Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations.

Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (~1000 ind.), suggesting that the evolutionary potential of the species is not assured.

Charring temperatures are driven by the fuel types burned in a peatland wildfire.

Peatlands represent a globally important carbon store; however, the human exploitation of this ecosystem is increasing both the frequency and severity of fires on drained peatlands. Yet, the interactions between the hydrological conditions (ecotopes), the fuel types being burned, the burn severity, and the charring temperatures (pyrolysis intensity) remain poorly understood. Here we present a post-burn assessment of a fire on a lowland raised bog in Co. Offaly, Ireland (All Saints Bog). Three burn severities were identified in the field (light, moderate, and deeply burned), and surface charcoals were taken from 17 sites across all burn severities. Charcoals were classified into two fuel type categories (either ground or aboveground fuel) and the reflectance of each charcoal particle was measured under oil using reflectance microscopy. Charcoal reflectance shows a positive relationship with charring temperature and as such can be used as a temperature proxy to reconstruct minimum charring temperatures after a fire event. Resulting median reflectance values for ground fuels are 1.09 ± 0.32%Romedian, corresponding to estimated minimum charring temperatures of 447°C ± 49°C. In contrast, the median charring temperatures of aboveground fuels were found to be considerably higher, 646°C ± 73°C (3.58 ± 0.77%Romedian). A mixed-effects modeling approach was used to demonstrate that the interaction effects of burn severity, as well as ecotope classes, on the charcoal reflectance is small compared to the main effect of fuel type. Our findings reveal that the different fuel types on raised bogs are capable of charring at different temperatures within the same fire, and that the pyrolysis intensity of the fire on All Saints Bog was primarily driven by the fuel types burning, with only a weak association to the burn severity or ecotope classes.

The effect of collective dispersal on the genetic structure of a subdivided population.

Correlated dispersal paths between two or more individuals are widespread across many taxa. The population genetic implications of this collective dispersal have received relatively little attention. Here we develop two-sample coalescent theory that incorporates collective dispersal in a finite island model to predict expected coalescence times, genetic diversities, and F-statistics. We show that collective dispersal reduces mixing in the system, which decreases expected coalescence times and increases FST . The effects are strongest in systems with high migration rates. Collective dispersal breaks the invariance of within-deme coalescence times to migration rate, whatever the deme size. It can also cause FST to increase with migration rate because the ratio of within- to between-deme coalescence times can decrease as migration rate approaches unity. This effect is most biologically relevant when deme size is small. We find qualitatively similar results for diploid and gametic dispersal. We also demonstrate with simulations and analytical theory the strong similarity between the effects of collective dispersal and anisotropic dispersal. These findings have implications for our understanding of the balance between drift-migration-mutation in models of neutral evolution. This has applied consequences for the interpretation of genetic structure (e.g., chaotic genetic patchiness) and estimation of migration rates from genetic data.

Genetic drift and collective dispersal can result in chaotic genetic patchiness.

Chaotic genetic patchiness denotes unexpected patterns of genetic differentiation that are observed at a fine scale and are not stable in time. These patterns have been described in marine species with free-living larvae, but are unexpected because they occur at a scale below the dispersal range of pelagic larvae. At the scale where most larvae are immigrants, theory predicts spatially homogeneous, temporally stable genetic variation. Empirical studies have suggested that genetic drift interacts with complex dispersal patterns to create chaotic genetic patchiness. Here we use a co-ancestry model and individual-based simulations to test this idea. We found that chaotic genetic patterns (qualified by global FST and spatio-temporal variation in FST's between pairs of samples) arise from the combined effects of (1) genetic drift created by the small local effective population sizes of the sessile phase and variance in contribution among breeding groups and (2) collective dispersal of related individuals in the larval phase. Simulations show that patchiness levels qualitatively comparable to empirical results can be produced by a combination of strong variance in reproductive success and mild collective dispersal. These results call for empirical studies of the effective number of breeders producing larval cohorts, and population genetics at the larval stage.

Baseline intrinsic flammability of Earth's ecosystems estimated from paleoatmospheric oxygen over the past 350 million years.

Atmospheric oxygen (O(2)) is estimated to have varied greatly throughout Earth's history and has been capable of influencing wildfire activity wherever fuel and ignition sources were present. Fires consume huge quantities of biomass in all ecosystems and play an important role in biogeochemical cycles. This means that understanding the influence of O(2) on past fire activity has far-reaching consequences for the evolution of life and Earth's biodiversity over geological timescales. We have used a strong electrical ignition source to ignite smoldering fires, and we measured their self-sustaining propagation in atmospheres of different oxygen concentrations. These data have been used to build a model that we use to estimate the baseline intrinsic flammability of Earth's ecosystems according to variations in O(2) over the past 350 million years (Ma). Our aim is to highlight times in Earth's history when fire has been capable of influencing the Earth system. We reveal that fire activity would be greatly suppressed below 18.5% O(2), entirely switched off below 16% O(2), and rapidly enhanced between 19-22% O(2). We show that fire activity and, therefore, its influence on the Earth system would have been high during the Carboniferous (350-300 Ma) and Cretaceous (145-65 Ma) periods; intermediate in the Permian (299-251 Ma), Late Triassic (285-201 Ma), and Jurassic (201-145 Ma) periods; and surprisingly low to lacking in the Early-Middle Triassic period between 250-240 Ma. These baseline variations in Earth's flammability must be factored into our understanding of past vegetation, biodiversity, evolution, and biogeochemical cycles.

Predicting the effects of body fatness on food intake and performance of sheep.

Adipose tissue produces signals that can have a profound effect on many physiological functions, including energy expenditure and food intake. The hypothesis that variation in food intake of sheep resulting from differences in animal fatness can be predicted from effects of animal fatness on energetic efficiency was subjected to three tests. First, an existing food intake model was adapted to account for effects of animal fatness, as estimated by condition score, on food intake. Parameter values were derived from data obtained with two of five treatment groups of an experiment where ewe lambs were fed either chopped hay or pelleted concentrates. The model predicted the intake of the remaining three treatment groups satisfactorily. The energy intake model was subsequently extended with a protein module based upon a Gompertz curve to simulate changes in body weight and condition score. The model predicted these changes satisfactorily for most treatment groups during the experimental period of 50 weeks. In a last test, the final body weights and body lipid contents of animals fed either hay or concentrates for a period of 3 years were predicted. The predictions for final body weight (77 or 118 kg) and lipid content in the empty body (26 or 58 %) were within the range of expectations for sheep with access to hay or concentrates, respectively. The biological implications of the hypothesis that body fatness acts upon voluntary intake via its effects on energetic efficiency are discussed.

Associations between basal metabolic rate and reproductive performance in C57BL/6J mice.

Basal metabolic rate (BMR) is highly variable, both between and within species. One hypothesis is that this variation may be linked to the capacity for sustained rate of energy expenditure, leading to associations between high BMR and performance during energy-demanding periods of life history, such as reproduction. However, despite the attractive nature of this hypothesis, previous studies have failed to show an association between BMR and fecundity. Our approach was to mate 304 C57BL/6J mice and allow them to wean pups before measuring BMR by indirect calorimetry. We did not find an association between BMR and litter mass, size or pup mass at birth or weaning that could not be accounted for by the body mass of the dam. There was also no relationship between BMR (or BMR corrected for body mass) and birth or weaning success, losses during weaning, or sex ratio. However, a significant relationship was found between BMR and gestational weight loss indicative of foetal resorption. This suggests that during pregnancy the available energy may be limited and partitioned away from the growing foetus and towards maintenance of the mother. In this context, a high BMR may actually be disadvantageous, conflicting with the idea that high BMR may bring reproductive benefits.

Transient population dynamics in periodic matrix models: methodology and effects of cyclic permutations.

Many biological populations are subject to periodically changing environments such as years with or without fire, or rotation of crop types. The dynamics and management options for such populations are frequently investigated using periodic matrix models. However the analysis is usually limited to long-term results (asymptotic population growth rate and its sensitivity to perturbations of vital rates). In non-periodic matrix models it has been shown that long-term results may be misleading as populations are rarely in their stable structure. We therefore develop methods to analyze transient dynamics of periodic matrix models. In particular, we show how to calculate the effects of perturbations on population size within and at the end of environmental cycles. Using a model of a weed population subject to a crop rotation, we show that different cyclic permutations produce different patterns of sensitivity of population size and different population sizes. By examining how the starting environment interacts with the initial conditions, we explain how different patterns arise. Such understanding is critical to developing effective management and monitoring strategies for populations subject to periodically recurring environments.

A theory of associating food types with their postingestive consequences.

Animals often face complex and changing food environments. While such environments are challenging, an animal should make an association between a food type and its properties (such as the presence of a nutrient or toxin). We use information theory concepts, such as mutual information, to establish a theory for the development of these associations. In this theory, associations are assumed to maximize the mutual information between foods and their consequences. We show that associations are invariably imperfect. An association's accuracy increases with the length of a feeding session and the relative frequency of a food type but decreases as time delay between consumption and postingestive consequence increases. Surprisingly, the accuracy of an association is independent of the number of additional food types in the environment. The rate of information transfer between novel foods and a forager depends on the forager's diet. In light of this theory, an animal's diet may have two competing goals: first, the provision of an appropriate balance of nutrients, and second, the ability to quickly and accurately learn the properties of novel foods. We discuss the ecological and behavioral implications of making associational errors and contrast the timescale and mechanisms of our theory with those of existing theory.

A life history model of somatic damage associated with resource acquisition: damage protection or prevention?

A resource acquisition-allocation model is developed to examine the trade-off between reproduction and somatic protection. Unlike previous studies, resource intake is not assumed to be constrained: instead, resource intake is free to vary, with increased intake being associated with an increased risk of somatic damage. This gives rise to an optimal resource intake as well as an optimal allocation strategy. This paper studies the relative importance of acquisition and allocation strategies in regulating acquisition-related mortality. Under the optimal allocation strategy mortality rate increases with age, in accordance with the disposable soma theory of aging. Contrary to the usual interpretation of the disposable soma theory, this increase in mortality can arise from an increase in the resource acquisition effort rather than a decrease in the resources allocated to protection. At early ages resource acquisition is found to be the primary path for regulating life history costs, whilst allocating resources to protection becomes more important later in life. Models for targeted and non-targeted damage repair are considered and the robustness of our results to the structure and parameterization of the model is discussed. The results from our models are discussed in light of published data. Resource acquisition is shown to be a potentially important mechanism for controlling somatic damage which deserves further study.

Optimal diet selection, frequency dependence and prey renewal.

This paper extends existing models of frequency-dependent diet selection by considering the optimal diet selection of a predator feeding upon prey populations which can be depleted but are also capable of renewal (e.g. immigration, growth, or reproduction). This model and existing models which include prey depletion, predict partial-preference and a generic diet preference for the commonest prey types (apostatic selection). Unlike previous diet selection models, it is found that the optimal diet selection of an individual predator can be to favour the rarest prey type (anti-apostatic selection) when encounter rates are high, even if the individual prey do not differ in their nutritional value. Studies have demonstrated that predators generally show apostatic selection, even when all prey have the same nutritional value. Anti-apostatic selection has also been observed when prey are crowded, and therefore at high density, consistent with the idea of high encounter rates. This anti-apostatic diet selection has previously been proposed as evidence for the use of prey search images by a predator, or variation in individual prey preference. In this paper it is suggested that prey renewal is a further factor, often confounded in experiments, which could favour anti-apostatic selection.

Equivalence relationships between stage-structured population models.

Matrix population models are widely applied in conservation ecology to help predict future population trends and guide conservation effort. Researchers must decide upon an appropriate level of model complexity, yet there is little theoretical work to guide such decisions. In this paper we present an analysis of a stage-structured model, and prove that the model's structure can be simplified and parameterised in such a way that the long-term growth rate, the stable-stage distribution and the generation time are all invariant to the simplification. We further show that for certain structures of model the simplified models require less effort in data collection. We also discuss features of the models which are not invariant to the simplification and the implications of our results for the selection of an appropriate model. We illustrate the ideas using a population model for short-tailed shearwaters (Puffinus tenuirostris). In this example, model simplification can increase parameter elasticity, indicating that an intermediate level of complexity is likely to be preferred.