CiteULike: marimo's method_model

From The Cover: Evolutionary cycles of cooperation and defection.

LA Imhof — 2005-08-30T19:49:35-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 31. (2 August 2005), pp. 10797-10800.

The main obstacle for the evolution of cooperation is that natural selection favors defection in most settings. In the repeated prisoner's dilemma, two individuals interact several times, and, in each round, they have a choice between cooperation and defection. We analyze the evolutionary dynamics of three simple strategies for the repeated prisoner's dilemma: always defect (ALLD), always cooperate (ALLC), and tit-for-tat (TFT). We study mutation-selection dynamics in finite populations. Despite ALLD being the only strict Nash equilibrium, we observe evolutionary oscillations among all three strategies. The population cycles from ALLD to TFT to ALLC and back to ALLD. Most surprisingly, the time average of these oscillations can be entirely concentrated on TFT. In contrast to the classical expectation, which is informed by deterministic evolutionary game theory of infinitely large populations, stochastic evolution of finite populations need not choose the strict Nash equilibrium and can therefore favor cooperation over defection.

Complementary sex determination substantially increases extinction proneness of haplodiploid populations.

A Zayed — 2005-08-17T09:26:10-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 30. (26 July 2005), pp. 10742-10746.

The role of genetic factors in extinction is firmly established for diploid organisms, but haplodiploids have been considered immune to genetic load impacts because deleterious alleles are readily purged in haploid males. However, we show that single-locus complementary sex determination ancestral to the haplodiploid Hymenoptera (ants, bees, and wasps) imposes a substantial genetic load through homozygosity at the sex locus that results in the production of inviable or sterile diploid males. Using stochastic modeling, we have discovered that diploid male production (DMP) can initiate a rapid and previously uncharacterized extinction vortex. The extinction rate in haplodiploid populations with DMP is an order of magnitude greater than in its absence under realistic but conservative demographic parameter values. Furthermore, DMP alone can elevate the base extinction risk in haplodiploids by over an order of magnitude higher than that caused by inbreeding depression in threatened diploids. Thus, contrary to previous expectations, haplodiploids are more, rather than less, prone to extinction for genetic reasons. Our findings necessitate a fundamental shift in approaches to the conservation and population biology of these ecologically and economically crucial insects.

Analyzing a bioterror attack on the food supply: the case of botulinum toxin in milk.

LM Wein — 2005-08-17T08:56:08-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 28. (12 July 2005), pp. 9984-9989.

We developed a mathematical model of a cows-to-consumers supply chain associated with a single milk-processing facility that is the victim of a deliberate release of botulinum toxin. Because centralized storage and processing lead to substantial dilution of the toxin, a minimum amount of toxin is required for the release to do damage. Irreducible uncertainties regarding the dose-response curve prevent us from quantifying the minimum effective release. However, if terrorists can obtain enough toxin, and this may well be possible, then rapid distribution and consumption result in several hundred thousand poisoned individuals if detection from early symptomatics is not timely. Timely and specific in-process testing has the potential to eliminate the threat of this scenario at a cost of <1 cent per gallon and should be pursued aggressively. Investigation of improving the toxin inactivation rate of heat pasteurization without sacrificing taste or nutrition is warranted.

Estimating the total genetic diversity of a spatial field population from a sample and implications of its dependence on habitat area.

EM Rauch — 2005-08-17T08:53:00-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 28. (12 July 2005), pp. 9826-9829.

The total genetic diversity of a species is a key factor in its persistence and conservation. Because realistic sample sizes are far smaller than the total population, it is impractical to exhaustively characterize diversity of most populations. Here, we demonstrate the possibility of calculating the genetic diversity of a spatial population from a sample using genealogical models. We trace the history of a population by simulating the locations of the ancestors of a particular sample of the population backwards in time. We use this method to estimate the genetic diversity of the global population of Pseudomonas bacteria. The same results are obtained whether using a global sample or a subsample restricted to a particular geographic region (California). The results are also validated by comparing additional predictions of the model to the data. Furthermore, we use these results to show that the level of genetic diversity in a population depends strongly on the size of its habitat, much more strongly than does biodiversity as measured by the number of species. The strong dependence of diversity on habitat area has significant implications for conservation strategies.

Coevolutionary arms races between bacteria and bacteriophage.

JS Weitz — 2005-08-17T08:39:02-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 27. (5 July 2005), pp. 9535-9540.

We propose a computational and theoretical framework for analyzing rapid coevolutionary dynamics of bacteriophage and bacteria in their ecological context. Bacteriophage enter host cells via membrane-bound surface receptors often responsible for nutrient uptake. As such, a selective pressure will exist for the bacteria to modify its receptor configuration and, in turn, for the phage to modify its tail fiber. A mathematical model of these trait adaptations is developed by using the framework of adaptive dynamics. Host strains differ in their efficiency of resource uptake and resistance to phage, whereas phage strains differ in their host preference for adsorption. We solve the evolutionary ecology model and find the conditions for coevolutionary branching and relevant dimensionless parameters leading to distinct quasispecies. We confirm these calculations using stochastic Monte Carlo simulations of populations evolving in a chemostat with fixed washout rate and inflow resource density. We find that multiple quasispecies of bacteria and phage can coexist in a homogeneous medium with a single resource. When diversification occurs, quasispecies of phage adsorb effectively to only a limited subset of the total number of quasispecies of bacteria, i.e., functional differences between quasispecies arise endogenously within the evolutionary ecology framework. Finally, we discuss means to relate predictions of this model to experimental studies in the chemostat, using the model organisms Escherichia coli and the virulent strain of lambda phage.

Plant coexistence depends on ecosystem nutrient cycles: extension of the resource-ratio theory.

T Daufresne — 2005-08-17T08:19:09-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 26. (28 June 2005), pp. 9212-9217.

We present a model of plant-nutrient interactions that extends classical resource competition theory to environments in which essential nutrients (resources) are recycled between plant and soil pools and dissolved nutrients are lost through plant-available (i.e., inorganic forms) or plant-unavailable (i.e., complex organic forms) pathways. Losses by dissolved organic pathways can alter ratios of nutrients that are recycled and supplied within the plant-soil system, thereby influencing competition and coexistence among plant species. In special cases, our extended model does not differ from classical models, but in more realistic cases our model introduces new dynamical behavior that influences competitive outcomes. At equilibrium, coexistence still depends on nutrient supply and consumption, but nutrient supply includes recycling and is highly sensitive to whether a species promotes more organic losses of the nutrient that limits its own growth than of nutrients that limit its competitors. Because recycling operates with a time delay compared with consumption, recycling-mediated effects on competition can, under certain conditions, lead to sustained population oscillations. Our findings have implications for how we understand nutrient competition, nutrient cycles, and plant evolutionary strategies.

Climate change threats to plant diversity in Europe.

W Thuiller — 2005-08-17T07:35:29-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 23. (7 June 2005), pp. 8245-8250.

Climate change has already triggered species distribution shifts in many parts of the world. Increasing impacts are expected for the future, yet few studies have aimed for a general understanding of the regional basis for species vulnerability. We projected late 21st century distributions for 1,350 European plants species under seven climate change scenarios. Application of the International Union for Conservation of Nature and Natural Resources Red List criteria to our projections shows that many European plant species could become severely threatened. More than half of the species we studied could be vulnerable or threatened by 2080. Expected species loss and turnover per pixel proved to be highly variable across scenarios (27-42% and 45-63% respectively, averaged over Europe) and across regions (2.5-86% and 17-86%, averaged over scenarios). Modeled species loss and turnover were found to depend strongly on the degree of change in just two climate variables describing temperature and moisture conditions. Despite the coarse scale of the analysis, species from mountains could be seen to be disproportionably sensitive to climate change (approximately 60% species loss). The boreal region was projected to lose few species, although gaining many others from immigration. The greatest changes are expected in the transition between the Mediterranean and Euro-Siberian regions. We found that risks of extinction for European plants may be large, even in moderate scenarios of climate change and despite inter-model variability.

Foliage shedding in deciduous forests lifts up long-distance seed dispersal by wind.

R Nathan — 2005-08-17T06:57:38-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 23. (7 June 2005), pp. 8251-8256.

Seed terminal velocity and release height are recognized as key biotic determinants of long-distance dispersal (LDD) of seeds by wind. Yet, potential determinants at the ecosystem level, such as seasonal dynamics in foliage density characterizing many deciduous forests, have received much less attention. We integrated detailed field observations and experiments with a mechanistic wind dispersal model to assess how seasonal variation in foliage density, estimated by leaf-area index (LAI), affects LDD in deciduous forests. We found that the model, previously shown to accurately predict seed dispersal by wind, also reliably describes the effects of LAI variation on wind statistics for a wide range of canopy types. Sparser canopies are characterized by more organized vertical eddy motion that promotes LDD by uplifting seeds to higher elevations where winds are stronger. Yet, sparser canopies are also characterized by reduced mean windspeed aloft. We showed that former effect more than compensates for the latter, i.e., conditions of low LAI are favorable for LDD. This may account for the tendency of many temperate tree species to restrict seed release to either early spring or late fall, when LAI is relatively low. Sensitivity analysis reveals that the typical seasonal variation in LAI can be more important to LDD of seeds by wind than the natural variation in seed terminal velocity. Because our model accurately describes the effects of LAI variation for distinctly different sites, species, and life forms, we suggest that its results reflect a general association between LDD and foliage density dynamics.

Altruistic punishment and the origin of cooperation.

JH Fowler — 2005-08-17T06:03:44-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 7047-7049.

How did human cooperation evolve? Recent evidence shows that many people are willing to engage in altruistic punishment, voluntarily paying a cost to punish noncooperators. Although this behavior helps to explain how cooperation can persist, it creates an important puzzle. If altruistic punishment provides benefits to nonpunishers and is costly to punishers, then how could it evolve? Drawing on recent insights from voluntary public goods games, I present a simple evolutionary model in which altruistic punishers can enter and will always come to dominate a population of contributors, defectors, and nonparticipants. The model suggests that the cycle of strategies in voluntary public goods games does not persist in the presence of punishment strategies. It also suggests that punishment can only enforce payoff-improving strategies, contrary to a widely cited "folk theorem" result that suggests that punishment can allow the evolution of any strategy.