literacy is nearly universal, as is access to accurate scientific and historical information, and to differing opinions on politics, religion, etc.
* original research to increase scientific understanding and improve technology is encouraged
* criticizing the government or the dominant culture is not a crime
* those accused of crime are entitled to some form of due process based on public examination of the evidence

At the low end:
* good and services are exchanged mostly through voluntary trade, at least within groups, but groups war among themselves and individuals can be executed for "witchcraft", "blasphemy", or "sedition."

The question is, if some natural or man-made disaster (a major epidemic, say, or failure of moderates to vote) reduces civilization to a given level, somewhere between these extremes, which direction will it tend to change, over the next thousand years or so? Will within-group processes tend to increase or decrease civilization? Some current trends in the US are not encouraging.

What about between-group processes? Will countries that respect science and other secular values be strong enough (economically? militarily?) to impose their values on countries that rely on "God, guns and guts", or will it be the other way around?

April 8, 2011

This week's picks

Workers influence royal reproduction
"worker aggressive and non-aggressive behaviour towards queens predicted which queen monopolized reproduction. In contrast, among-queen interactions were rare and did not predict queen reproduction. Furthermore, parentage analysis showed workers favoured their mother when present"
[Maybe "inclusive fitness" is useful after all!]

Updated chronology for the Miocene hominoid radiation in Western Eurasia
"Eurasian pongines [orangutans and extinct relatives] and African hominines [humans, chimps, bonobos, and extinct relatives] might have independently evolved in their respective continents from similar kenyapithecin ancestors [apes living 14 million years ago], resulting from an early Middle Miocene [5-23 MYA] intercontinental range extension followed by vicariance [geographic separation, reducing or eliminating interbreeding so allowing evolutionary divergence]. "

Ribozyme-Catalyzed Transcription of an Active Ribozyme "we recombined traits evolved separately in different ribozyme [catalytic enzyme made of RNA rather than protein] lineages. This yielded a more general polymerase ribozyme that was able to synthesize a wider spectrum of RNA sequences, as we demonstrate by the accurate synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme. "

An evolutionary process that assembles phenotypes through space rather than through time "assortative mating between fast-dispersing individuals at the invasion front results in an evolutionary increase in dispersal rates in successive generations"

Fork-tailed drongos use deceptive mimicked alarm calls to steal food
"false alarm calls when watching target species handling food, in response to which targets flee to cover abandoning their food"

Moving calls: a vocal mechanism underlying quorum decisions in cohesive groups
"a sharp increase in the probability of changing foraging patch when the number of group members joining the chorus increased from two up to three"

Differences in the temporal dynamics of phenotypic selection among fitness components in the wild "The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival."

Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias "Rickettsia sp. nr. bellii swept into a population of an invasive agricultural pest, the sweet potato whitefly, Bemisia tabaci, in just 6 years. Compared with uninfected whiteflies, Rickettsia-infected whiteflies produced more offspring, had higher survival to adulthood, developed faster, and produced a higher proportion of daughters. The symbiont thus functions as both mutualist and reproductive manipulator. "

The evolutionary biology of child health "cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes"

Tradeoffs associated with constitutive and induced plant resistance against herbivory "Across all 58 plant species, we demonstrate a tradeoff between constitutive and induced resistance, which was robust to accounting for phylogenetic history of the species. Moreover, the tradeoff was driven by wild species and was not evident for cultivated species."

Towards a quantitative understanding of the late Neoproterozoic carbon cycle
"all of the main features of the carbonate and organic carbon isotope record can be explained by the release of methane hydrates from an anoxic dissolved organic carbon-rich ocean into an atmosphere containing oxygen levels considerably less than today"

March 31, 2011

This week's picks

Chimpanzees help conspecifics obtain food and non-food items "...given that the donor cannot get the food herself.... the key factor... is the recipients' attempts to either get the food or get the attention of the potential donor."

On the earliest evidence for habitual use of fire in Europe
"...spectacular cases of Neandertal pyrotechnological knowledge..."

Sizing up your enemy: individual predation vulnerability predicts migratory probability
"trade-off between seasonal fluctuations in predation risk and growth potential... Smaller, high-risk individuals migrate with a higher probability"

Plant-ants feed their host plant, but above all a fungal symbiont to recycle nitrogen
"In many ant-plant symbioses, a fungal patch grows within each domatium."

More closely related species are more ecologically similar in an experimental test
"Species also competed more with close relatives than with distant relatives in field soils; however, in potting soil this pattern reversed..."

Assassin bug uses aggressive mimicry to lure spider prey "vibrations from bugs had a temporal structure and amplitude... similar to vibrations generated by leg and body movements of prey and distinctly different... from courting males or leaves..."

Social and Ecological Synergy: Local Rulemaking, Forest Livelihoods, and Biodiversity Conservation "participation in forest governance institutions by local forest users is strongly associated with jointly positive outcomes"

Oxygen isotopes of East Asian dinosaurs reveal exceptionally cold Early Cretaceous climates "cold local climatic conditions linked to the paleolatitudinal position of northeastern China and global icehouse climates..."

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia
"we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations."

March 25, 2011

The beaks of the finches

This week's paper is "Divergence with gene flow as facilitated by ecological differences: within-island variation in Darwin's finches", published in Philosophical Transactions of the Royal Society.

"If humans evolved from chimps", ask the creationists, "why are there still chimps?" Good question! Humans didn't evolve from modern chimps, any more than I am descended from my cousins. We just share ancestors.

But still... why are there now chimps and humans, rather than one species? More generally, how does one species split in two? If part of a species becomes isolated enough to be inaccessible for mating, or at least "geographically undesirable," then the two populations can diverge through natural selection or random genetic drift, eventually losing the ability to reproduce with each other.

But genetic divergence doesn't always require geographical isolation. For example, if birds with medium-size beaks get less food than those with large or small beaks (on an island with many large and small seeds but few medium seeds), will the resulting "disruptive selection" tend to split the population into two subpopulations, with genes for small and large beaks? Maybe, but not if small- and large-beaked birds interbreed, combining genes for large and small beaks. And why wouldn't they?

Continue reading "The beaks of the finches" »

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"

November 12, 2010

So many papers, so little time

Here are the papers I'm considering this week. Any requests? Otherwise, I'll probably discuss one of my own recent papers, on the implications of evolutionary tradeoffs for agriculture and human health.
Why genes overlap in viruses

Identification of an ant queen pheromone regulating worker sterility

DDS, 4,4′-diaminodiphenylsulfone, extends organismic lifespan

Evolutionary history of partible paternity in lowland South America

The evolution of cultural adaptations: Fijian food taboos protect against dangerous marine toxins

Conditional Cooperation and Costly Monitoring Explain Success in Forest Commons Management

Periodic climate cooling enhanced natural disasters and wars in China during AD 10-1900

A climate for contemporary evolution

The evolution of menopause in cetaceans and humans: the role of demography

Prosocial behaviour emerges independent of reciprocity in cottontop tamarins

Fossilized glycolipids reveal past oceanic N2 fixation by heterocystous cyanobacteria

November 3, 2010

Is it really bet-hedging?

Before the ink is even dry on our Current Biology paper on bet-hedging in rhizobia (actually, before it's even printed), Xue-Xian Zhang and Paul B Rainey have critiqued it in Genome Biology. They summarize Will Ratcliff's results, then ask "whether it is an evolutionary response to fluctuating selection shaped by natural selection." Experimental evolution, an approach Rainey and colleagues have used successfully, would be a good way to answer this question.

But is it really even bet-hedging? To qualify as bet-hedging, you need to sacrifice arithmetic-average fitness to gain greater geometric-average fitness. That would obviously depend on the environment, but it seems reasonable to assume that having half your progeny go dormant would sacrifice fitness when food is abundant, while increasing the chances of having at least one surviving progeny under starvation.

Zhang and Rainey seem to think there's an additional requirement to qualify as bet-hedging, namely, "switching rates to suit prevailing conditions." I disagree. Isn't a 50:50 mix of stocks and bonds (rather than 100% stocks, which have higher average return but are riskier) considered bet-hedging, even if you never change that ratio? But I do agree that it's important to know whether the ratio of dormant to growing cells changes in response to conditions, which I would call phenotypic plasticity. We are working on that.

August 24, 2010

Another way to alarm aphids

A new paper in Current Biology shows that aphids drop off their host plant when breathed on by an animal that's about to eat the plant: Mammalian herbivore breath alerts aphids to flee host plant.

Last week I discussed a paper about transgenic plants that make aphid alarm signals, scaring them away (at least for a generation or two). This latest paper suggests a related approach. Getting crops to release hot, humid "breath" might be hard, but could we make a machine to blast crops with artificial breath, maybe in greenhouses?

August 19, 2010

Evolution-proof pest-resistant crops?

This week's paper is "Alarm pheromone habituation in Myzus persicae has fitness consequences and causes extensive gene expression changes", published in PNAS by Martin de Vos and others.

Aphids suck. This wouldn't be too big a problem for their host plants, except that they sometimes transmit viruses. Some plants repel these pests by giving off gases very similar to the chemical alarm signals aphids release when attacked by predators. Could crops be genetically engineered to do this? Probably, but would it work, or would the aphids evolve to ignore these signals and keep on sucking?

To answer this question, the authors studied aphids on plants genetically engineered to make aphid alarm signal.

Continue reading "Evolution-proof pest-resistant crops?" »

June 25, 2010

Are scientists smarter than squirrels?

"Monkey-watchers often use the word "aunt" for an adopting female." -- Richard Dawkins, The Selfish Gene
The willingness of animals to adopt and care for orphans has been shaped by past natural selection. Often, Dawkins suggested, adoption represents "misfiring of a built-in rule... a mistake that happens too seldom for natural selection to have 'bothered' to change the rule by making the maternal instinct more selective." This seems a reasonable explanation for the failure of bird parents to kick "brood parasites" out of their nests, a situation I discussed recently.

But this week's paper, by Jamieson Gorrell and colleagues, seems to show that squirrels have a more-sophisticated understanding of selfish-gene theory than I would have expected. "Adopting kin enhances inclusive fitness in asocial red squirrels" was recently published in the new online journal Nature Communications. The authors analyzed five cases of orphaned squirrels being adopted, all by close relatives, and two cases where they were left to die, even though a relative had a territory nearby. In each case, they asked whether adopting would likely increase or decrease the frequency of the adopter's genes in future generations.

Closely related individuals tend to share gene variants (alleles) even if those alleles are rare in the overall population, so adopting a younger sister or a nephew who would otherwise die could increase one's genetic representation in future generations. On the other hand, adding an orphan to one's litter puts one's own offspring at somewhat greater risk. The authors were able to estimate this risk and compare it to the increased survival chances of the adoptee, weighted by its relatedness to the foster mother. If this benefit exceeds the risk, then Hamilton's rule (the fundamental equation of social evolution) predicts adoption. All of the adoptions that did occur met this criterion -- two cases were right on the line -- whereas the two potential adoptions that didn't occur failed the Hamilton's-rule test. Yet another example of squirrels solving challenging problems.

At least, that's what the data seemed to show. But the "relatedness" term in Hamilton's rule isn't necessarily equal to the relatedness we could calculate from a family tree or from genetic similarity. It would be, if helping an orphan had no negative effect on anyone outside one's current litter. But if there are more red squirrels than red-squirrel territories, then a surviving orphan may end up displacing another squirrel. So the question is, how closely related is that displaced squirrel likely to be to the adoptive mother? In the cases studied, 1/4 to 1/2 of the lactating females nearby were kin to the adopting mother. If that's a representative sample, then a surviving orphan might often end up displacing another squirrel that was as closely related to the mother as the orphan was. In such cases, the mother would have exposed her own litter to increased risk, without doing much to increase her genetic representation in future generations. Even so, the adoptive mothers aren't acting as maladaptively as Dawkins suggested (as if they adopted orphans at random), but their behavior wouldn't be optimal (by Hamilton's rule) unless there were unoccupied territories available nearby. Thanks to Dr. Carin Bondar, whose blog alerted me to this interesting paper.

Meanwhile, over at Science, Jeff Smith and colleagues propose "A generalization of Hamilton's rule for the evolution of microbial cooperation." When one cooperative act (releasing an expensive enzyme, say) benefits all microbes nearby, it's common to assume we can add up all the costs and benefits over a population. But what if twice the enzyme gives three times the benefit? The authors developed some high-powered math to deal with such problems and concluded that certain kinds of cheaters would have a harder time getting established than we would have expected from the simpler version of Hamilton's rule. Scientists are definitely smarter than squirrels, but they can't jump as well.

May 28, 2010

Sexual imprinting in redheads

We may disagree on who's most attractive, but most of us prefer to mate with a member of our own species. But that can be tricky for redheads. Redhead mothers often lay their eggs -- I'm talking about ducks, of course -- in canvasback nests, saving themselves the trouble of raising the chicks. But what if chicks raised by canvasbacks end up thinking of themselves as canvasbacks? Or, however, they may think of themselves, what if their earlier experience makes them prefer canvasbacks as mates? They might end up mating with the wrong species.

This apparently doesn't happen very often in nature, but why not? One possibility is that redheads are genetically programmed to prefer redheads, even if they grow up with canvasbacks. After all, brush turkeys grow up to prefer mating with brush turkeys (below), even though they're incubated in compost piles managed mostly by males. Michael Sorenson, Mark Hauber, and Scott Derrickson, the authors of this week's paper, "Sexual imprinting misguides species recognition in a facultative interspecific brood parasite", published in Proceedings of the Royal Society, set out to test this hypothesis for redheads.
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Brush turkey and brush turkey mound in Australia. Photo by Ford Denison.

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July 24, 2009

Microbes evolve; flies evolve and learn

"Can plants predict the future?" asked one of my Crop Ecology lectures at UC Davis. Yes, they can. Plants use decreasing daylength to predict oncoming winter, and flower early enough to finish seed development before it gets too cold. Some plants detect early signs of drying soil and reduce their own water use, saving water in the soil for later.(Davies & Zhang. 1991, Bano, et al. 1993) Others detect "distress signals" from neighbors under insect attack, turning on chemical defenses in anticipation (Karban, et al. 2004).

But these anticipatory responses do not require learning: a beneficial change in individual behavior in response to individual experience. An alfalfa plant will never learn that the farmer always irrigates before it actually runs out of water. At least, I assume it won't. An evolving alfalfa population is a different story. Over a few generations under irrigation, genotypes that reduce their water use as the soil starts to dry (thereby reducing their growth) will be out-competed by genotypes that keep using water and growing.

Like plants, microbes can predict the future. As in plants, this trait can evolve. As they pass through the gut, bacteria typically see lactose before they see maltose. So they have evolved to "anticipate" maltose availability, turning genes for maltose use on as soon as they are exposed to lactose. After 500 generations of evolution on lactose without maltose, however, the bacteria have lost lose this anticipatory response, so that they turn maltose genes on only when they actually see maltose.(Mitchell, et al. 2009) The title of the news story in Nature about this work asked whether microbes can "learn from history", but this is clearly not an example of individual cells modifying their responses to lactose based on their individual experience.

Individual insects can learn. But is learning always a good thing? Aimee Dunlap, a grad student in my department working with David Stephens, just published a paper in Proceedings of the Royal Society exploring the conditions under which natural selection will favor learning (Dunlap & Stephens. 2009).
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May 31, 2008

Traditional values in bees

The beehive was an early Mormon icon, symbolizing hard work and cooperation. To an evolutionary biologist, however, a beehive could symbolize reproductive skew, a situation where some individuals reproduce much more than others. Extreme reproductive skew is one of the defining characteristics of eusocial species, of which honey bees are a prime example. Reproductive skew can differ between the sexes. In honey bees, the queen lays most of the eggs, and most females don't reproduce at all. Polygamous species and groups show the opposite pattern: males vary much more in reproductive success than females do. Maybe an inverted beehive would have been a better symbol. Note that the cells in our bodies behave somewhat like a eusocial bee colony; any children we have are directly descended from a few sex cells, while brain cells and skin cells play the supporting role of worker bees.

This week's paper, "Ancestral monogamy shows kin selection is key to the evolution of eusociality" was published in Science by William Hughes and others. Like humans, some bees are monogamous, meaning that the queen mates with only one male, so her daughters (the workers) are all sisters. In other bee species, the queen mates with several males, so her daughters are half-sisters. Relatedness generally favors cooperation, although there are some possible complications, discussed below.

This week's paper asks how mating behavior affects the evolution of eusociality. They reasoned that, if mating system doesn't matter, then today's eusocial species could be descended from either monogamous, polygamous, polyandrous (each female has multiple mates), or promiscuous ancestors. Alternatively, eusociality may evolve more easily with one of these mating systems than with the others.

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