Selection on sporulation strategies in a metapopulation can lead to coexistence.

In constant environments the coexistence of similar species or genotypes is generally limited. In a metapopulation context, however, types that utilize the same resource but are distributed along a competition-colonization trade-off, can coexist. Much thought in this area focuses on a generic trade-off between within-deme competitive ability and between-deme dispersal ability.

Ancient Secretory Pathways Contributed to the Evolutionary Origin of an Ecologically Impactful Bioluminescence System.

Evolutionary innovations in chemical secretion-such as the production of secondary metabolites, pheromones, and toxins-profoundly impact ecological interactions across a broad diversity of life. These secretory innovations may involve a "legacy-plus-innovation" mode of evolution, whereby new biochemical pathways are integrated with conserved secretory processes to create novel products. Among secretory innovations, bioluminescence is important because it evolved convergently many times to influence predator-prey interactions, while often producing courtship signals linked to increased rates of speciation.

Modeling the metabolic evolution of mixotrophic phytoplankton in response to rising ocean surface temperatures.

Background: Climate change is expected to lead to warming in ocean surface temperatures which will have unequal effects on the rates of photosynthesis and heterotrophy. As a result of this changing metabolic landscape, directional phenotypic evolution will occur, with implications that cascade up to the ecosystem level. While mixotrophic phytoplankton, organisms that combine photosynthesis and heterotrophy to meet their energetic and nutritional needs, are expected to become more heterotrophic with warmer temperatures due to heterotrophy increasing at a faster rate than photosynthesis, it is unclear how evolution will influence how these organisms respond to warmer temperatures.

Selection on modifiers of genetic architecture under migration load.

Gene flow between populations adapting to differing local environmental conditions might be costly because individuals can disperse to habitats where their survival is low or because they can reproduce with locally maladapted individuals. The amount by which the mean relative population fitness is kept below one creates an opportunity for modifiers of the genetic architecture to spread due to selection. Prior work that separately considered modifiers changing dispersal, recombination rates, or altering dominance or epistasis, has typically focused on the direction of selection rather than its absolute magnitude.

Testing the adaptive value of sporulation in budding yeast using experimental evolution.

Saccharomyces yeast grow through mitotic cell division, converting resources into biomass. When cells experience starvation, sporulation is initiated and meiosis produces haploid cells inside a protective ascus. The protected spore state does not acquire resources and is partially protected from desiccation, heat, and caustic chemicals.

How differing modes of non-genetic inheritance affect population viability in fluctuating environments.

Different modes of non-genetic inheritance are expected to affect population persistence in fluctuating environments. We here analyse Caenorhabditis elegans density-independent per capita growth rate time series on 36 populations experiencing six controlled sequences of challenging oxygen level fluctuations across 60 generations, and parameterise competing models of non-genetic inheritance in order to explain observed dynamics. Our analysis shows that phenotypic plasticity and anticipatory maternal effects are sufficient to explain growth rate dynamics, but that a carryover model where 'epigenetic' memory is imperfectly transmitted and might be reset at each generation is a better fit to the data.

Partial Selfing Can Reduce Genetic Loads While Maintaining Diversity During Experimental Evolution.

Partial selfing, whereby self- and cross- fertilization occur in populations at intermediate frequencies, is generally thought to be evolutionarily unstable. Yet, it is found in natural populations. This could be explained if populations with partial selfing are able to reduce genetic loads and the possibility for inbreeding depression while keeping genetic diversity that may be important for future adaptation.

Slower environmental change hinders adaptation from standing genetic variation.

Evolutionary responses to environmental change depend on the time available for adaptation before environmental degradation leads to extinction. Explicit tests of this relationship are limited to microbes where adaptation usually depends on the sequential fixation of de novo mutations, excluding standing variation for genotype-by-environment fitness interactions that should be key for most natural species. For natural species evolving from standing genetic variation, adaptation at slower rates of environmental change may be impeded since the best genotypes at the most extreme environments can be lost during evolution due to genetic drift or founder effects.

What Kind of Maternal Effects Can Be Selected For in Fluctuating Environments?

Just as phenotypic plasticity can evolve when developing individuals get informational cues about their future adult environment, deterministic maternal effects, where offspring trait values depend on the maternal environment, can evolve when mothers gain reliable information about the environments their offspring will face. Randomizing maternal effects (a type of diversifying bet hedging), where offspring trait values are randomized, can evolve by natural selection even when information about future environments is unavailable. We investigate selection on both randomizing and deterministic maternal effects in environments that show correlated fluctuations between two environmental states.

Adaptation to Temporally Fluctuating Environments by the Evolution of Maternal Effects.

All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e.

Migration-selection balance at multiple Loci and selection on dominance and recombination.

A steady influx of a single deleterious multilocus genotype will impose genetic load on the resident population and leave multiple descendants carrying various numbers of the foreign alleles. Provided that the foreign types are rare at equilibrium, and all immigrant genes are eventually eliminated by selection, the population structure can be inferred explicitly from the branching process taking place within a single immigrant lineage. Unless the migration and recombination rates were high, this novel method gives a close approximation to the simulation with all possible multilocus genotypes considered.

Evolution of transcription networks in response to temporal fluctuations.

Organisms respond to changes in their environment over a wide range of biological and temporal scales. Such phenotypic plasticity can involve developmental, behavioral, physiological, and genetic shifts. The adaptive value of a plastic response is known to depend on the nature of the information that is available to the organism as well as the direct and indirect costs of the plastic response.

Multiple routes to subfunctionalization and gene duplicate specialization.

Gene duplication is arguably the most significant source of new functional genetic material. A better understanding of the processes that lead to the stable incorporation of gene duplications into the genome is important both because it relates to interspecific differences in genome composition and because it can shed light on why some classes of gene are more prone to duplication than others. Typically, models of gene duplication consider the periods before duplication, during the spread and fixation of a new duplicate, and following duplication as distinct phases without a common underlying selective environment.

The rate of multi-step evolution in Moran and Wright-Fisher populations.

Several groups have recently modeled evolutionary transitions from an ancestral allele to a beneficial allele separated by one or more intervening mutants. The beneficial allele can become fixed if a succession of intermediate mutants are fixed or alternatively if successive mutants arise while the previous intermediate mutant is still segregating. This latter process has been termed stochastic tunneling.

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences.

Background: The reptiles, characterized by both diversity and unique evolutionary adaptations, provide a comprehensive system for comparative studies of metabolism, physiology, and development. However, molecular resources for ectothermic reptiles are severely limited, hampering our ability to study the genetic basis for many evolutionarily important traits such as metabolic plasticity, extreme longevity, limblessness, venom, and freeze tolerance. Here we use massively parallel sequencing (454 GS-FLX Titanium) to generate a transcriptome of the western terrestrial garter snake (Thamnophis elegans) with two goals in mind.

The evolutionary origins of gene regulation.

One way that organisms cope with constantly changing physical and biological conditions is by regulating the expression of genes and thereby altering protein production. Clearly, altering the protein production to match the environmental demands can be adaptive, but there may be evolutionary barriers to the transition from constitutive expression to regulated expression. In particular, down-regulating a gene when it is not needed means that there will necessarily be a delay in protein production when the protein is up-regulated in the future.

Sex allocation based on relative and absolute condition.

Traditional models predict that organisms should allocate to sex based on their condition relative to the condition of their competitors, tracking shifts in mean condition in fluctuating environments, and maintaining an equilibrium sex ratio. In contrast, when individuals are constrained to define their condition absolutely, environmental fluctuations induce fluctuating sex ratios and the evolutionary loss of condition-dependent sex allocation in short-lived organisms. Here, we present a simulation model of temperature-dependent sex determination (TSD) in fluctuating environments that specifically examines the importance of relativity in defining individual condition.

Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants.

Transposable elements, particularly LTR-retrotransposons, comprise the primary vehicle for genome size expansion in plants, while DNA removal through illegitimate recombination and intrastrand homologous recombination serve as the most important counteracting forces to plant genomic obesity. Despite extensive research, the relative impact of these opposing forces and hence the directionality of genome size change remains unknown. In Gossypium (cotton), the 3-fold genome size variation among diploids is due largely to copy number variation of the gypsy-like retrotransposon Gorge3.

Gene expression dynamics in randomly varying environments.

A simple model of gene regulation in response to stochastically changing environmental conditions is developed and analyzed. The model consists of a differential equation driven by a continuous time 2-state Markov process. The density function of the resulting process converges to a beta distribution.

Dissecting selection on female mating preferences during secondary contact.

Population-specific preferences involved in premating isolation may be based on several different types of mating cues. Here, we compare the rates of spread of 12 different mating preferences that reflect preferences for local adaptation, male condition, and reinforcement. We introduce methods to dissect the components of the rate of spread to determine why certain mating preferences spread more quickly than others.

Mutual information reveals variation in temperature-dependent sex determination in response to environmental fluctuation, lifespan and selection.

Quantifying the degree to which sex determination depends on the environment can yield insight into the evolution, ecological dynamics, and functional aspects of sex determination. In temperature-dependent sex determination (TSD), theory often predicts a complete dependence of sex on temperature, with a switch-like reaction norm. However, empirical data suggest more shallow relationships between sex and temperature.

Quasi-species evolution in subdivided populations favours maximally deleterious mutations.

Most models of quasi-species evolution predict that populations will evolve to occupy areas of sequence space with the greatest concentration of neutral sequences, thus minimizing the deleterious mutation rate and creating mutationally 'robust' genomes. In contrast, empirical studies of the principal model of quasi-species evolution, RNA viruses, suggest that the effects of deleterious mutations are more severe than in similar DNA-based microbes. We demonstrate that populations divided into discrete patches connected by dispersal may favour genotypes where the deleterious effect of non-neutral mutations is maximized.

Direct selection on genetic robustness revealed in the yeast transcriptome.

Background: Evolutionary theory predicts that organisms should evolve the ability to produce high fitness phenotypes in the face of environmental disturbances (environmental robustness) or genetic mutations (genetic robustness). While several studies have uncovered mechanisms that lead to both environmental and genetic robustness, we have yet to understand why some components of the genome are more robust than others. According to evolutionary theory, environmental and genetic robustness will have different responses to selective forces.

The role of life cycle and migration in selection for variance in offspring number.

For two genotypes that have the same mean number of offspring but differ in the variance in offspring number, naturalselection will favor the genotype with lower variance. In such cases, the average growth rate is not sufficient as a measure of fitness or as a predictor of fixation probability. However, the effect of variance in offspring number on the fixationprobability of mutant strategies has been calculated under several scenarios with the general conclusion that variance in offspring number reduces fitness in proportion to the inverse of the population size [Gillespie, J.

Allelic divergence precedes and promotes gene duplication.

One of the striking observations from recent whole-genome comparisons is that changes in the number of specialized genes in existing gene families, as opposed to novel taxon-specific gene families, are responsible for the majority of the difference in genome composition between major taxa. Previous models of duplicate gene evolution focused primarily on the role that neutral processes can play in evolutionary divergence after the duplicates are already fixed in the population. By instead including the entire cycle of duplication and divergence, we show that specialized functions are most likely to evolve through strong selection acting on segregating alleles at a single locus, even before the duplicate arises.