June 21, 2013

Aging, intelligence, cooperation, and ecology

The age-specific force of natural selection and biodemographic walls of death "Nonlinear interactions cause the collapse of Hamilton-style predictions in the most commonly studied case..."

GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment "A linear polygenic score from all measured SNPs accounts for ≈2% of the variance in both educational attainment and cognitive function."

Fusing enacted and expected mimicry generates a winning strategy that promotes the evolution of cooperation "reducing conflict intensities among human populations necessitates (i) instigation of social initiatives that increase the perception of similarity among opponents"

Global human appropriation of net primary production doubled in the 20th century

Several scales of biodiversity affect ecosystem multifunctionality

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."

April 12, 2013

This week's picks

Here are some papers that look interesting this week. See also my Darwinian Agriculture blog

Stable isotope evidence of meat eating and hunting specialization in adult male chimpanzees "sex differences in food acquisition and consumption may have persisted throughout hominin evolution, rather than being a recent development"

New World cattle show ancestry from multiple independent domestication events "pre-Columbian introgression of genes from African cattle into southern Europe"

Key role for a glutathione transferase in multiple-herbicide resistance in grass weeds "When the black-grass A. myosuroides (Am) AmGSTF1 was expressed in Arabidopsis thaliana, the transgenic plants acquired resistance to multiple herbicides"

Potential shortfall of pyramided transgenic cotton for insect resistance management "results from 21 selection experiments with eight species of lepidopteran pests indicates that some cross-resistance typically occurs between Cry1A and Cry2A toxins."

The Upper Limb of Australopithecus sediba "use of the forelimb primarily for prehension and manipulation appears to arise later, likely with the emergence of Homo erectus" [There are several articles on A. sediba in this issue.]

Achieving the triple bottom line in the face of inherent trade-offs among social equity, economic return, and conservation "three very different case studies in California (United States), Raja Ampat (Indonesia), and the wider Coral Triangle region (Southeast Asia). We show that equity tends to trade off nonlinearly with the potential to achieve conservation objectives, such that similar conservation outcomes can be possible with greater equity, to a point."

Decreased water flowing from a forest amended with calcium silicate "An unexpected outcome of the Ca amendment was a change in watershed hydrology; annual evapotranspiration increased by 25%, 18%, and 19%, respectively, for the 3 y following treatment before returning to pretreatment levels. "

Responses of Mn2+ speciation in Deinococcus radiodurans and Escherichia coli to γ-radiation by advanced paramagnetic resonance "extreme radiation resistance of D. radiodurans cells cannot be attributed to SodA"

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."

January 25, 2013

What's for dinner?

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

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

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

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

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

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

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

November 9, 2012

Cooking key to cognition; corals recruit bodyguards; etc.

Metabolic constraint imposes tradeoff between body size and number of brain neurons in human evolution "This limitation was probably overcome in Homo erectus with the shift to a cooked diet."

Corals Chemically Cue Mutualistic Fishes to Remove Competing Seaweeds "Mutualistic gobies and corals appear to represent a marine parallel to terrestrial ant-plants, in that the host provides shelter and food in return for protection from natural enemies."

Bateman in Nature: Predation on Offspring Reduces the Potential for Sexual Selection "substantial yearly variation in the Bateman slope [number of offspring as a function of the number of mates] due to predation on fawns was evident."

Drift-barrier hypothesis and mutation-rate evolution "selection appears to reduce the mutation rate... to a level that scales negatively with both the effective population size (Ne)... and the genomic content "

For a list of my upcoming talks around the world, see my new Darwinian Agriculture Blog.

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.

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

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?

July 15, 2011

Evolution of human cooperation

Two papers this week help explain why humans cooperate, even with nonrelatives. Cooperation with relatives (activities that tend to decrease one's own reproductive success, while increasing that of others likely to share many of one's genes) is predicted by "selfish gene" theory, as formalized in Hamilton's rule. I've assumed that cooperation with nonrelatives is a beneficial side-effect of behavioral genes that evolved when most of our neighbors were relatives, as is still the case in parts of the Amazon and West Virginia. But other explanations have been proposed.

One hypothesis is that "human cooperation evolved as a result of high levels of lethal competition (i.e. warfare) between genetically differentiated groups." In other words, some groups of unrelated individuals happened, by chance, to have a higher fraction of individuals whose genes tended to increase within-group cooperation -- particularly, willingness to risk injury in battles with other groups -- and the overall frequency of those genes increased as victorious groups killed groups that happened to have a lower frequency of "cooperation genes." This process would tend to be undermined by within-group evolution (assuming selfish individuals tend to have more descendants) and by migration between groups. The latter could include abductions.

But are genetic differences between groups big enough for this "group selection" mechanism to work? In "Genetic differentiation and the evolution of cooperation in chimpanzees and humans", recently published in Proceedings of the Royal Society, Kevin Langergraber and colleagues compared genetic differences among competing aboriginal human groups with differences among competing chimpanzee groups. They found that genetic differences among chimpanzee troops were at least as great as differences among human groups. So, if humans are more cooperative than chimps -- budget deadlocks in the US Congress and my state legislature call this into question -- it's probably not because group selection is more effective in humans than in chimps, in increasing the frequency of genes favoring cooperation. The authors suggest that "both genetic and cultural differentiation between groups played a role in the evolution of altruistic cooperation."

What sorts of cultural differences among groups might be important? This week's second paper, recently published in PNAS by Sarah Mathew and Robert Boyd, claims that "Punishment sustains large-scale cooperation in prestate warfare." This paper addresses the issue mentioned briefly above, the problem of within-group increases in selfishness (if selfish individuals have more descendants) undermining increases in cooperation from between-group processes. In particular, they asked whether individuals that deserted during battles between groups were punished.

The researchers obtained data for 88 raids involving the Turkana tribe, and found that: 1) the chance of a man being killed is >1% for each raid he participates in, 2) desertion or acts of cowardice occur in at least 45% of raids, and 3) these acts often lead to severe beatings, after group discussion. Getting beaten could certainly cause an individual to change his behavior, but what effect, if any, do such sanctions have on the frequency of genes that affect willingness to take risks in battle? Do those who fight bravely end up with more wives and, more important, more descendants? Unfortunately, "distinguishing the effect of behavior during warfare from the effect of other factors that affect a person's value as a social or mating partner is beyond the scope of the present study."

July 2, 2011

The "boy pill", assortative mating, and human evolution

There's a debate underway about whether we should oppose sex-selective abortion because it's abortion or because it's sex-selective. Matthew Yglesias argues for the latter. What if scientists developed a "boy pill" that would make a man produce only Y-chromosome sperm? He suggests that:

if we found out that use of the "boy" pill was extremely widespread, this might still legitimately worry us for three kinds of reasons. One is that widespread use of the boy pill would express the inegalitarian idea that men are more valuable than women. A second is that widespread use of the boy pill would reflect the existence of ongoing inequities in society that make it the case that a male child is more valuable than a female child. The third is that there are plausible reasons to believe that even a relatively small gender gap in the population could have problematic macro-scale consequences for society.
I'm not sure about his first and second points. Yes, the lower the status of women, the more likely parents might be to want a son rather than a daughter, even if they personally deplored discrimination against women. But would a male-biased sex ratio contribute to lower status for women, or perhaps alleviate it? If there were twice as many men as women, would women have more opportunities to choose partners who would support their aspirations?

A male-biased sex ratio could certainly cause "problematic macro-scale consequences for society", but would those consequences be all negative? Population growth can have negative macro-scale consequences, but every country except China has decided that those consequences are not negative enough to justify the "mutual coercion, mutually agreed upon" that Garrett Hardin thought necessary to limit population growth.

Making the hypothetical "boy pill" freely available would hardly qualify as coercion, but a male-biased sex ratio would tend to slow population growth. Could the net benefits of slower population growth (mostly positive) outweigh the net costs of a male-biased sex ratio (probably negative)?

Things get more interesting when we ask who it is that would prefer sons to daughters. In the US, men strongly prefer sons, by 49 to 22%, while women value sons and daughters equally. Conservatives prefer sons, 41 to 25%, while liberals value both equally. If this tendency applies worldwide, then widespread availability of the hypothetical "boy pill" would lead to male-biased sex ratios mainly in more-conservative countries and subcultures where men dominate decision making.

Would a shortage of females slow the population growth of conservatives? That's far from clear. If conservatism were highly heritable, either genetically or culturally, and if conservatives didn't marry outside of their subculture (i.e., if mating were highly assortative), then conservative societies with male-biased sex ratios would tend to grow more slowly. To the extent that conservatism (or a preference for sons) has a genetic basis, those genes would become less common than if the "boy pill" were not available.

Similarly, a "girl pill" could perhaps slow the population growth of any society with a strong preference for girls, assuming both assortative mating and lifelong monogamy.

Sex selection is just one example of the choices that parents may be able to make within the next few decades. Would it matter whether parental choices for the skin pigmentation of their offspring were motivated by their own prejudices, societal prejudices that they personally abhor, or the relative risks of skin cancer versus vitamin-D deficiency at their latitude?

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."

February 24, 2011

This week's picks

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

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

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

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

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

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

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

February 10, 2011

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

Some recent papers that look interesting:

The evolution of host protection by vertically transmitted parasites

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

Before senescence: the evolutionary demography of ontogenesis

Costs of memory: lessons from 'mini' brains

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

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

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

Multiple strategies in structured populations

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

December 22, 2010

Our secret is out !

Fort_Denison.jpgFor millennia, we Denisovans have hidden in our secret fortress laboratories, underground in Siberia and out at sea, like Fort Denison, occasionally interbreeding with humans from neighboring islands. We didn't expect you to discover the traces of the latter activity so soon. Looks like we'll have to use our interstellar spaceship earlier than planned. So long, and thanks for all the fish!

December 12, 2010

Conditional cooperation and forest management

A while ago, I asked readers which of several papers they would most like me to discuss. The only request was for a paper which, though related to my own interests in the evolution of cooperation, isn't exactly evolutionary biology, "Conditional cooperation and costly monitoring explain success in forest commons management". I decided to discuss it anyway. Anyone particularly interested in the tragedy of the commons might also find some older posts in my moribund blog, The Comedy of the Trojans, worth reading.

Continue reading "Conditional cooperation and forest management" »

March 10, 2010

Why hasn't natural selection eliminated Alzheimer's?


The Alzheimer's Disease-Associated Amyloid beta-Protein Is an Antimicrobial Peptide
[See comment below for an earlier paper making this suggestion.]

Life-long protection against brain infections, in exchange for increased risk of dementia at an age few of our ancestors reached? Sounds like a reasonable tradeoff to me. Except that now we may have better options:

"it raises the possibility of preventing amyloidosis from initiating by pre-emptive targeting of pathogens/insults that stimulate the brain's innate immune system."

All we need is a good noninvasive way to detect brain infections early, so we can treat them with nonAlzheimer's-inducing antibiotics before amyloid beta-protein gets into the act.

October 2, 2009

Local TV new blows Ardipithecus story

If you don't believe in evolution, you might not want to listen to this next story. Scientists reported this week on a new fossil, possibly a human ancestor, older than Lucy. The good news is, we're not descended from chimps after all. The bad news is, chimps and humans are descended from the same ancestor.

That's a paraphrase of how our local TV news covered Ardipithecus ramidus, the fossil hominid discussed in a series of papers in this week's issue of Science. Read all about it on Carl Zimmer's blog. The TV anchor didn't say which scientists claimed we are descended from chimps, perhaps because no scientist has made that claim. Chimps have evolved over the six million years or so since our last common ancestor, including their split with bonobos. Can we expect the story below on the TV soon?

Startling breakthrough in human genetics! You aren't descended from brother after all, or even from your cousin. You and your brother still have the same parents, and you and your cousin have the same grandparents, though. I hope that doesn't upset you too much.

We don't know for sure that present-day humans are descended from Ardipithecus . It's a reasonable hypothesis, but any hypothesis is, by definition, subject to possible disproof. For example, if we found another fossil that was clearly much more similar to modern humans, dating from the same time or earlier, then we'd conclude that Ardipithecus probably has no surviving descendants.

But this species probably isn't too far from the direct line of descent between our common ancestor with chimps and modern humans. Suppose you wanted to know what your great grandmother looked like, but there was no surviving picture of her. If you had pictures of her sister or her daughter, that would give you some idea, even if all her living descendants are descended from a son.

Of course, much of what we know about our ancestors now comes from analyzing DNA in humans and closely related species. We can figure out when vitamin C synthesis was lost or adult lactose tolerance gained, for example. But we don't yet understand development enough to predict height, foot shape, etc., from inferred DNA sequences of ancestral species. So keep those fossils coming!

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?

July 6, 2009

Throwing the longevity switch

If you could choose a longer, healthier life, but only by having fewer kids, would you? What if you could eventually have the same number of kids, but only by having sex more often, and with no possibility of becoming a parent as a teen-ager?

Is this really possible? Based on the paper we published last week, we are pretty sure it is, although we don't yet know how much of an increase in lifespan is achievable, nor how much it will "cost" in reduced fertility.

A key assumption is that there are tradeoffs between longevity and reproduction, especially early reproduction. There is plenty of evidence for this antagonistic pleiotropy hypothesis: some gene variants that increase longevity nonetheless stay rare, because individuals with those variants have fewer kids. There are many possible reasons for this tradeoff. Calories used for reproduction aren't available for maintaining our bodies. Blood pressure and insulin levels optimal for reproduction are unlikely to be exactly optimal for longevity. Other risks associated with reproduction include sexually transmitted diseases and direct risks of childbirth. When there is a conflict between reproduction and longevity, natural selection will often favor reproduction.

There are, however, two ways we may be able to choose differently, increasing longevity at the expense of (potential, but maybe not actual) reproduction. First, once germ-line gene therapy is perfected and available (initially, perhaps, only in one or two "outlaw states"), maybe we could reverse some of the effects of past natural selection. We might be able to produce genetically engineered kids who would reach puberty later and with low enough intrinsic fertility that occasional unprotected sex would rarely lead to pregnancy, but who would still be healthy at age 100.

Second, what about people already born? Is there some biological "switch" we can throw, that tilts the longevity-vs.-reproduction tradeoff more towards longevity? Or has past natural selection welded the switch in the "reproduce now" position?

We think the switch is free to move, depending on environmental cues that affected our ancestors' survival and reproduction. Our paper shows that the switch position that maximizes Darwinian fitness depends on whether the overall population is increasing or decreasing. If population is decreasing, then individuals that live longer and reproduce later can contribute a larger fraction to their species' (shrunken) gene pool than those that reproduce earlier, on average, even if a few of them die before they get a chance to reproduce, and even if their lifetime reproduction is less than they might have achieved earlier.

Therefore, even though gene variants that always sacrifice early reproduction to increase longevity may not have persisted in the gene pool, variants that delay reproduction (thereby increasing longevity) only when populations were decreasing are likely to be with us, in each of our DNA molecules, today.

If this is true, all we need to do to increase our longevity is to give our bodies (false) cues that, over our evolutionary history, usually predicted population declines. To the extent that population declines were caused by food shortage, eating less may work, as it does in most species tested. Eating "famine foods" (leaves rather than meat, maybe) may also trigger physiological responses that reduce fertility but extend lifespan. On the other hand, if population declines were usually caused by cold winters, is there some reasonably comfortable way to trigger similar responses?

Delaying reproduction can only increase fitness if it increases the chances of surviving the famine or cold winter and reproducing later. So stresses that often predicted the death of the stressed individual (those associated with violent conflict, perhaps) won't necessarily delay reproduction or increase longevity. But there are lots of examples of mild stress increasing longevity. These stresses presumably trigger health-and-longevity-promoting mechanisms, but we may be the first to explain why such beneficial mechanisms aren't turned on all the time: they tend to reduce fertility.

Now, here's a question for you: would increasing human longevity be a good thing? I've seen this issue discussed in various places, but rather superficially. Assume that this option was made available to everyone, given that the cost could be quite low: inexpensive drugs or lifestyle changes that might even save money. Death rates would go down, in the short run, but so would birth rates, especially in countries where birth control is now rare. Death from old age is a fairly small component of overall population trends in these countries (relative to birth rate and infant mortality), so their rate of population increase might actually slow. But, if people expected to live longer, would they have more children (despite lower intrinsic fertility) or fewer, and at what age? Assuming some increase in population, we might need to grow more food -- a significant challenge -- but how would the overall impact of two healthy 90-year-olds who are still working (perhaps as doctors or nurses) and driving compare to that of one 90-year old who doesn't drive but needs expensive medical care? If professors keep working into their 90's, will that slow the spread of good new ideas, or only of stupid ideas that younger faculty may not know were debunked long ago? Would a longer-lived population produce too many bloggers?

June 25, 2009

The bitter fountain of youth

"When stress predicts a shrinking gene pool, trading early reproduction for longevity can increase fitness, even with lower fecundity." That's the title of a paper that Will Ratcliff, Mike Travisano, Peter Hawthorne and I just published in PloS-One. This was a spin-off from Ratcliff's work on the timing of reproduction in bacteria, but our main conclusions should apply broadly to plants and animals, with important implications for human health. Our entire paper is available on-line, but here is some additional background and explanation.

Earlier, I blogged about our research at UC Davis showing that tomatoes grown using organic methods have higher concentrations of a specific chemical (Mitchell, et al. 2007). Plants make this chemical to defend themselves against insects, which may be why there was more of it in tomatoes not protected by artificial pesticides. Surprisingly, this chemical actually seems to benefit human health. At the time, I thought this might just be coincidence, and wrote that "some of the natural insecticides plants make... are likely to be harmful to humans, rather than beneficial."

Now, I'm not so sure. It turns out that many toxins, including natural insecticides, can have health benefits in low doses, a phenomenon known as hormesis (Mattson & Cheng. 2006). Other forms of mild stress, such as dietary restriction (calorie restriction, intermittent fasting) or high temperature, have also been shown to increase longevity.

How can stress be beneficial? Some stresses trigger various protection mechanisms, such as antioxidants or heat-shock proteins, which may increase lifespan, even relative to individuals not exposed to stress. But why aren't these protective mechanisms turned on all the time, rather than only under stress? Don't individuals with longer lifespans leave more descendants than those with shorter lifespans? Not necessarily.

What if some mechanisms that increase lifespan also delay sexual maturity or decrease the rate of reproduction? For example, what if the blood pressure that maximizes lifespan is lower than that which maximizes reproduction? Then a gene for lower blood pressure would not necessarily increase in frequency over generations. A trade-off between early reproduction and longevity (and later reproduction) was central to the "antagonistic pleiotropy" hypothesis of Williams (1957). Our paper builds on this widely accepted hypothesis.

Given trade-offs between early and late reproduction, when will natural selection favor genes that potentially increase longevity but delay reproduction? Sometimes, resources not used for reproduction can be invested in growth, increasing reproduction in future years. Also, more experienced individuals may care for their offspring better. But what if delaying reproduction doesn't increase either the number of offspring or their survival?

We showed that delaying reproduction can still increase Darwinian fitness, that is, proportional representation in the gene pool, provided that overall population size is decreasing. Hamilton (1966) pointed out that an offspring added to a smaller population represents a larger fraction of the total gene pool. Therefore, if total population is increasing, offspring produced earlier have a larger effect on fitness. But if population size is decreasing, then offspring produced later have a larger effect on fitness. This means that delaying reproduction can sometimes increase fitness, even if delay does not increase the number of offspring.

Most populations will alternate between increasing and decreasing in numbers. If the population is stable or increasing, delaying reproduction can only decrease fitness. This is especially true if there is a high risk of death from causes unrelated to reproduction. But if the size of the gene pool is likely to decrease, delaying reproduction can increase fitness. This is especially true if risks directly or indirectly associated with reproduction are large relative to other risks.

Our mathematical models show that the best strategy is to delay reproduction only when an individual's chance of surviving to reproduce later is high, and only when an individual has reliable information predicting a decrease in overall population size. This is where stress comes in.

Past population declines were often caused by shortages of food, which can affect both the amount and types of food eaten. For example, natural insecticides in plants often have an unpleasant taste. Over most of our evolutionary history, therefore, these plants may have been eaten only when preferred foods, like meat or fruit, were not available. Consumption of these "famine foods" would therefore have been a reasonably good predictor of population decline, so they may trigger physiological changes (lower testosterone, etc.) that increase longevity while tending to delay reproduction.

A remarkable result, seen in both nematode worms and fruit flies, is that food odors can reverse the beneficial effects of dietary restriction on longevity (Libert, et al. 2007). If an individual smells food, others may be eating that food, so population size may be increasing. In that case, delaying reproduction would be a losing strategy, even if reproducing now increases the chance of an early death.

What about humans? Our models assumed that individuals reproduce only once, then die, like salmon or soybeans. However, we expect that some of our results will apply to species, like humans, with more complex life histories. One result for humans that is consistent with our hypothesis is that artificially sweetened soft drinks are just as likely to cause metabolic syndrome (related to diabetes) as sugared soft drinks are (Lutsey, et al. 2008). Like food odors, sweet foods may have been correlated, over much of our evolutionary history, with abundance, and therefore with impending increases in population size. If we want to live longer, maybe we should instead eat foods whose chemical composition or flavor remind our bodies of past famines. The health benefits we get from eating vegetables like kale may be due, in part, to the chemicals that give them their slightly bitter taste.

High levels of toxins, including natural ones, are still presumably harmful. But low doses of plant toxins, perhaps especially those found in traditional famine foods, may often improve health. This assumes that our hypothesis is correct, so you might want to wait for the results of experiments we are planning before making major changes in your diet.

We are also assuming that most people would consider some decrease in potential reproduction to be acceptable. For the many humans that already choose to limit their own reproduction, this need not result in any decrease in actual family size. For example, if people don't expect to marry until after college, the risks of early fertility may outweigh the benefits, even apart from health effects of hormone levels etc. in the teenage years on health later in life. Delaying puberty might, however, result in larger adults, with possible negative implications for automobile fuel economy and other resource issues.

Another popular hypothesis has been that individuals benefit from delaying reproduction in a bad year and waiting until conditions are better. This may increase the number of offspring produced, but we show that it does not increase proportional representation if the entire population also reproduces more in the good year.

"How is putting our entire kingdom to sleep for 100 years better for my family than losing one daughter, however much we love her?" asked the queen. "In 100 years, our other children would have had countless grandchildren. Meanwhile, those in neighboring kingdoms will multiply. By the time the impenetrable thorn forest you put around our kingdom dies and we awake, our enemies will vastly outnumber us."

"Not necessarily", replied the fairy scientist, "My computer models predict 100 years of wars, famines, and plagues. It's true that your population won't grow, but those of your enemies will shrink. This would have been a winning strategy, even if there were another way to save your daughter's life."

Ratcliff, Travisano, Hawthorne, and Denison. Can you spot the model?


Hamilton WD. 1966. The moulding of senescence by natural selection. Journal of Theoretical Biology. 12 : 12-45

Libert S, Zwiener J, Chu X, VanVoorhies W, Roman G, Pletcher SD. 2007. Regulation of Drosophila life span by olfaction and food-derived odors. Science. 315 : 1133-7

Lutsey PL, Steffen LM, Stevens J. 2008. Dietary intake and the development of the metabolic syndrome: The atherosclerosis risk in communities study. Circulation. 117 : 754-61

Mattson MP, Cheng A. 2006. Neurohormetic phytochemicals: Low-dose toxins that induce adaptive neuronal stress responses. Trends in Neurosciences. 29 : 632-9

Mitchell AE, Hong YJ, Koh E, Barrett DM, Bryant DC, et al. 2007. Ten-year comparison of the influence of organic and conventional crop management practices on the content of flavonoids in tomatoes. Journal of Agricultural and Food Chemistry. 55 : 6154-9

Williams GC. 1957. Pleiotropy, natural selection, and the evolution of senescence. Evolution. 11 : 398-411

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.

Continue reading "Oxytocin and the genetics of altruism" »

April 8, 2009


Which animals kill the most humans? Lions and tigers and bears? Oh no, malaria-transmitting mosquitoes! The risks of using insecticides to kill mosquitoes may be outweighed by the benefits, but those benefits only last until mosquito populations evolve resistance. Careful use (insecticide-treated bed-nets, for example, rather than spraying wetlands) can slow the evolution of resistance, but we haven't yet achieved a goal I recently saw on a bumper sticker, namely, to "Stop Evolution Now!"

Can we do better? A paper published today suggests a new approach. "How to make evolution-proof insecticides for malaria control" was written by Andrew Read and colleagues. It's in the open-access journal, PLoS Biology, so you can read the whole article for details, but here's my summary:

Continue reading "Evolution-Proof?" »

February 20, 2009

20 February 2009

Here are some links to some papers that looked interesting this week. I hope I will have time to write about one of them this weekend.

Market forces affect patterns of polygyny in Uganda

Harmonic Convergence in the Love Songs of the Dengue Vector Mosquito

Monoamine oxidase A gene (MAOA) predicts behavioral aggression following provocation

A “crown of thorns” is an inducible defense that protects Daphnia against an ancient predator

The feeding biomechanics and dietary ecology of Australopithecus africanus

Isotopic Evidence for an Aerobic Nitrogen Cycle in the Latest Archean

Risk assessment in man and mouse

Duplicate genes increase expression diversity in closely related species and allopolyploids

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...

Continue reading "Inferring details of past evolution from DNA is tricky" »

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?

Continue reading "Staying ahead in the evolutionary arms race with viruses" »

January 19, 2009

Safe-crackers have vaults in their cells

This is the most amazing thing I've seen in awhile. Vaults are abundant in our cells and bigger than ribosomes and apparently I'm not the only biologist who had never heard of them. They seem to be important in defense against bacteria, but nobody understands them in detail yet, apparently.

January 2, 2009

Ford Denison, amateur scientist

My NSF grant will run out soon, so I get to spend the year in which we celebrate the 200th anniversary of Darwin's birth and the 150th anniversary of The Origin of Species as an amateur scientist, like Darwin himself. I'm not as smart or as rich as he was, but I do have imaginative and hard-working students and much better equipment.

I'm working on two grant proposals and several papers while dreaming of getting back to writing my book, so no detailed paper analysis this week. But Nature is highlighting 15 major papers on evolution they have published in the last few years.

September 12, 2008

Evolution of mental illness

I usually only discuss papers with original data, but I'm going to make an exception this week.

"Battle of the sexes may set the brain" was published in Nature by Christopher Badcock and Bernard Crespi. It's labeled "Opinion" but it is based on facts as well as theory. Their central hypothesis is that mental illness in humans is often the result of conflicts between genes inherited from the mother and father.

Imagine a gene -- let's call it IGF2, since that's it's name -- that causes a fetus to grow faster, resulting in somewhat higher birth weight. Babies with slightly higher birth weight tend to be healthier, up to a point, but they may endanger the health of the mother, at least a little. So most women shut down the copy of IGF2 in their eggs. Therefore, most babies get an active copy from their father and an inactive copy from their mother. Occasionally, though, the mother's copy is also active in the fetus, resulting in larger-than-normal babies. It turns out that these babies have a higher risk of autism.

Continue reading "Evolution of mental illness" »

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.

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.

Continue reading "Sharing diseases with relatives and neighbors" »

March 23, 2008

Oestrus Island

"A struggle for existence inevitably follows from the high rate at which all organic beings tend to increase... It is the doctrine of Malthus applied with manifold force to the whole animal and vegetable kingdoms" -- Charles Darwin, Chapter 3, The Origin of Species
This week's paper is more about ecology and sustainability than evolution per se. In recognition of Easter, a holiday that originally honored Oestre (the goddess of spring, who also lent her name to oestrus), and which, at least in the US, retains its association with fecundity in the the egg-laying Easter Bunny, I will discuss "The simple economics of Easter Island: A Ricardo-Malthus model of renewable resource use", written by J.A. Brander and M.S. Taylor and published in 1998 (Am. Econ. Rev. 88:119).

Although this paper focuses on Easter Island, it also discusses many of the same societies in Jared Diamond's 2005 book "Collapse." The book includes much that is not in the paper, but the paper has the advantage of being shorter and of supporting specific points with specific citations, in contrast to the diffuse "Further Reading" approach used in Collapse.

Continue reading "Oestrus Island" »

January 22, 2008

Altruistic punishment? Maybe not.

Punishing cheaters selects against cheating, but what selects for punishing? Are the answers different, depending on whether the species involved have brains? A recent internet experiment suggests that altruistic punishment, perhaps unique to humans, doesn't promote cooperation as effectively as previously thought.

My own research focuses on cooperation in species without brains. We showed that "sanctions" imposed by legume plants limit the evolution of "cheating" rhizobium bacteria (those that divert more plant resources to their own reproduction, relative to other rhizobia, by investing less in fixing the nitrogen needed by the plant). We think individual plants help themselves by imposing sanctions that limit wasteful resource use by less-beneficial rhizobia - they don't do it for the benefit other legumes.

In theory "altruistic punishment" (paying some cost or taking some risk to punish noncooperators) could help explain why there is more cooperation among unrelated humans than might otherwise be expected. (Cooperation among relatives is explained by kin selection.) But how much are individuals willing to pay to punish noncooperators?
The latest experiments attempting to answer this question were just published on-line in Proceedings of the Royal Society, by Martijn Egas and Arno Riedl: The economics of altruistic punishment and the maintenance of cooperation.

Continue reading "Altruistic punishment? Maybe not." »

November 16, 2007

Communication doesn't automatically prevent cheating

There are enough examples of ‘‘cheating’’ in bacteria ... that mindless obedience to such [quorum-sensing] chemical signals cannot be assumed. Mindlessness can be assumed, but not obedience. -- Denison et al. (2003) Ecology 84:838-845
Millions of cooperating cells can do things far beyond the ability of an individual cell. This is most obvious in multicellular organisms, whose cells cooperate because they are all genetically identical, or nearly so. Genetically diverse populations of cells could often benefit from cooperating, but do they? For example, the mixed bacteria populations associated with plant roots might benefit from keeping the plant healthy, so that it can continue to feed them with its root exudates. But for this to happen, they need some method of coordinating their plant-benefiting activities. Furthermore, cells whose genes lead to this form of cooperation must, on average, survive and reproduce more than "cheaters" who don't invest in cooperative activities. Otherwise, cooperative traits will disappear.

Quorum sensing, an exchange of chemical signals among bacteria, can solve the coordination problem. But this week's paper Cooperation and conflict in quorum-sensing bacterial populations shows that quorum sensing doesn't automatically solve the problem of cheaters. The paper is by Stephen Diggle, Ashleigh Griffin, Genevieve Campbell, and Stuart West and published in Nature.

Continue reading "Communication doesn't automatically prevent cheating" »

October 11, 2007

Evolution of language

Ed Yong beat me again, this time discussing an interesting paper in Nature on the evolution of language, but I'm going to comment anyway. Actually, there are two papers in the same issue, both showing that frequently used words change more slowly. For example, irregular past tenses of rarely-used verbs (bide, delve, etc.) have tended to disappear, but we still say "came and saw" not "goed and seed." Lieberman et al. (Nature 449:713) note that:

It is much rarer for regular verbs to become irregular: for every ‘sneak’ that ‘snuck’ in there are many more ‘flews’ that ‘flied’ out.

I bet this is also true of less-used definitions of words and of collective nouns: a group of football players will still be a "team" long after a "bouquet" of pheasants has become a "flock" and then a "group."

Languages evolve, but analogies with evolution of genes may be misleading. Genes pass only from parent(s) to offspring and their frequency changes over generations. Words and ideas can spread much more rapidly, including from child to parent. Cultural evolution seems more analogous to the spread of viruses, only some of which come from our parents.

Some ideas (e.g., religions) come packaged with explicit instructions to proselytize, like the rabies virus making its victims bite others. But the desire to spread our tastes in music, for example, seems intrinsic to us, not to the music. So cultural evolution seems similar enough to epidemiology that analogies will sometimes be useful, but only sometimes.

September 20, 2007

Menopause trade-offs

Why do women, in contrast to our closest relatives, stop giving birth while they are still relatively young and healthy? This week's paper. "Testing Evolutionary Theories of Menopause", by Daryl Shanley and coauthors, published in Proceedings of the Royal Society, uses data from people living in The Gambia to test two different hypotheses.

Continue reading "Menopause trade-offs" »

September 15, 2007

The pirate code

R_RRR R_!R_!R!!_R!R !R!!_!!_R!R_! !R !RR!_!!_!R!_!R_R_! !!_!!! !!R!_!!_R!_! R!!!_!!R_R R_!!!!_!!_!!! R!R!_RRR_R!!_! RRR_!RR!_! R!_!!! R_!!!!_! !RR!_RRR_!R!_R_!!!!_RRR_!R!!_! R_RRR !R_!!!R_!R_!!!_R !RR_RRR_!R!_!R!!_R!! RRR_!!R! !RR!_!!_!R!_!R_R_! !R!_!R_R!!_!!_RRR !RR_!!_R_!!!! !R_R!!_R!!_!!_R_!!_RRR_R!_!R_!R!! !_R!_R!R!_!R!_R!RR_!RR!_R_!!_RRR_R! !!_ !!R! R_!_!_R!!_!_R!!

August 29, 2007

Selfish sperm cells

Usually, those alleles (versions of a gene) that become more common over generations are those that are most beneficial to the organisms in whose cells they live. But not always.

The latest issue of PLoS Biology has an open-access article on a particularly selfish gene responsible for Apert syndrome in humans.

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August 3, 2007

Left behind: social amoebae

This week's paper, published in Science (317:679) is "Immune-like phagocyte activity in the social amoeba" by Guokai Chen, Olga Zhuchenko, and Adam Kuspa of the Baylor College of Medicine.

Cells of the social amoeba, Dictyostyleium discoideum forage individually, but eventually group together into a "slug", which crawls through the soil for days before eventually forming a spore-tipped stalk. Previous work with this species has looked at conflicts of interest over which cells have to sacrifice future reproduction (as spores) and become part of the stalk. This week's paper uncovers another example of apparent altruism in Dictyostelium, which may shed light on the evolution of a key part of our immune system.

As a Dictyostelium slug crawls through the soil, some cells are left behind. Are these just random sluggards? Or do they function like human phagocytes, the immune system cells that gobble up bacteria?

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June 30, 2007

Tracing the spread of agriculture with stone-age human DNA

This week's paper is "Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe" by M.L. Sampietro and others, published online in Proceedings of the Royal Society. The paper is interesting both for its findings and for its methods.

We know that agriculture spread from the Near East -- do people in Asia call this the Near West? -- to western Europe, starting around 10,000 years ago. But did this mostly involve farmers moving, or the spread of agriculture without major movement of people?

People have tried to figure out past population movements using genetic differences among modern populations, but it would help to have genetic information from people who lived thousands of years ago, as well. This is technically challenging, however...

Continue reading "Tracing the spread of agriculture with stone-age human DNA" »

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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May 2, 2007


What did our early ancestors and related species eat? Different data seemed to give different answers. This week’s paper may have helped to solve this mystery.

Isotope data suggest that tropical grasses were a big part of the diet of the hominins Australopithecus africanus and Paranthropus robustus. These grasses have CO2-concentrating C4 photosynthesis. As a result, they have a little more of the rare carbon-13 isotope, and a little less C12, relative to most other plants. So do the fossil teeth of these early human relatives, as if they ate these grasses. But the shape of their teeth, and wear patterns, are wrong if they mostly ate grass leaves or animals that ate grass. What about roots, or underground storage organs? These are an important food for some human foragers today, especially in dry climates. If our early relatives mostly ate these “USOs?, then the isotope ratios in their teeth should be like those of other species with a similar diet. Mole rats, for example.

Continue reading "Roots" »

April 17, 2007

Darwinian agriculture II

Last week, I was at a meeting in the Netherlands on "Darwinian agriculture: the evolutionary ecology of agricultural symbiosis." Topics included: the effects of cows on human evolution, the independent invention of "agriculture" by ants and termites, and some disadvantages of diversity. As promised, here are a few highlights.

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March 27, 2007

Evolution of color vision: transgenic mice see red

This week’s paper, "Emergence of novel color vision in mice engineered to express human cone pigment", by Gerald Jacobs and colleagues at UC Santa Barbara and Johns Hopkins Medical School (Science 315:1723), is yet another experimental study that increases our understanding of how repeated cycles of natural selection, each producing a fairly small change, can lead to adaptations that may seem irreducibly complex.

Most humans have three different photopigment color sensors, as do our closest relatives. Many other mammals, including mice, have only two. Three-color vision is useful for many purposes, from identifying higher-protein leaves to eat (Nature 410:363) to telling which wire to cut to disarm the nuclear bomb buried under the stadium. But eventual usefulness isn’t enough for a trait to evolve. If a series of steps is required, each step must be beneficial, or at least not lethal. Such a series of steps has been worked out for the evolution of optically sophisticated eyes from light-sensitive spots (Proc. Roy. Soc. B 256:53), but what about color vision?

Continue reading "Evolution of color vision: transgenic mice see red" »