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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.]

May 31, 2013

This week's picks

Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size "areas deprived of large avian frugivores for several decades present smaller seeds than nondefaunated forests, with negative consequences for palm regeneration"

Molecular evolution of peptidergic signaling systems in bilaterians "phylogenetic reconstruction tools... show that a large fraction of human PSs [peptide-based signaling systems] were already present in the last common ancestor of flies, mollusks, urchins, and mammals"

Honey constituents up-regulate detoxification and immunity genes in the western honey bee Apis mellifera "apicultural use of honey substitutes, including high-fructose corn syrup, may thus compromise the ability of honey bees to cope with pesticides and pathogens and contribute to colony losses"

Palaeontological evidence for an Oligocene divergence between Old World monkeys and apes" "the oldest known fossil 'ape', represented by a partial mandible... the oldest stem member of the Old World monkey clade, represented by a lower third molar... recovered from a precisely dated 25.2-Myr-old stratum in... the East African Rift in Tanzania."

Experimental evidence that evolutionarily diverse assemblages result in higher productivity "Species produced more biomass than predicted from their monocultures when they were in plots with distantly related species and produced the amount of biomass predicted from monoculture when sown with close relatives."

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 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"

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.

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

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 11, 2011

Aging primates, agricultural ants, efficent cooperation, etc.

Lots of interesting papers this week, but I only have time for some brief comments.

I can't believe Obama's response to the earthquake in Japan was to go ahead with a speech on gasoline prices. (BBC cut him off!) Higher prices for nonrenewable resources are an efficient way (relative to rationing, say, or complicated mandates) to encourage us to use them more slowly, so they'll last longer. And although adding more carbon dioxide to the atmosphere may increase photosynthetic efficiency and make our winters here in Minnesota a little less cold, I'm not willing to bet that those benefits will outweigh risks such as rising sea level from melting glaciers. If civilization must be at war with nature, I'm on the side of civilization, but let's not shoot ourselves in the foot. For example, we can stay warm inside insulated houses, while agricultural pests perish in the cold, reducing the need for pesticides later. Cold winters are good! Hmmm... maybe I should turn comments back on; but I'm still deleting all commercial links.

Aging in the Natural World: Comparative Data Reveal Similar Mortality Patterns Across Primates "in neither females nor males did we find evidence of a negative correlation between IMR [initiral mortality risk, at onset of adulthood] and RoA [rate of aging, increase in mortality with age],which would be indicative of a trade-off..."
[I wouldn't have expected a trade-off between those parameters, but what about a tradeoff with reproduction (mentioned only in the definition of adulthood)?]

How within-group behavioural variation and task efficiency enhance fitness in a social group "females of both phenotypes [aggressive versus docile] experience increased fitness when occupying colonies containing unlike individuals"

Experimental peripheral administration of oxytocin elevates a suite of cooperative behaviours in a wild social mammal

Co-Residence Patterns in Hunter-Gatherer Societies Show Unique Human Social Structure

The influence of maternal effects on indirect benefits associated with polyandry

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

Evolution of cold-tolerant fungal symbionts permits winter fungiculture by leafcutter ants at the northern frontier of a tropical ant-fungus symbiosis

Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog

Global CO2 rise leads to reduced maximum stomatal conductance in Florida vegetation

March 4, 2011

Sex, sexiness, viruses, nematodes, and horses

Haploinsufficiency and the sex chromosomes from yeasts to humans
"orthologues of S. cerevisiae HI genes (those for which a reduction in copy number in a diploid from two to one results in significantly reduced fitness) are significantly under-represented on the X chromosomes of mammals... accumulation of HI genes on the sex chromosomes would compromise fitness in both sexes, given X chromosome inactivation in females"

Natural selection stops the evolution of male attractiveness
"lack of genetic variation that would allow an increase in sexual fitness while simultaneously maintaining nonsexual fitness"

A Virophage at the Origin of Large DNA Transposons

Computational and phylogenetic validation of nematode horizontal gene transfer

Dietary Change and Evolution of Horses in North America

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 15, 2010

Evolution of DNA methylation in animals, plants, and fungi

This week, I will try to explain what DNA methylation is and some of the reasons why it's important, before discussing this week's paper on how DNA methylation has evolved.

The paper is "Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation", published in Science by Assaf Zemach and others from the lab of Daniel Zilberman.

DNA methylation usually refers to the attachment of a methyl (CH3) group to a cytosine, one of four DNA bases (C, in DNA's A,T,C,G alphabet). Here's a link showing one way cytidine can get methylated. And this Wikipedia article shows cytosine in place in double-stranded RNA. (DNA would be similar, but with T instead of U.)

The functions of DNA methylation mostly come from the reduced transcription of RNA from methylated stretches of DNA. Surprisingly, when a new DNA copy is made (e.g., when one of our cells divide), methylation patterns are generally copied, too. Together, these two facts explain many of DNA methylation's functions.

First, DNA methylation is key to imprinting, whereby genes inherited from one parent are often shut down, perhaps for life, by methylation. Imprinting often reflects an unconscious battle between male and female parents over whether to maximize growth of this particular offspring, whatever the consequences for the mother's future survival and reproduction, or take or more long-term view. Earlier, I discussed the possible role of imprinting in mental illness.

Continue reading "Evolution of DNA methylation in animals, plants, and fungi" »

March 5, 2010

Evolution via less-fit intermediates

A central hypothesis in my forthcoming book, "Darwinian agriculture: where does Nature's wisdom lie?" is that past natural selection is unlikely to have missed simple, tradeoff-free improvements. This implies (as discussed in a recent post on drought-tolerant wheat) that tradeoff-blind biotechnology is less likely to succeed, relative to crop-improvement methods that consider tradeoffs, as long as biotechnology is limited to simple changes, like increasing the expression of an existing gene.

More complex improvements (those whose evolution would require a series of steps) are another story, however. Just because some hypothetical horse would kick ass, if it did evolve, doesn't guarantee that it will evolve. The problem is that you can't get from genotype A to some very different genotype Z, except through one or more generations of individuals with intermediate genotypes.

It's fairly easy to get from A to Z, provided that B is at least as fit as A, while C is at least as fit as B, and so on. This can be the case, as shown by experiments on the five-step evolution of antibiotic resistance, discussed in a previous post. But is this the only way a population can evolve a superior genotype? Or does evolution sometimes reach new heights (faster-flying birds, scummier pond scum, etc.) through intermediates that are significantly less fit?

Evolution via less-fit intermediates would expand evolution's options, making it even harder for biotechnology folks to come up with something missed by evolution. And that's what this week's paper seems to show.

"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness" was recently published in Nature by Margarita Meer and colleagues.

Continue reading "Evolution via less-fit intermediates" »

September 4, 2009

Where do new genes come from?

When a few members of a family have a gene not found in most other members, one explanation is that the gene is newly evolved, rather than inherited from the common ancestor of that family. (The other possibility is that their ancestor had it, but most descendants lost it.)

New genes often turn out to be copies of old genes, sometimes with modifications that give them very different functions. But a paper just published in Current Biology reports "Emergence of a new gene from an intergenic region", rather than duplication of an existing gene....

Continue reading "Where do new genes come from?" »

July 9, 2009

Has natural selection been asleep at the switch?

"This new forage has great insect resistance", effused a former colleague, "we just need to eliminate the toxins that keep sheep from eating it."

Genetically engineered drought-tolerant crops are introduced with great fanfare, only to disappear when they turn out to have low yield under nondrought conditions.

When natural selection falls short of perfection, it may be because "you can't get there (some desirable adaptation) from here (current genotypes)" without passing through a series of intermediate generations that would have lower fitness. Natural selection favors genotypes best-adapted to current conditions, which are not necessarily steps towards any long-term improvement.

But natural selection often seems to miss even "simple" improvements, that might be achieved by changing as little as one DNA base. Such small changes are often enough to increase or decrease expression of key genes, for example. This sort of evolutionary progress may be blocked by tradeoffs, e.g., between seed production under different conditions (e.g., wet vs. dry), or between the competitiveness of individual plants and their collective seed production.

So what are we to make of two recent papers (in Science and Nature, respectively, discussed in Science News) on extending lifespan, one using calorie restriction and the other using the antibiotic, rapamycin?

Calorie restriction has been shown to increase longevity in model species like nematode worms and mice, but this latest study shows clear benefits in monkeys. The obvious question -- at least, it was obvious to me -- is why has past natural selection given monkeys (and fruitflies, and nematodes, and mice...) appetites that make them eat more than is good for them?

At least, that seemed to be the question, until it was shown that food odors can reverse the beneficial effects of calorie restriction, at least in fruitflies and nematodes. In humans, soft drinks with artificial sweeteners turn out to be just as likely to cause "metabolic syndrome" (related to diabetes) as those with sugar. So apparently our lives can be shortened by a perception of abundance, not just by actually eating too much. What is going on here?

In this case, the evolutionary tradeoff seems to be between current and future reproduction. As discussed in last week's post, delaying reproduction usually decreases fitness (representation in the next generation, relative to others) when population is increasing, but delaying reproduction can increase fitness when population is decreasing. Calorie restriction predicts population decline, triggering physiological responses that delay reproduction and thereby increase longevity. So do bitter-tasting foods, traditionally eaten only during famines. Food odors or sweet tastes have the opposite effect, because they predict population increase.

But what about life extension by rapamycin? One known tradeoff is suppression of the immune system, so we might get longer lives only in a hypothetical germ-free environment. But could the protein target of rapamycin (TOR) also be important to reproduction? Is this yet another example of a longevity-vs.-reproduction tradeoff?

May 22, 2009

Oxytocin and the genetics of altruism

Where to publish a paper on the genetics of altruism? In an open-access journal, of course! One day after publishing the fossil primate paper that's creating so much excitement -- it's a great fossil, but too old to tell us anything about our recent ancestors, shared with other apes, or the less-recent ones shared with monkeys -- PLoS One published "The Oxytocin Receptor (OXTR) Contributes to Prosocial Fund Allocations in the Dictator Game and the Social Value Orientations Task", by Salomon Israel and colleagues. Like all papers in open-access journals, the full text is available on-line.

These researchers measured altruism in 200 students, based on how each chose to divide a pool of money with another unknown individual. Their hypothesis, based on various past studies, was that the hormone oxytocin is important for social interactions in general and for human altruism in particular. For example, Zak and colleagues showed that sniffing oxytocin made people offer a more generous split when the recipient had the chance to retaliate for a low offer (the "Ultimatum Game"), although not when there was no chance to retaliate, as in the Dictator Game used in the current study.

The researchers tested for statistically significant relations between and different variants of the oxytocin receptor gene, which codes for the protein that responds to this hormone signal in the brain, and "prosocial responses" (generosity) in the Dictator Game and a more-complex version, the SVO. Interestingly, none of the genetic differences they looked at were in the protein-coding part of the gene (orange). Most were in an intron, which would be transcribed from DNA into messenger RNA but then cut out before the mRNA is translated into protein. So I assume these genetic differences could affect how much oxytocin receptor protein is made where and when, but not the structure of the protein itself.
receptor.jpg

Continue reading "Oxytocin and the genetics of altruism" »

January 30, 2009

Inferring details of past evolution from DNA is tricky

Last week I discussed one of many papers that use the ratio of protein-changing to "neutral" genetic changes, along the branches of an evolutionary tree, to infer past natural selection. This week's paper presents data calling that approach into question. This does not necessarily undermine the overall conclusions of last week's paper, which were based on a variety of methods, including testing the actual performance of mutant proteins.

"Hotspots of biased nuclear substitutions in human genes" was published in PLoS Biology by Jonas Berglund and colleagues. I am not a molecular biologist, so will just summarize their main points. The paper is open access.

Most of our DNA does not code for proteins. Some of the noncoding DNA is known to have important regulatory functions. But there is lots of DNA whose function, if any, is unknown, but which is nonetheless highly similar among species, as if any change was lethal. Except, when someone tried deleting this DNA, a bit at a time, most of the deletions were not lethal or even (as far as they could tell) harmful. I discussed this work earlier.

Anyway, much of this noncoding DNA that differs little among most species is different in humans. Could these differences be what makes us different from other apes? Quite possibly. But are all these human-vs.-chimp differences important? Maybe not. An unexpectedly high fraction of the changes from the ape ancestor we share with chimps involved a change from A bound to T (a weak bond) to G bound to C (a strong bond). Unless noncoding DNA with stronger bonds is consistently better somehow (and only in humans!), this suggests that these changes are caused by some DNA-specific process and not by natural selection. In other words, these changes occurred whether or not they were beneficial, just as mutations do. Could similar AT=>GC changes have changed protein-coding sections of DNA?

The researchers compared 10,238 genes in humans, chimps, and macaques...

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January 23, 2009

Staying ahead in the evolutionary arms race with viruses

This week's paper uses molecular methods to reveal new details of the evolutionary arms race between primates, including humans, and viruses. "Protein kinase R reveals an evolutionary model for defeating viral mimicry" was published in Nature by Nels Elde and colleagues in Seattle.

Protein kinase R (PKR) is an important defense against viruses in many species, from humans to yeast. When it detects a virus inside a cell, it activates eIF2-alpha, which shuts down protein production in that cell. With protein production blocked, the virus can't replicate and spread to other cells. Viruses, however, have evolved counter-measures. These include molecules that resemble eIF2-alpha. These molecular mimics interact with PKR and prevent its normal defensive activity.

Viral epidemics can be a major cause of death, so we expect populations to evolve PKR resistant to the eIF2-alpha-mimics produced by viruses. Can we find evidence of such evolution in primates?

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November 3, 2008

Ook! Another librarian for Obama

With the US election imminent, I interview the Librarian of Unseen University.

TWiE: Your endorsement of Obama has created quite a stir on this planet and might help swing the election. Were you influenced by Sarah Palin's firing a librarian for refusal to censor library books or for her views on evolution?

Librarian: Ook.

TWie: OK, but she would have limited power (you know, like Cheney) unless McCain dies in the next four years. Are you worried that some Christian terrorist would assassinate him to put her in power? Or are there problems with McCain as well?

Librarian: Ook!

TWiE: A macaca? But those aren't even apes; they're...

Librarian: Ook. Ook.

TWiE: OK, OK. Moving on to another topic, are you supporting anyone for Patrician?

Librarian: Eek. Ook.

TWiE: OK, thanks for your time. I did have a few more questions, but good luck straightening out Wall Street.

September 26, 2008

Social intelligence

The other day, my brother was telling me about playing mandolin on songs he didn't know, with a band he'd just met. Then there are people who can play several chess games at once or write crossword puzzles for the New York Times. How did humans get so smart? Over most of our evolutionary history, mandolin players and crossword writers probably had a hard time making a living.

This week's paper tests the hypothesis that natural selection favored intelligence largely because it was important in social interactions. If that's true, then species that interact with more different individuals should evolve greater intelligence. Federica Amici and colleagues tested this hypothesis using apes and monkeys and reported their results in Current Biology. Their paper is titled "Fission-fusion dynamics, behavioral flexibility, and inhibitory control in primates."

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September 6, 2008

Brief note on thumbs and junk DNA

I was going to write about this paper about a gene that evolved rapidly in humans since our lineage split from that leading to chimps. But Ed Yong at Not Exactly Rocket Science has already done a great post on it, including a picture showing its likely link to thumbs.

Comments on Ed's blog and a more complete treatment on Carl Zimmer's "The Loom" (both favorites of mine) point out the fallacy of some popular press coverage claiming this is the first evidence that "junk DNA" isn't junk after all. They both make the important point that we've known for decades that some DNA that doesn't code for protein is nonetheless very important.

On the other hand, lots of our DNA really does seem to be junk. Much of it is the product of "jumping genes" that copy themselves and insert themselves into existing DNA. These are common because they copy themselves, not because they do us any good (although, just by chance, they may occasionally be beneficial).

About 5% of DNA that doesn't code for protein is nonetheless "highly conserved", as if it were somehow beneficial and therefore maintained by natural selection. But a paper I reviewed earlier showed that much of this conserved noncoding DNA can be deleted without apparent ill effects. So if it's beneficial, it's not very beneficial. Or maybe it's beneficial only under special circumstances.

August 21, 2008

The bird in the mirror

This week’s paper is “Mirror-induced behavior in the magpie (Pica pica): evidence of self-recognition?, by Helmut Prior and colleagues, available online in PLoS Biology.

When confronted with mirrors, apes (including humans) react very differently from monkeys. Monkeys never seem to recognize that they are seeing a reflection of themselves rather than another monkey. Recently, dolphins and elephants have been added to the list of species that can recognize themselves in mirrors and use them for self-exploration. Most other species can not. Is this because their brains are too small? Or is the tendency to self-exploration using a mirror a side-effect of a mental ability that evolved for other reasons? If the latter is true (even if there is also some minimum brain size requirement), then more species that need to pay more attention to what others of their species are doing might be more likely to evolve this mental ability.

Some birds, for example, hide food, raid each other’s food caches, and pay attention to who was around when they were hiding food. How do these birds respond to mirrors?

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May 3, 2008

Sharing diseases with relatives and neighbors

Not enough people voted on the Reader’s Choice, so this week’s paper is “Phylogeny and geography predict pathogen community similarity in wild primates and humans? by Jonathan Davies and Amy Pedersen, published in Proceedings of the Royal Society.

Many humans diseases, from flu to AIDS, come from other species. Similarly, diseases from dogs are an increasing threat to lions, while cat diseases kill sea otters. Are there general rules that predict how likely two species are to share diseases?

To find out, the authors analyzed several large data sets on diseases of humans and 117 other species of primate (apes, monkeys, etc.). They hypothesized that species are more likely to share diseases if they live near each other and/or if they are more closely related, that is if they share a more recent common ancestor. This is similar to how we define relatedness in humans: brothers and sisters have more recent common ancestors (parents) than cousins do (grandparents). Fortunately, the family tree for primates is relatively uncontroversial, at least among scientists.

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April 19, 2008

Separate vacations and other sexual differences

Three recent papers in Proceedings of the Royal Society discuss differences between males and females or, in one case, among males.

The costs of risky male behaviour: sex differences in seasonal survival in a small sexually monomorphic primate? by Cornelia Kraus and others, is based on a 10-year study of differences between male and female behavior in grey mouse lemurs. During the breeding season, males had lower survival than females, despite any possible risks associated with pregnancy or raising young. The higher risk for males apparently resulted from their tendency to travel more, looking for females.

The sexes also differ in winter behavior: females hibernate, while males remain active. Is there something about female physiology that makes hibernation healthier for them than it would be for males? Maybe, but there was no difference in winter survival between the sexes, which don’t differ much in size in this lemur species. The authors suggest that hibernation might have longer-term benefits in females, such as increased lifespan, whereas males need to stay active to bulk up in preparation for the breeding season.

This paper reminded me of an earlier paper on albatrosses, in which "in each pair, the male spent the winter just north of the pack ice in Antarctic waters whereas the female stayed south of Madagascar." It’s not hard to understand why males and females might differ in various ways (size, color, etc.) but differences in behavior outside of the breeding season are more interesting.

The second paper addresses an old argument between Charles Darwin and Alfred Russel Wallace, who developed similar explanations of evolution by natural selection at about the same time.

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November 2, 2007

When did social learning evolve?

Two papers this week may shed some light on human evolution. We aren't descended from modern monkeys or lemurs, but we can often learn something about our ancestors by studying our distant cousins.

colugo.jpg

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September 14, 2007

Money for monkeys

This week's paper is "Do capuchin monkeys (Cebus apella) use tokens as symbols?" by E. Addessi and coauthors, published in Proceedings of the Royal Society.

Humans use symbols in various ways, from drawings that somewhat resemble the object represented to national flags and religious symbols that represent complex ideologies (or at least group identity). Is symbolic reasoning a uniquely human trait, at least on this planet?

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June 24, 2007

Trade-offs in defense against retroviruses

I have written about evolutionary trade-offs before, starting with early posts about trade-offs between seed size and seed number in plants, and trade-offs between the ability of insects to escape predators by flying away, versus the ability to hide from them by playing dead. I have also given some examples of the increasing use of sophisticated experimental (often molecular) methods in evolutionary biology. This week's paper combines both themes.

The paper is "Restriction of an extinct retrovirus by the human TRIM5-alpha antiviral protein" by Shari Kaiser, Harmit Malik, and Michael Emerman, published in Science (vol.316 p.1756).

Retroviruses are made of RNA, but make DNA copies of themselves that can insert into the DNA of host cells they infect. HIV, the cause of AIDS, is a well-known example, but there are many others. If DNA copies of the retrovirus are inserted into cells giving rise to sperm or eggs, they can be passed to the next generation, as endogenous retroviruses. If the DNA inserts somewhere where it turns an important gene on or off, it may kill the host. Or, once in a while, this change may turn out to be beneficial. The few beneficial changes are the ones that survive and spread, just as the few mutations that are beneficial are the ones that persist.

VWXYNot has an interesting discussion of how a creationist web site misused one of her papers as evidence of "intelligent design." She shows how shared endoviruses can be used to infer shared ancestry, providing yet more evidence that we share a recent ancestor with apes, less-recent ancestors with monkeys, etc. But that's not what this week's paper is about....

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March 7, 2007

Teenage chimps with spears and hammers

Two related papers this week: “Savanna chimpanzees, Pan troglodytes verus, hunt with tools? by Jill Preutz and Paco Bertolani, published in Current Biology (17:1-6), and “4,300-year-old chimpanzee sites and the origins of percussive stone technology? by Julio Mercader et al., published in Proceedings of the National Academy of Science (104:3043-3048).

Preutz and Bertolani report field observations of chimpanzees in Senegal making simple wooden spears and using them to kill bushbabies (sleeping in hollow trees) for food. Several individuals were seen making and using the spears, although apparently they only saw one successful “hunt.?

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