The role of reservoir species in mediating plague's dynamic response to climate.

The distribution and transmission of Yersinia pestis, the bacterial agent of plague, responds dynamically to climate, both within wildlife reservoirs and human populations. The exact mechanisms mediating plague's response to climate are still poorly understood, particularly across large environmentally heterogeneous regions encompassing several reservoir species. A heterogeneous response to precipitation was observed in plague intensity across northern and southern China during the Third Pandemic. This has been attributed to the response of reservoir species in each region. We use environmental niche modelling and hindcasting methods to test the response of a broad range of reservoir species to precipitation. We find little support for the hypothesis that the response of reservoir species to precipitation mediated the impact of precipitation on plague intensity. We instead observed that precipitation variables were of limited importance in defining species niches and rarely showed the expected response to precipitation across northern and southern China. These findings do not suggest that precipitation-reservoir species dynamics never influence plague intensity but that instead, the response of reservoir species to precipitation across a single biome cannot be assumed and that limited numbers of reservoir species may have a disproportional impact upon plague intensity.

Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe.

Understanding the biological processes involved in genetic differentiation and divergence between populations within species is a pivotal aim in evolutionary biology. One particular phenomenon that requires clarification is the maintenance of genetic barriers despite the high potential for gene flow in the marine environment. Such patterns have been attributed to limited dispersal or local adaptation, and to a lesser extent to the demographic history of the species. The corkwing wrasse (Symphodus melops) is an example of a marine fish species where regions of particular strong divergence are observed. One such genetic break occurred at a surprisingly small spatial scale (FST ~0.1), over a short coastline (<60 km) in the North Sea-Skagerrak transition area in southwestern Norway. Here, we investigate the observed divergence and purported reproductive isolation using genome resequencing. Our results suggest that historical events during the post-glacial recolonization route can explain the present population structure of the corkwing wrasse in the northeast Atlantic. While the divergence across the break is strong, we detected ongoing gene flow between populations over the break suggesting recent contact or negative selection against hybrids. Moreover, we found few outlier loci and no clear genomic regions potentially being under selection. We concluded that neutral processes and random genetic drift e.g., due to founder events during colonization have shaped the population structure in this species in Northern Europe. Our findings underline the need to take into account the demographic process in studies of divergence processes.

Effects of size- and sex-selective harvesting: An integral projection model approach.

Harvesting is often size-selective, and in species with sexual size dimorphism, it may also be sex-selective. A powerful approach to investigate potential consequences of size- and/or sex-selective harvesting is to simulate it in a demographic population model. We developed a population-based integral projection model for a size- and sex-structured species, the commonly exploited pike (Esox lucius). The model allows reproductive success to be proportional to body size and potentially limited by both sexes. We ran all harvest simulations with both lower size limits and slot limits, and to quantify the effects of selective harvesting, we calculated sex ratios and the long-term population growth rate (λ). In addition, we quantified to what degree purely size-selective harvesting was sex-selective, and determined when λ shifted from being female to male limited under size- and sex-selective harvesting. We found that purely size-selective harvest can be sex-selective, and that it depends on the harvest limits and the size distributions of the sexes. For the size- and sex-selective harvest simulations, λ increased with harvest intensity up to a threshold as females limited reproduction. Beyond this threshold, males became the limiting sex, and λ decreased as more males were harvested. The peak in λ, and the corresponding sex ratio in harvest, varied with both the selectivity and the intensity of the harvest simulation. Our model represents a useful extension of size-structured population models as it includes both sexes, relaxes the assumption of female dominance, and accounts for size-dependent fecundity. The consequences of selective harvesting presented here are especially relevant for size- and sex-structured exploited species, such as commercial fisheries. Thus, our model provides a useful contribution toward the development of more sustainable harvesting regimes.

Spatial heterogeneity as a genetic mixing mechanism in highly philopatric colonial seabirds.

How genetic diversity is maintained in philopatric colonial systems remains unclear, and understanding the dynamic balance of philopatry and dispersal at all spatial scales is essential to the study of the evolution of coloniality. In the King penguin, Aptenodytes patagonicus, return rates of post-fledging chicks to their natal sub-colony are remarkably high. Empirical studies have shown that adults return year after year to their previous breeding territories within a radius of a few meters. Yet, little reliable data are available on intra- and inter-colonial dispersal in this species. Here, we present the first fine-scale study of the genetic structure in a king penguin colony in the Crozet Archipelago. Samples were collected from individual chicks and analysed at 8 microsatellite loci. Precise geolocation data of hatching sites and selective pressures associated with habitat features were recorded for all sampling locations. We found that despite strong natal and breeding site fidelity, king penguins retain a high degree of panmixia and genetic diversity. Yet, genetic structure appears markedly heterogeneous across the colony, with higher-than-expected inbreeding levels, and local inbreeding and relatedness hotspots that overlap predicted higher-quality nesting locations. This points towards heterogeneous population structure at the sub-colony level, in which fine-scale environmental features drive local philopatric behaviour, while lower-quality patches may act as genetic mixing mechanisms at the colony level. These findings show how a lack of global genetic structuring can emerge from small-scale heterogeneity in ecological parameters, as opposed to the classical model of homogeneous dispersal. Our results also emphasize the importance of sampling design for estimation of population parameters in colonial seabirds, as at high spatial resolution, basic genetic features are shown to be location-dependent. Finally, this study stresses the importance of understanding intra-colonial dispersal and genetic mixing mechanisms in order to better estimate species-wide gene flows and population dynamics.

Biotic interactions and temporal dynamics of the human gastrointestinal microbiota.

The human gastrointestinal (GI) microbiota is important to human health and imbalances or shifts in the gut microbial community have been linked to many diseases. Most studies of the GI microbiota only capture snapshots of this dynamic community at one or a few time points. Although this is valuable in terms of providing knowledge of community composition and variability between individuals, it does not provide the foundation for going beyond descriptive studies and toward truly predictive ecological models. In order to achieve this goal, we need longitudinal data of appropriate temporal and taxonomic resolution, so that established time series analysis tools for identifying and quantifying putative interactions among community members can be used. Here, we present new analyses of existing data to illustrate the potential usefulness of this approach. We discuss challenges related to sampling and data processing, as well as analytical approaches and considerations for future studies of the GI microbiota and other complex microbial systems.

Twelve years of change in coastal upwelling along the central-northern coast of Chile: spatially heterogeneous responses to climatic variability.

We use time-series analyses to characterize the effects of recent climate variability upon the local physical conditions at 11 study sites along the northern-central coast of Chile (29-34°S). Environmental indices show that the 1° Bakun upwelling index in this coastal region has fluctuated in time, starting from a stable period around the 1980's, peaking during the mid 90s, decreasing during the next ten years and increasing at a steep rate since 2010. Upwelling intensity decreased with increasing latitude, showing also a negative correlation with climate patterns (El Niño3 sea surface temperature-SST anomalies and the Multivariate El Niño Index). We hypothesize that the impacts of climate variability on upwelling events seem to be spatially heterogeneous along the region. Non-sheltered locations and, particularly, sites on prominent headlands show an immediate (lag = 0) and negative correlation between local SST, upwelling events and wind stress. We suggest that near-shore thermal conditions are closely coupled to large-scale forcing of upwelling variability and that this influence is modulated through local topographic factors.

Fundamental population-productivity relationships can be modified through density-dependent feedbacks of life-history evolution.

The evolution of life histories over contemporary time scales will almost certainly affect population demography. One important pathway for such eco-evolutionary interactions is the density-dependent regulation of population dynamics. Here, we investigate how fisheries-induced evolution (FIE) might alter density-dependent population-productivity relationships. To this end, we simulate the eco-evolutionary dynamics of an Atlantic cod (Gadus morhua) population under fishing, followed by a period of recovery in the absence of fishing. FIE is associated with increases in juvenile production, the ratio of juveniles to mature population biomass, and the ratio of the mature population biomass relative to the total population biomass. In contrast, net reproductive rate (R 0 ) and per capita population growth rate (r) decline concomitantly with evolution. Our findings suggest that FIE can substantially modify the fundamental population-productivity relationships that underlie density-dependent population regulation and that form the primary population-dynamical basis for fisheries stock-assessment projections. From a conservation and fisheries-rebuilding perspective, we find that FIE reduces R 0 and r, the two fundamental correlates of population recovery ability and inversely extinction probability.

Predator transitory spillover induces trophic cascades in ecological sinks.

Understanding the effects of cross-system fluxes is fundamental in ecosystem ecology and biological conservation. Source-sink dynamics and spillover processes may link adjacent ecosystems by movement of organisms across system boundaries. However, effects of temporal variability in these cross-system fluxes on a whole marine ecosystem structure have not yet been presented. Here we show, using 35 y of multitrophic data series from the Baltic Sea, that transitory spillover of the top-predator cod from its main distribution area produces cascading effects in the whole food web of an adjacent and semi-isolated ecosystem. At varying population size, cod expand/contract their distribution range and invade/retreat from the neighboring Gulf of Riga, thereby affecting the local prey population of herring and, indirectly, zooplankton and phytoplankton via top-down control. The Gulf of Riga can be considered for cod a "true sink" habitat, where in the absence of immigration from the source areas of the central Baltic Sea the cod population goes extinct due to the absence of suitable spawning grounds. Our results add a metaecosystem perspective to the ongoing intense scientific debate on the key role of top predators in structuring natural systems. The integration of regional and local processes is central to predict species and ecosystem responses to future climate changes and ongoing anthropogenic disturbances.

To make the most of what we have: extracting phenological data from nestling measurements.

To study the ecological and evolutionary effects of climate change on timing of annual events, scientists need access to data that have been collected over long time periods. High-quality long-term phenology data are rare and costly to obtain and there is therefore a need to extract this information from other available data sets. Many long-term studies on breeding birds include detailed information on individually marked parents and offspring, but do not include information on timing of breeding. Here, we demonstrate how a study of repeated standard measurements of white-throated dipper Cinclus cinclus nestlings in our study system in southernmost Norway can be used for modeling nestling growth, and how this statistical model can be used to estimate timing of breeding for birds with sparser data. We also evaluate how the accuracies of nestling growth models based on different morphological traits (mass and feather length) differ depending on the nestling age, present user guidelines and demonstrate how they can be applied to an independent data set. In conclusion, the approach presented is likely to be useful for a wide variety of species, even if the preferred measurement may differ between species.

Pathogen-induced rapid evolution in a vertebrate life-history trait.

Anthropogenic factors, including climate warming, are increasing the incidence and prevalence of infectious diseases worldwide. Infectious diseases caused by pathogenic parasites can have severe impacts on host survival, thereby altering the selection regime and inducing evolutionary responses in their hosts. Knowledge about such evolutionary consequences in natural populations is critical to mitigate potential ecological and economic effects. However, studies on pathogen-induced trait changes are scarce and the pace of evolutionary change is largely unknown, particularly in vertebrates. Here, we use a time series from long-term monitoring of perch to estimate temporal trends in the maturation schedule before and after a severe pathogen outbreak. We show that the disease induced a phenotypic change from a previously increasing to a decreasing size at maturation, the most important life-history transition in animals. Evolutionary rates imposed by the pathogen were high and comparable to those reported for populations exposed to intense human harvesting. Pathogens thus represent highly potent drivers of adaptive phenotypic evolution in vertebrates.

Diversity, transmission and persistence of Escherichia coli in a cohort of mothers and their infants.

Despite that Escherichia coli is one of the most important bacteria in early infant colonization and immune modulation, we have limited knowledge about diversity, transmission and persistence within human populations for this bacterium. Here we have utilized a novel, growth-independent, direct typing approach to describe E. coli mother-to-child transmission and persistence within infants in a well-defined cohort of 86 mothers and their infants in Norway. Seven gene multilocus sequence typing of 28 study isolates, three probiotic strains, eight Norwegian pathogenic isolates and the ECOR strain collection added a phylogenetic framework to the direct sequencing data. We found that a type B2 subpopulation of the maternal E. coli strains was the main group transmitted to the infants and that the proportion of children carrying their mothers' strain decreased as the children age. Using species richness estimates we also found a limited number of strains within the cohort compared with total E. coli diversity, constraints on infant colonization, and that infant strain diversity levels increased towards maternal diversity levels over time. This knowledge about inheritance and diversity forms a foundation for future understanding of E. coli in human health and disease.

Convergent temporal dynamics of the human infant gut microbiota.

Temporal dynamics of the human gut microbiota is of fundamental importance for the development of proper gut function and maturation of the immune system. Here we present a description of infant gut ecological dynamics using a combination of nonlinear data modeling and simulations of the early infant gut colonization processes. Principal component analysis of infant microbiota 16S rRNA gene microarray data showed that the main directions of variation were defined by three phylum-specific probes targeting Bacteroides, Proteobacteria and Firmicutes. Nonlinear regression analysis identified several dynamic interactions between these three phyla. Simulations of the early phylum-level colonization process showed the relatively rapid establishment of an equilibrium community after an unstable initial phase. In general, varying the initial composition of phyla in the simulations had little bearing on the final equilibrium. The dynamic interaction model was found to maintain its predictive ability for Proteobacteria and Firmicutes well into the simulation, whereas Bacteroides densities tended to be underestimated, possibly due to host top-down selection for Bacteroides. In accordance with our model, initial perturbation of the microbiota by different mode of delivery (vaginal and C-section) did not affect the later phylum composition in the infants investigated. Considering the predictive ability and convergence of our phylum-level model, we now propose that deterministic bacterial-bacterial interactions are more important for shaping the human infant gut microbiota than previously anticipated.

Ecosystem oceanography for global change in fisheries.

Overexploitation and climate change are increasingly causing unanticipated changes in marine ecosystems, such as higher variability in fish recruitment and shifts in species dominance. An ecosystem-based approach to fisheries attempts to address these effects by integrating populations, food webs and fish habitats at different scales. Ecosystem models represent indispensable tools to achieve this objective. However, a balanced research strategy is needed to avoid overly complex models. Ecosystem oceanography represents such a balanced strategy that relates ecosystem components and their interactions to climate change and exploitation. It aims at developing realistic and robust models at different levels of organisation and addressing specific questions in a global change context while systematically exploring the ever-increasing amount of biological and environmental data.

Changes in selection and evolutionary responses in migratory brown trout following the construction of a fish ladder.

Brown trout (Salmo trutta) are extensively harvested and its habitat highly influenced by human encroachments. Using a 40-year time series of mark-recapture data we estimate vital rates for a piscivorous trout population. This population spawns upstream of a waterfall, which historically acted as a migration barrier for smaller trout. In 1966, the waterfall was dammed and a fish ladder constructed. All fish ascending the fish ladder were individually tagged and measured for a variety of traits. The fish ladder overall favoured access to upstream spawning areas for middle-sized trout, resulting in stabilizing selection acting on size at spawning. Over time, natural and fishing mortality have varied, with fishing mortality generally decreasing and natural mortality increasing. The average and, particularly, variance in size-at-first-spawning, and growth rates during the first years of lake residence have all decreased over the 1966-2003 period. These changes are all consistent with a shift from directional to stabilizing selection on age and size at spawning. Estimated rates of phenotypic change are relatively high, in particular for size at first spawning, adding further support for the growing notion that human interference may lead to rapid life-history trait evolution.