Changes in size and trends of North American sea duck populations associated with North Pacific oceanic regime shifts

Broad-scale multi-species declines in populations of North American sea ducks for unknown reasons is cause for management concern. Oceanic regime shifts have been associated with rapid changes in ecosystem structure of the North Pacific and Bering Sea. However, relatively little is known about potential effects of these changes in oceanic conditions on marine bird populations at broad scales. I examined changes in North American breeding populations of sea ducks from 1957 to 2011 in relation to potential oceanic regime shifts in the North Pacific in 1977, 1989, and 1998. There was strong support for population-level effects of regime shifts in 1977 and 1989, but little support for an effect of the 1998 shift. The continental-level effects of these regime shifts differed across species groups and time. Based on patterns of sea duck population dynamics associated with regime shifts, it is unclear if the mechanism of change relates to survival or reproduction. Results of this analysis support the hypothesis that population size and trends of North American sea ducks are strongly influenced by oceanic conditions. The perceived population declines appear to have halted >20 years ago, and populations have been relatively stable or increasing since that time. Given these results, we should reasonably expect dramatic changes in sea duck population status and trends with future oceanic regime shifts.     

A novel participatory and remote-sensing-based approach to mapping annual land use change on forest frontiers in Laos,Myanmar, and Madagascar

Tropical forests are under pressure from both commercial and smallholder agriculture. Forest frontiers are seeing dynamic land use changes that frequently lead to land system regime shifts, posing challenges for the sustainability of entire local social-ecological systems. Monitoring highly dynamic land use change and detecting land system regime shifts is methodologically challenging due to trade-offs between spatial and temporal data resolution. We propose an innovative approach that combines analysis of very-high-resolution satellite imagery with participatory mapping based on workshops and field walks. Applying it in Laos, Myanmar, and Madagascar, we were able to collect annual land use information over several decades. Unlike conventional land use change mapping approaches, which assess only few points in time, our approach provides information at a temporal resolution that enables detection of gradual and abrupt land system regime shifts.     

Reproductive success in male savanna baboons

Summary Different techniques have been utilized to ascertain male savanna baboon reproductive success based upon behavioral data. A 19 month field study of the reproductive behavior of savanna baboons in Kenya revealed a high degree of concordance among five different measures of male baboon reproductive success. The number of ejaculations showed the highest correlation with time spent in consort. Male reproductive success was not correlated with the number of females mated with because most males mated with most females. Female baboons regularly undergo multiple cycles prior to conception and the penultimate cycle showed no behavioral or physiological differences from the conception cycle. In nearly one-third of conception cycles a single consort partner was responsible for almost two-thirds of ejaculations during the four day optimal conception period. One may be able to reasonably infer paternity in these cases, but the available data are insufficient to support the idea that the variance in male baboon reproductive success is greater than the variance in female baboon reproductive success. The variance in male savanna baboon reproductive success will remain uncertain until genetic paternity studies are undertaken. It is suggested that mate selectivity, longevity, and stochastic factors are important components influencing male baboon reproductive success.     

Dynamic resource management under the risk of regime shifts

This paper provides a framework through which a dynamic resource management problem with potential regime shifts can be analyzed both in a strategic environment and from a social planner?s perspective. Based on a fairly general model, a condition for a precautionary policy is discussed. By applying the framework to a common-property resource problem with a linear production technology, we illustrate how the qualitative as well as quantitative nature of equilibrium is altered due to the possibility of regime shifts. In particular, when the risk is endogenously affected by the players? behavior, potential regime shifts can facilitate the precautionary management of resources as long as the resource stock is in good shape. As the stock of resource becomes scarce, however, the precautionary effect vanishes and more aggressive resource exploitation emerges. The impacts of irreversibility on the equilibrium behavior are highlighted. It is also shown that there can exist a resource-depletion trap in which a regime shift, once it happens, triggers a continuous decline of resource stock no matter which regime materializes in the subsequent periods.     

On metapopulation resistance to drift and extinction

The spatial configuration of metapopulations (numbers, sizes, and localization of patches) affects their ability to resist demographic extinction and genetic drift, but sometimes with opposite effects. Small and isolated patches, for instance, contribute marginally to demography but may play a large role in genetics by maintaining a sizeable amount of genetic variance among demes. In source-sink systems, similarly, connectivity may be beneficial in terms of effective size, but detrimental in terms of survival, by lowering the reproductive value of source populations. How to reconcile these opposite effects? Here we propose an analytical framework that integrates fixation time (ability to resist genetic drift) and extinction time (ability to resist demographic extinction) into a single index of resistance, measuring the ability of a metapopulation to maintain its demo-genetic integrity. We then illustrate with numerical examples how conflicting demands may be resolved.     

Emissions cap or emissions tax? A multi-sector business cycle analysis

We develop a multi-sector business cycle model to analyze stochastic implications of reducing CO₂ emissions with carbon permits or with carbon taxes in the presence of multiple sources of macroeconomic uncertainty. The model is calibrated to reflect the U.S. experience. As in previous studies, using a single-sector version of our model, we find that the cap regime generates lower volatility of real variables than the tax regime, but the latter may be preferable from the welfare perspective. Still, our multi-sector analysis points to the importance of the origin of the shocks in the ranking of the two instruments and to the desirability of going beyond a single-sector analysis in evaluating their merits. We find no significant difference between the cap and the tax regimes when shocks come from non-energy sectors. In contrast, the cap has lower volatility but higher welfare costs than the tax for the shocks to energy production.     

Scalar mixing in an urban canyon

The scalar dynamics within a unit-aspect-ratio street canyon are studied using large-eddy simulation. The key processes of ventilation and mixing are analysed with the canyon-averaged concentration, mean tracer age and variance. The results are sensitive to the source location and can be classified according to the streamline geometry. The canyon-averaged concentrations for the corner vortices, vortex sea and central vortex do not converge to the same value at large times, though the mean decay rates do. The variance measured with respect to the canyon average shows two distinct decay regimes: the early regime reflects large-scale straining and enhanced diffusion across streamlines, while the late regime is associated with escape from the canyon, i.e., ventilation. Analytical predictions for the variance-decay or mixing time scales are verified for the early regime. It is argued that the presence of an open boundary at the roof level suppresses rapid mixing of the scalar field and is responsible for differences with respect to scalar dynamics within closed domains.

     

Temporal Changes in Allele Frequencies and a Population's History of Severe Bottlenecks

Monitoring temporal changes in genetic variation has been suggested as a means of determining if a population has experienced a demographic bottleneck. Simulations have shown that the variance in allele frequencies over time ( F ) can provide reasonable estimates of effective population size ( N_e ). This relationship between F and N_e suggests that changes in allele frequencies may provide a way to determine the severity of recent demographic bottlenecks experienced by a population. We examined allozyme variation in experimental populations of the eastern mosquitofish ( Gambusia holbrooki ) to evaluate the relationship between the severity of demographic bottlenecks and temporal variation in allele frequencies. Estimates of F from both the fish populations and computer simulations were compared to expected rates of drift. We found that different methods for estimating F had little effect on the analysis. The variance in estimates of F was large among both experimental and simulated populations experiencing similar demographic bottlenecks. Temporal changes in allele frequencies suggested that the experimental populations had experienced bottlenecks, but there was no relationship between observed and expected values of F . Furthermore, genetic drift was likely to be underestimated in populations experiencing the most severe bottlenecks. The weak relationship between F and bottleneck severity is probably due to both sampling error associated with the number of polymorphic loci examined and the loss of alleles during the bottlenecks. For populations that may have experienced severe bottlenecks, caution should be used in making evolutionary interpretations or management recommendations based on temporal changes in allele frequencies.     

Negative effects of stress-resistant drift algae and high temperature on a small ephemeral seagrass species

Seagrasses are threatened by multiple anthropogenic stressors, such as accumulating drift algae and increasing temperatures (associated with eutrophication and global warming, respectively). However, few seagrass experiments have examined whether exposure to multiple stressors causes antagonistic, additive, or synergistic effects, and this has limited our ability to predict the future health status of seagrass beds. We conducted a laboratory experiment to test whether abundance of Gracilaria comosa (3 levels; 0, 1.2, and 3.4 kg WW m⁻²), an algae that is resistant to wide environmental fluctuations (e.g. light, temperature, salinity, and oxygen levels), has negative effects on the small ephemeral seagrass, Halophila ovalis and whether the effects are exacerbated by high temperature (3 levels; 20, 25, and 30°C). We found an additive negative effect of the two stressors when tested simultaneously on 14 seagrass performance measures, with most data variability explained by the drift algae. For the individual plant performance measures (above- and below-ground growth and mortality, leaf area, internode distance, and root length and root volume), we found 5 additive effects, 4 synergistic effects, and 5 effects that were significant only for drift algae. We also documented a significant additive effect of drift algae and temperature on dissolved porewater sulphide (DS). A follow-up correlation analysis between DS and the 14 plant performance measures revealed significant or near-significant linear correlations on 9 of these responses (above- and below-ground growth, leaf area and weight, leaf mortality, and internode distance). In summary, we showed (a) that a stress-resistant drift algae can have strong negative effects on a small ephemeral seagrass, (b) this negative effect can increase both additively and synergistically with increasing temperature depending on performance measure, and (c) the negative effects may be mediated by a build-up of porewater DS. An implication of our findings is that resource managers aiming to preserve healthy seagrass beds in an almost certain future warmer world should increase efforts to keep drift algae populations low.     

Mutation and Conservation

Mutation can critically affect the viability of small populations by causing inbreeding depression, by maintaining potentially adaptive genetic variation in quantitative characters, and through the erosion of fitness by accumulation of mildly detrimental mutations. I review and integrate recent empirical and theoretical work on spontaneous mutation and its role in population viability and conservation planning. I analyze both the maintenance of potentially adaptive genetic variation in quantitative characters and the role of detrimental mutations in increasing the extinction risk of small populations. Recent experiments indicate that the rate of production of quasineutral, potentially adaptive genetic variance in quantitative characters is an order of magnitude smaller than the total mutational variance because mutations with large phenotypic effects tend to be strongly detrimental. This implies that, to maintain normal adaptive potential in quantitative characters under a balance between mutation and random genetic drift (or among mutation, drift, and stabilizing natural selection), the effective population size should be about 5000 rather than 500 (the Franklin-Soulé number). Recent theoretical results suggest that the risk of extinction due to the fixation of mildly detrimental mutations may be comparable in importance to environmental stochasticity and could substantially decrease the long-term viability of populations with effective sizes as large as a few thousand. These findings suggest that current recovery goals for many threatened and endangered species are inadequate to ensure long-term population viability.     

Experimental floods cause ecosystem regime shift in a regulated river.

Reservoirs have altered the flow regime of most rivers on the globe. To simulate the natural flow regime, experimental floods are being implemented on regulated rivers throughout the world to improve their ecological integrity. As a large-scale disturbance, the long-term sequential use of floods provides an excellent empirical approach to examine ecosystem regime shifts in rivers. This study evaluated the long-term effects of floods (15 floods over eight years) on a regulated river. We hypothesized that sequential floods over time would cause a regime shift in the ecosystem. The floods resulted in little change in the physicochemistry of the river, although particulate organic carbon and particulate phosphorus were lower after the floods. The floods eliminated moss cover on bed sediments within the first year of flooding and maintained low periphyton biomass and benthic organic matter after the third year of flooding. Organic matter in transport was reduced after the third year of flooding, although peaks were still observed during rain events due to tributary inputs and side slopes. The floods reduced macroinvertebrate richness and biomass after the first year of floods, but density was not reduced until the third year. The individual mass of invertebrates decreased by about one-half after the floods. Specific taxa displayed either a loss in abundance, or an increase in abundance, or an increase followed by a loss after the third year. The first three flood years were periods of nonequilibrium with coefficients of variation in all measured parameters increasing two to five times from those before the floods. Coefficients of variation decreased after the third year, although they were still higher than before the floods. Analysis of concordance using Kendall's W confirmed the temporal changes observed in macroinvertebrate assemblage structure. An assessment of individual flood effects showed that later floods had approximately 30% less effect on macroinvertebrates than early floods of similar magnitude, suggesting that the new assemblage structure is more resilient to flood disturbance. We conclude that the floods caused an ecosystem regime shift that took three years to unfold. Additional long-term changes or shifts are expected as new taxa colonize the river from other sources.     

Market design in cap and trade programs: Permit validity and compliance timing

Cap and trade programs have considerable heterogeneity in permit validity and compliance timing. For example, permits have different validities across time (e.g., banking, borrowing, and seasons) and space (e.g., zonal restrictions), and compliance timing can be annual, in overlapping cycles, or in multi-year periods. We discuss nine prominent cap and trade programs along these dimensions and construct a general model of permit validity and compliance timing. We derive sufficient conditions under which abatement is invariant to compliance timing, i.e., compliance timing cannot smooth abatement cost shocks. Under these conditions, (i) expected compliance costs are invariant, (ii) the variance of compliance costs increases with the delayed compliance, (iii) equilibrium prices may not be unique, and (iv) the delayed compliance equilibrium may rely on “degenerate” prices not determined by marginal abatement costs. We demonstrate the model's broad applicability by illustrating different types of temporal permit validity.     

Environmental policy and macroeconomic dynamics in a new Keynesian model

This paper studies the dynamic behavior of an economy under different environmental policy regimes in a New Keynesian model with nominal and real uncertainty. We find the following results: (i) an emissions cap policy is likely to dampen macroeconomic fluctuations; (ii) staggered price adjustment alters significantly the performance of the environmental policy regime put in place; (iii) the optimal environmental policy response to shocks is strongly influenced by the degree to which prices adjust and by the monetary policy reaction.     

The CPCAT as a novel tool to overcome the shortcomings of NOEC/LOEC statistics in ecotoxicology: a simulation study to evaluate the statistical power

Species reproduction is an important determinant of population dynamics. As such, this is an important parameter in environmental risk assessment. The closure principle computational approach test (CPCAT) was recently proposed as a method to derive a NOEC/LOEC for reproduction count data such as the number of juvenile Daphnia. The Poisson distribution used by CPCAT can be too restrictive as a model of the data-generating process. In practice, the generalized Poisson distribution could be more appropriate, as it allows for inequality of the population mean \(\mu\) and the population variance \(\sigma ^2\). It is of fundamental interest to explore the statistical power of CPCAT and the probability of determining a regulatory relevant effect correctly. Using a simulation, we varied between Poisson distribution (\(\mu =\sigma ^2\)) and generalized Poisson distribution allowing for over-dispersion (\(\mu <\sigma ^2\)) and under-dispersion (\(\mu >\sigma ^2\)). The results indicated that the probability of detecting the LOEC/NOEC correctly was \(\ge 0.8\) provided the effect was at least 20% above or below the mean level of the control group and mean reproduction of the control was at least 50 individuals while over-dispersion was missing. Specifically, under-dispersion increased, whereas over-dispersion reduced the statistical power of the CPCAT. Using the well-known Hampel identifier, we propose a simple and straight forward method to assess whether the data-generating process of real data could be over- or under-dispersed.     

Biological responses to environmental forcing: the linear tracking window hypothesis

Determining the relative contributions of intrinsic and extrinsic processes to the regulation of biological populations has been a recurrent ecological issue. Recent discussions concerning ecosystem "regime shifts" again raise the question of whether population fluctuations are mainly controlled by external forcing. Results of nonlinear time series analyses indicate that pelagic populations typically do not passively track stochastic environmental variables. Rather, population dynamics are better described as nonlinear amplification of physical forcing by biological interactions. However, we illustrate that in some cases populations do show linear tracking of the physical environment. To explain why population dynamics can sometimes be linear, we propose the linear tracking window hypothesis: populations are most likely to track the stochastic environmental forcing when their generation time matches the characteristic time scale of the environmental signal. While our observations follow this hypothesis well, our results indicate that the linear tracking window is a necessary but not a sufficient condition.     

A Hierarchical View of Genetic Structure in the Rare Annual Plant Clarkia springvillensis

Genetic structure at several spatial scales was examined in the rare California annual, Clarkia springvillensis . Using seven isozyme-encoding loci as genetic markers, we assessed the amount and distribution of genetic variation among three populations and eight subpopulations. Total genetic variation was lower than in species with similar life history traits but equivalent to that of other endemic plants. Spatial autocorrelation showed some evidence for very limited differentiation within subpopulations at a scale of 1–2 m. The subpopulations, separated by tens of meters, were found to be more differentiated from each other ( F _sp = 0.084) on average than were populations ( F,pt = 0.017). This local genetic differentiation was not correlated with physical distance between subpopulations. The low F_pt estimates suggest that substantial gene flow is occurring among populations. However, the lack of correlation between genetic and geographic distances and the significant differentiation of subpopulations suggest that genetic drift is occurring within populations. Therefore, we believe the apparent homogeneity of populations is due to each population's gene frequencies' being an average of several divergent subpopulations. If drift is causing differentiation within populations, it may eventually cause differentiation between populations. The importance of using a hierarchical approach to evaluating genetic structure is clear. Patterns occurring at one spatial scale may not be evident at others. One should not necessarily conclude that gene flow is substantial and that the risk of genetic erosion via drift is negligible just because differentiation between populations is small; the system may not be at equilibrium. This lesson is particularly important when recent changes in climate or land use are apparent.     

Supportive Breeding and Variance Effective Population Size

The practice of supporting weak, wild populations through release of individuals bred in captivity is becoming an increasingly important conservation measure. A frequently recommended form of such breeding-release activity refers to supportive breeding: a fraction of the target population is brought into captivity for reproduction, and the resulting progeny are released to mix with the wild segment of the population. We derived an expression for the variance effective size of a population managed through supportive breeding and discuss its relationship to previously published equations that are based on the assumption of random mating. We show that the effect of supportive breeding may be quite different on the inbreeding and the variance effective sizes. Whereas supportive breeding always results in a reduction of the inbreeding effective number, the variance effective number may either decrease, increase, or remain unchanged. We discuss these observations in relation to conservation management and suggest some general guidelines for supportive breeding situations. Our recommendations include making a distinction between inbreeding and variance effective numbers; taking particular care when dealing with organisms with high reproductive potential; assuring that the amount of drift be no larger than it would be without supportive breeding; and focusing primarily on the variance effective size of a population-that is, on the effective number directly related to the rate of loss of gene diversity.     

Increased spatial variance accompanies reorganization of two continental shelf ecosystems

Phase transitions between alternate stable states in marine ecosystems lead to disruptive changes in ecosystem services, especially fisheries productivity. We used trawl survey data spanning phase transitions in the North Pacific (Gulf of Alaska) and the North Atlantic (Scotian Shelf) to test for increases in ecosystem variability that might provide early warning of such transitions. In both time series, elevated spatial variability in a measure of community composition (ratio of cod [Gadus sp.] abundance to prey abundance) accompanied transitions between ecosystem states, and variability was negatively correlated with distance from the ecosystem transition point. In the Gulf of Alaska, where the phase transition was apparently the result of a sudden perturbation (climate regime shift), variance increased one year before the transition in mean state occurred. On the Scotian Shelf, where ecosystem reorganization was the result of persistent overfishing, a significant increase in variance occurred three years before the transition in mean state was detected. However, we could not reject the alternate explanation that increased variance may also have simply been inherent to the final stable state in that ecosystem. Increased variance has been previously observed around transition points in models, but rarely in real ecosystems, and our results demonstrate the possible management value in tracking the variance of key parameters in exploited ecosystems.     

Predicting the Deleterious Effects of Mutation Load in Fragmented Populations

Abstract:  Human-induced habitat fragmentation constitutes a major threat to biodiversity. Both genetic and demographic factors combine to drive small and isolated populations into extinction vortices. Nevertheless, the deleterious effects of inbreeding and drift load may depend on population structure, migration patterns, and mating systems and are difficult to predict in the absence of crossing experiments. We performed stochastic individual-based simulations aimed at predicting the effects of deleterious mutations on population fitness (offspring viability and median time to extinction) under a variety of settings (landscape configurations, migration models, and mating systems) on the basis of easy-to-collect demographic and genetic information. Pooling all simulations, a large part (70%) of variance in offspring viability was explained by a combination of genetic structure ( F_ST ) and within-deme heterozygosity ( H_S ). A similar part of variance in median time to extinction was explained by a combination of local population size ( N ) and heterozygosity ( H_S ). In both cases the predictive power increased above 80% when information on mating systems was available. These results provide robust predictive models to evaluate the viability prospects of fragmented populations.     

The unified neutral theory of biodiversity: do the numbers add up?

Hubbell's unified neutral theory is a zero-sum ecological drift model in which population sizes change at random in a process resembling genetic drift, eventually leading to extinction. Diversity is maintained within the community by speciation. Hubbell's model makes predictions about the distribution of species abundances within communities and the turnover of species from place to place (beta diversity). However, ecological drift cannot be tested adequately against these predictions without independent estimates of speciation rates, population sizes, and dispersal distances. A more practical prediction from ecological drift is that time to extinction of a population of size N is approximately 2N generations. I test this prediction here using data for passerine birds (Passeriformes). Waiting times to speciation and extinction were estimated from genetic divergence between sister populations and a lineage-through-time plot for endemic South American suboscine passerines. Population sizes were estimated from local counts of birds in two large forest plots extrapolated to the area of wet tropical forest in South America and from atlas data on European passerines. Waiting times to extinction (ca. 2 Ma) are much less than twice the product of average population size (4.0 and 14.4 x 10(6) individuals in South America and Europe) and generation length (five and three years) for songbirds, that is, 40 and 86 Ma, respectively. Thus, drift is too slow to account for turnover in regional avifaunas. Presumably, other processes, involving external drivers, such as climate and physiographic change, and internal drivers, such as evolutionary change in antagonistic interactions, predominate. Hubbell's model is historical and geographic, and his perspective importantly links local and regional process and pattern. Ecological reality can be added to the mix while retaining Hubbell's concept of continuity of communities in space and time.