Density-dependent habitat selection of spawning Chinook salmon: broad-scale evidence and implications

Estimating migration speed of glass eels during their colonization of a Mediterranean lagoon

Migration speed can have important evolutionary consequences as it can affect the timing of arrival, remaining energy reserves, and habitat choice. Environmental conditions and individual phenotypic traits can impact the migration speed of individuals. In this way, estimating migration speed is of particular importance, especially for species under strong management strategies and colonizing highly diversified habitats, as is the case for the European eel. However, estimating the migration speed of glass eels, which is the life stage when eels colonize continental habitats, presents challenges due to typically low re-capture probabilities and difficulties in tagging individuals. Using recruitment time series at two sites, one at the sea connection and another inland, we estimated the temporal lag between the two migration peaks to compute migration speed. Because we worked on the Mediterranean coasts and in a lagoon, the weak tidal amplitudes may inhibit individuals from efficiently performing the selective tidal stream transport. We obtained migration speed values coherent with the few values available in the literature for Atlantic estuaries. The values we obtained that are lower than those obtained for Atlantic estuaries are also coherent with the weak tides along the Mediterranean coasts and lead to necessary further studies to understand the migratory behavior of glass eels in such hydro-systems.

From spawner habitat selection to stock-recruitment: Implications for assessment

The relationship between the spawning stock size and subsequent number of recruits is a central concept in fisheries ecology. The influence of habitat selection of spawning individuals on the stock-recruitment relationship is poorly known. Here we explore how each of four different spawner behaviors might influence the stock-recruitment relationship and estimates of its parameters in the two most commonly used stock-recruitment functions (Beverton-Holt and Ricker). Using simulated stock-recruitment data generated by four different spawner behaviors applied to multiple discrete habitats, we show that when spawners were distributed proportionally to local carrying capacities, there was small or no bias in estimated recruitment and stock-recruitment parameters. For an ideal free distribution of spawners, larger bias in the estimates of recruitment and stock-recruitment parameters was obtained, whereas a random and a stepwise spawner behavior introduced the largest bias. Using stock-recruitment data corresponding to a "realistic" range of population densities and adding measurement error (20%-60%) to the simulated stock-recruitment data generated larger variation in the estimation bias than what was introduced by the spawner behavior. Thus, for exploited stocks at low population density and where spawning stock size and recruitment cannot be observed perfectly, partial observation of the possible spawner abundance range and measurement error might be of higher concern for management.

Landscape-scale giant panda conservation based on metapopulations within China's national park system

Historically, giant panda conservation in China has been compromised by disparate management of protected areas. It is thus crucial to address how giant panda populations can be managed cohesively on a landscape scale, an opportunity offered by China's newly established Giant Panda National Park. Here, we evaluated giant panda populations in a metapopulation context, based on range-wide data from the Fourth National Giant Panda Survey. We delineated metapopulations by geographic range, relative abundance, and relative density and assessed the extent of human disturbance each metapopulation faced. We found density-dependent and disturbance-influenced effects on habitat selection across metapopulations. We determined the main effects faced by each metapopulation regarding area sensitivity, population size, intraspecific competition, and disturbance. To enhance the landscape-scale conservation of giant pandas and various other wildlife across China's national park system, we propose that metapopulation management incorporates population status along with density-dependent and disturbance-related effects on habitat selection.

Social competition as a driver of phenotype-environment correlations: implications for ecology and evolution

While it is universally recognised that environmental factors can cause phenotypic trait variation via phenotypic plasticity, the extent to which causal processes operate in the reverse direction has received less consideration. In fact individuals are often active agents in determining the environments, and hence the selective regimes, they experience. There are several important mechanisms by which this can occur, including habitat selection and niche construction, that are expected to result in phenotype–environment correlations (i.e. non‐random assortment of phenotypes across heterogeneous environments). Here we highlight an additional mechanism – intraspecific competition for preferred environments – that may be widespread, and has implications for phenotypic evolution that are currently underappreciated. Under this mechanism, variation among individuals in traits determining their competitive ability leads to phenotype–environment correlation; more competitive phenotypes are able to acquire better patches. Based on a concise review of the empirical evidence we argue that competition‐induced phenotype–environment correlations are likely to be common in natural populations before highlighting the major implications of this for studies of natural selection and microevolution. We focus particularly on two central issues. First, competition‐induced phenotype–environment correlation leads to the expectation that positive feedback loops will amplify phenotypic and fitness variation among competing individuals. As a result of being able to acquire a better environment, winners gain more resources and even better phenotypes – at the expense of losers. The distinction between individual quality and environmental quality that is commonly made by researchers in evolutionary ecology thus becomes untenable. Second, if differences among individuals in competitive ability are underpinned by heritable traits, competition results in both genotype–environment correlations and an expectation of indirect genetic effects (IGEs) on resource‐dependent life‐history traits. Theory tells us that these IGEs will act as (partial) constraints, reducing the amount of genetic variance available to facilitate evolutionary adaptation. Failure to recognise this will lead to systematic overestimation of the adaptive potential of populations. To understand the importance of these issues for ecological and evolutionary processes in natural populations we therefore need to identify and quantify competition‐induced phenotype–environment correlations in our study systems. We conclude that both fundamental and applied research will benefit from an improved understanding of when and how social competition causes non‐random distribution of phenotypes, and genotypes, across heterogeneous environments.

Assessing the Viability of American Horseshoe Crab (Limulus polyphemus) Embryos in Salt Marsh and Sandy Beach Habitats

AbstractFor animal embryos that develop externally, the physio-chemical environment can substantially affect offspring viability. In the case of the American horseshoe crab (Limulus polyphemus), sediment conditions along estuarine shorelines influence development rates and embryonic viability. Sandy beach habitats are considered to have optimal conditions for horseshoe crab embryonic development; however, spawning is often observed outside of these optimal habitats, in areas such as salt marshes, where reduced oxygen availability is thought to decrease the viability of eggs laid in these sediments. We excavated horseshoe crab eggs, embryos, and trilobites laid naturally in marsh and beach sediments in South Carolina to compare their development and viability between habitats. We found all developmental stages in both marsh and beach habitats. For two of three sampling areas, trilobites were more likely to be found at beaches than at marshes. Multivariate analyses demonstrate that the prevalence of early and middle developmental stages was similar between habitats but that beaches had a greater proportion of late-stage trilobites than marshes. The lower likelihood of finding trilobites at some marshes may reflect differences in spawning phenology between habitats or reduced rates of embryonic development in marshes compared to beaches, leading to potentially different developmental timelines rather than a true reduction in viability. Nevertheless, the substantial proportions of eggs laid in salt marshes that survive to the trilobite stage indicate that spawning in this habitat could represent a previously underappreciated source of recruitment for horseshoe crab populations that may need to be incorporated into population assessments.

Habitat selection patterns are density dependent under the ideal free distribution

Despite being widely used, habitat selection models are rarely reliable and informative when applied across different ecosystems or over time. One possible explanation is that habitat selection is context-dependent due to variation in consumer density and/or resource availability. The goal of this paper is to provide a general theoretical perspective on the contributory mechanisms of consumer and resource density-dependent habitat selection, as well as on our capacity to account for their effects. Towards this goal we revisit the ideal free distribution (IFD), where consumers are assumed to be omniscient, equally competitive and freely moving, and are hence expected to instantaneously distribute themselves across a heterogeneous landscape such that fitness is equalised across the population. Although these assumptions are clearly unrealistic to some degree, the simplicity of the structure in IFD provides a useful theoretical vantage point to help clarify our understanding of more complex spatial processes. Of equal importance, IFD assumptions are compatible with the assumptions underlying common habitat selection models. Here we show how a fitness-maximising space use model, based on IFD, gives rise to resource and consumer density-dependent shifts in consumer distribution, providing a mechanistic explanation for the context-dependent outcomes often reported in habitat selection analysis. Our model suggests that adaptive shifts in consumer distribution patterns would be expected to lead to nonlinear and often non-monotonic patterns of habitat selection. These results indicate that even under the simplest of assumptions about adaptive organismal behaviour, habitat selection strength should critically depend on system-wide characteristics. Clarifying the impact of adaptive behavioural responses may be pivotal in making meaningful ecological inferences about observed patterns of habitat selection and allow reliable transferability of habitat selection predictions across time and space.

Territoriality drives preemptive habitat selection in recovering wolves: Implications for carnivore conservation

According to the ideal-free distribution (IFD), individuals within a population are free to select habitats that maximize their chances of success. Assuming knowledge of habitat quality, the IFD predicts that average fitness will be approximately equal among individuals and between habitats, while density varies, implying that habitat selection will be density dependent. Populations are often assumed to follow an IFD, although this assumption is rarely tested with empirical data, and may be incorrect when territoriality indicates habitat selection tactics that deviate from the IFD (e.g. ideal-despotic distribution or ideal-preemptive distribution). When territoriality influences habitat selection, species' density will not directly reflect components of fitness such as reproductive success or survival. In such cases, assuming an IFD can lead to false conclusions about habitat quality. We tested theoretical models of density-dependent habitat selection on a species known to exhibit territorial behaviour in order to determine whether commonly applied habitat models are appropriate under these circumstances. We combined long-term radiotelemetry and census data from grey wolves Canis lupus in the Upper Peninsula of Michigan, USA to relate spatiotemporal variability in wolf density to underlying classifications of habitat within a hierarchical state-space modelling framework. We then iteratively applied isodar analysis to evaluate which distribution of habitat selection best described this recolonizing wolf population. The wolf population in our study expanded by >1,000% during our study (~50 to >600 individuals), and density-dependent habitat selection was most consistent with the ideal-preemptive distribution, as opposed to the ideal-free or ideal-despotic alternatives. Population density of terrestrial carnivores may not be positively correlated with the fitness value of their habitats, and density-dependent habitat selection patterns may help to explain complex predator-prey dynamics and cascading indirect effects. Source-sink population dynamics appear likely when species exhibit rapid growth and occupy interspersed habitats of contrasting quality. These conditions are likely and have implications for large carnivores in many systems, such as areas in North America and Europe where large predator species are currently recolonizing their former ranges.

Territorial landscapes: incorporating density-dependence into wolf habitat selection studies

Habitat selection is a process that spans space, time and individual life histories. Ecological analyses of animal distributions and preferences are most accurate when they account for inherent dynamics of the habitat selection process. Strong territoriality can constrain perception of habitat availability by individual animals or groups attempting to colonize or establish new territory. Because habitat selection is a function of habitat availability, broad-scale changes in habitat availability or occupancy can drive density-dependent habitat functional responses. We investigated density-dependent habitat selection over a 19-year period of grey wolf (Canis lupus) recovery in Michigan, USA, using a generalized linear mixed model framework to develop a resource selection probability function (RSPF) with habitat coefficients conditioned on random effects for wolf packs and random year intercepts. In addition, we allowed habitat coefficients to vary as interactions with increasing wolf density over space and time. Results indicated that pack presence was driven by factors representing topography, human development, winter prey availability, forest structure, roads, streams and snow. Importantly, responses to many of these predictors were density-dependent. Spatio-temporal dynamics and population changes can cause considerable variation in wildlife-habitat relationships, possibly confounding interpretation of conventional habitat selection models. By incorporating territoriality into an RSPF analysis, we determined that wolves' habitat use in Michigan shifted over time, for example, exhibiting declining responses to winter prey indices and switching from positive to negative responses with respect to stream densities. We consider this an important example of a habitat functional response in wolves, driven by colonization, density-dependence and changes in occupancy during a time period of range expansion and population increase.

Tree lizard (Urosaurus ornatus) growth decreases with population density, but increases with habitat quality

Habitat selection models can explain spatial patterns in the relative abundance of animals in different habitats based on the assumption that fitness declines as density in a habitat increases. Ectotherms, such as lizards, may not follow predictions of density-dependent habitat selection models because temperature, which is unaffected by density, strongly influences their habitat selection. If competition for limited resources decreases fitness, then crowding should cause a decrease in body size and growth rates. We used skeletochronology and body size data from tree lizards (Urosaurus ornatus) at six sites that each spanned two habitats varying in quality to test the hypothesis that habitat selection is density dependent because growth is limited by competition for resources and by habitat quality. First, we tested that the maximum body size of lizards decreased with higher densities in a habitat by comparing growth between sites. Second, we tested whether body size and growth were higher in the habitat with more resources by controlling for density in a habitat and comparing growth between habitats in different sites. We found evidence of density-dependent growth in females, but not in males. Females in more crowded sites reached a smaller maximum size. Females in the higher quality habitat also grew larger than females in the lower quality habitat after controlling for differences in density between the habitats. Therefore, we found partial support for our hypothesis that competition for resources limits growth and causes density-dependent habitat selection.

The role of density-dependent and -independent processes in spawning habitat selection by salmon in an Arctic riverscape

Density-dependent (DD) and density-independent (DI) habitat selection is strongly linked to a species’ evolutionary history. Determining the relative importance of each is necessary because declining populations are not always the result of altered DI mechanisms but can often be the result of DD via a reduced carrying capacity. We developed spatially and temporally explicit models throughout the Chena River, Alaska to predict important DI mechanisms that influence Chinook salmon spawning success. We used resource-selection functions to predict suitable spawning habitat based on geomorphic characteristics, a semi-distributed water-and-energy balance hydrologic model to generate stream flow metrics, and modeled stream temperature as a function of climatic variables. Spawner counts were predicted throughout the core and periphery spawning sections of the Chena River from escapement estimates (DD) and DI variables. Additionally, we used isodar analysis to identify whether spawners actively defend spawning habitat or follow an ideal free distribution along the riverscape. Aerial counts were best explained by escapement and reference to the core or periphery, while no models with DI variables were supported in the candidate set. Furthermore, isodar plots indicated habitat selection was best explained by ideal free distributions, although there was strong evidence for active defense of core spawning habitat. Our results are surprising, given salmon commonly defend spawning resources, and are likely due to competition occurring at finer spatial scales than addressed in this study.

Proxies in Practice: Calibration and Validation of Multiple Indices of Animal Abundance

The abundance of individuals in a population is a fundamental metric in basic and applied ecology, but sampling protocols yielding precise and unbiased estimates of abundance are often cost-prohibitive. Proxies of abundance are therefore common, but require calibration and validation. There are many ways to calibrate a proxy, and it is not obvious which will perform best. We used data from eight populations of Chinook salmon Oncorhynchus tshawytscha on the Oregon coast where multiple proxies of abundance were obtained contemporaneously with independent mark–recapture estimates. We combined multiple proxy values associated with a single level of abundance into a composite index and then calibrated the composite index to mark–recapture estimates using several different techniques. We tested our calibration methods using leave-one-out cross-validation and simulation. Our cross-validation analysis did not definitively identify a single best calibration technique for all populations, but we could identify consistently inferior approaches. The simulations suggested that incorporating the uncertainty associated with mark–recapture estimates into the calibration technique reduced precision and introduced bias when mark–recapture estimate uncertainty increased with point estimate values. Cross-validation techniques can be used to test multiple methods of calibrating multiple proxies to an estimate of abundance. Critical uncertainties with the application of calibrated proxies still exist, and cost-benefit analysis should be performed to help identify optimal monitoring designs.