Habitat Size, Recruitment, and Longevity as Factors Limiting Population Size in Stage‐Structured Species

Evaluating intra- and inter-life stage density-dependent dynamics for management of perennial amphidromous fish

Compensatory density-dependent (DD) processes play an integral role in fisheries management by underpinning fundamental population demographics. However, DD processes are often assessed only for specific life stages, likely resulting in misleading evaluations of population limitations. Here, we assessed the relative roles of intra- and inter-life stage DD interactions in shaping the population dynamics of perennial freshwater fish with demographically open populations. Specifically, we monitored populations of amphidromous banded kōkopu (Galaxias fasciatus), giant kōkopu (Galaxias argenteus), and shortjaw kōkopu (Galaxias postvectis) in five streams where migratory post-larvae are fished and in three no-take ("closed") streams located on New Zealand's South Island for two years. Using mark-recapture data, we investigated whether fishing altered densities of "small" (non-territorial recruits ≤1-year-old) and "large" (territorial fish >1-year-old) kōkopu size classes, and how subsequent density shifts affected the apparent survival and growth of each class while controlling for other confounding factors (e.g., habitat characteristics). We found that closed areas had substantially greater biomass of small kōkopu, particularly following the two-month fishing season. Despite this greater influx of recruits, there was no difference in the biomass of large kōkopu at the species level, or as a combined assemblage between stream types. This indicated that although fishing of post-larvae reduced recruit influxes into adult habitats, there was no subsequent evidence of recruitment-limitation within adult populations. Instead, kōkopu demographics were underpinned by intra- and inter-life stage DD competition and predation. Greater large fish densities played a key role in regulating the survival, growth, and/or presence of various kōkopu classes. In contrast, greater small fish densities had positive effects on the growth of opportunistic and insectivorous congeners, likely due to cannibalism and altered foraging behaviors, respectively. Our study details the prominent role of intra- and inter-life stage DD interactions in regulating the population dynamics of perennial migratory freshwater fishes, even in populations with inhibited recruit and juvenile availability. We emphasize the importance for fisheries management to implement recruitment dependencies and complex interactions between distinct life stages to avoid deleterious DD responses and ensure population persistence.

Multicomponent assessment of the impact of hydropower cascade on fish metrics

The water sector is one of the priority areas of the European Union; therefore, legislation encourages the development of methods to protect the river ecosystem. The key to this is the characterization of the river's physical features with respect to ecological quality. Rivers are a complex system in which geomorphic conditions, hydrological regime, and ecological indicators interact. The group of hydropower plants (HPPs) that forms a hydropower cascade disturbs the natural continuity of river system components. Analysis of the spatial and temporal alterations in the river environment is important for understanding the potential impact of the hydropower cascade on ecological indicators. In a current study, the multicomponent assessment was used to evaluate the impact of the hydropower cascade of five HPPs on fish metrics as ecological indicators in the case study Varduva River. The research involved field surveys to collect hydrological data in highly affected ungauged river to estimate indicators of hydrologic alterations under HPPs operation, use of Unmanned Aerial Vehicles and digital photogrammetry to map geomorphic units, fish sampling to estimate composition of fish species and guilds, and fish habitat availability modelling based on the collected data and the conditional habitat suitability criteria using the MesoHABSIM modelling approach. Results revealed that the technical characteristics of HPPs determined their individual operation mode, which had a crucial impact on the hydrologic alterations of the river and, together with the distance between the dams, on the variation of fish metrics in the hydropower cascade. The intensive operation of the hydropower cascade created adverse effects for intolerant fish but was advantageous for tolerant fish species. The proposed HPP multimetric correlated with the fish metrics and showed similar tendencies between HPPs as habitat integrity index (IH), derived from MesoHABSIM modelling.

Predicting biomass of resident kōkopu (Galaxias) populations using local habitat characteristics

With the global decline of freshwater fishes, quantifying the body size-specific habitat use of vulnerable species is crucial for accurately evaluating population health, identifying the effects of anthropogenic stressors, and directing effective habitat restoration. Populations of New Zealand's endemic kōkopu species (Galaxias fasciatus, G. argenteus, and G. postvectis) have declined substantially over the last century in response to anthropogenic stressors, including habitat loss, migratory barriers, and invasive species. Despite well-understood habitat associations, key within-habitat features underpinning the reach-scale biomass of small and large kōkopu remain unclear. Here, we investigated whether the total biomass of large (> 90 mm) size classes of each kōkopu species and the composite biomass of all small (≤ 90 mm) kōkopu were associated with components of the physical environment that provided refuge and prey resources across fifty-seven 50-m stream reaches. Because kōkopu are nocturnal, populations were sampled by removal at night using headlamps and hand-nets until reaches were visually depleted. Based on Akaike's information criterion, greater large banded kōkopu biomass was most parsimoniously explained by greater pool volume and forest cover, greater large giant kōkopu biomass by greater bank cover and pool volume, and greater large shortjaw kōkopu biomass by greater substrate size and pool volume. In contrast, greater composite small kōkopu biomass was best explained by smaller substrate size, reduced bank cover, and greater pool volume. Local habitat associations therefore varied among kōkopu species and size classes. Our study demonstrates the importance of considering the ontogenetic shift in species' habitat use and provides an effective modelling approach for quantifying size-specific local habitat use of stream-dwelling fish.

The role of continental shelf bathymetry in shaping marine range shifts in the face of climate change

As a consequence of anthropogenic climate change, marine species on continental shelves around the world are rapidly shifting deeper and poleward. However, whether these shifts deeper and poleward will allow species to access more, less, or equivalent amounts of continental shelf area and associated critical habitats remains unclear. By examining the proportion of seabed area at a range of depths for each large marine ecosystem (LME), we found that shelf area declined monotonically for 19% of LMEs examined. However, the majority exhibited a greater proportion of shelf area in mid-depths or across several depth ranges. By comparing continental shelf area across 2° latitudinal bands, we found that all coastlines exhibit multiple instances of shelf area expansion and contraction, which have the potential to promote or restrict poleward movement of marine species. Along most coastlines, overall shelf habitat increases or exhibits no significant change moving towards the poles. The exception is the Southern West Pacific, which experiences an overall loss of area with increasing latitude. Changes in continental shelf area availability across latitudes and depths are likely to affect the number of species local ecosystems can support. These geometric analyses help identify regions of conservation priority and ecological communities most likely to face attrition or expansion due to variations in available area.

Local prey shortages drive foraging costs and breeding success in a declining seabird, the Atlantic puffin

As more and more species face anthropogenic threats, understanding the causes of population declines in vulnerable taxa is essential. However, long-term datasets, ideal to identify lasting or indirect effects on fitness measures such as those caused by environmental factors, are not always available. Here we use a single year but multi-population approach on populations with contrasting demographic trends to identify possible drivers and mechanisms of seabird population changes in the north-east Atlantic, using the Atlantic puffin, a declining species, as a model system. We combine miniature GPS trackers with camera traps and DNA metabarcoding techniques on four populations across the puffins' main breeding range to provide the most comprehensive study of the species' foraging ecology to date. We find that puffins use a dual foraging tactic combining short and long foraging trips in all four populations, but declining populations in southern Iceland and north-west Norway have much greater foraging ranges, which require more (costly) flight, as well as lower chick-provisioning frequencies, and a more diverse but likely less energy-dense diet, than stable populations in northern Iceland and Wales. Together, our findings suggest that the poor productivity of declining puffin populations in the north-east Atlantic is driven by breeding adults being forced to forage far from the colony, presumably because of low prey availability near colonies, possibly amplified by intraspecific competition. Our results provide valuable information for the conservation of this and other important North-Atlantic species and highlight the potential of multi-population approaches to answer important questions about the ecological drivers of population trends.

Assessing the evolutionary persistence of ecological relationships: A review and preview

Species interactions, such as pollination, parasitism and predation, form the basis of functioning ecosystems. The origins and resilience of such interactions therefore merit attention. However, fossils only occasionally document ancient interactions, and phylogenetic methods are blind to recent interactions. Is there some other way to track shared species experiences? "Comparative demography" examines when pairs of species jointly thrived or declined. By forging links between ecology, epidemiology, and evolutionary biology, this method sheds light on biological adaptation, species resilience, and ecosystem health. Here, we describe how this method works, discuss examples, and suggest future directions in hopes of inspiring interest, imitators, and critics.

Climate-driven shift in coral morphological structure predicts decline of juvenile reef fishes

Rapid intensification of environmental disturbances has sparked widespread decline and compositional shifts in foundation species in ecosystems worldwide. Now, an emergent challenge is to understand the consequences of shifts and losses in such habitat-forming species for associated communities and ecosystem processes. Recently, consecutive coral bleaching events shifted the morphological makeup of habitat-forming coral assemblages on the Great Barrier Reef (GBR). Considering the disparity of coral morphological growth forms in shelter provision for reef fishes, we investigated how shifts in the morphological structure of coral assemblages affect the abundance of juvenile and adult reef fishes. We used a temporal dataset from shallow reefs in the northern GBR to estimate coral convexity (a fine-scale quantitative morphological trait) and two widely used coral habitat descriptors (coral cover and reef rugosity) for disentangling the effects of coral morphology on reef fish assemblages. Changes in coral convexity, rather than live coral cover or reef rugosity, disproportionately affected juvenile reef fishes when compared to adults, and explained more than 20% of juvenile decline. The magnitude of this effect varied by fish body size with juveniles of small-bodied species showing higher vulnerability to changes in coral morphology. Our findings suggest that continued large-scale shifts in the relative abundance of morphological groups within coral assemblages are likely to affect population replenishment and dynamics of future reef fish communities. The different responses of juvenile and adult fishes according to habitat descriptors indicate that focusing on coarse-scale metrics alone may mask fine-scale ecological responses that are key to understand ecosystem functioning and resilience. Nonetheless, quantifying coral morphological traits may contribute to forecasting the structure of reef fish communities on novel reef ecosystems shaped by climate change.

Characterizing ontogenetic habitat shifts in marine fishes: advancing nascent methods for marine spatial management

Niche requirements and habitat resource partitioning by conspecific fishes of different sizes are significant knowledge gaps in the species distribution modelling domain. Management actions and operations are typically concentrated on static habitats, or specific areas of interest, without considering movement patterns of species associated with ontogenetic shifts in habitat usage. Generalized additive models were used to model the body-length-habitat relationships of six fish species. These models were used to identify subsets of environmental parameters that drive and explain the continuous length-habitat relationships for each of the study species, which vary in their degree of ecological and/or commercial importance. Continuous predictive maps of the length distributions for each of the six study species across approximately 200 km² of the study area were created from these models. The spatial patterns in habitat partitioning by individuals of different body lengths for all six study species provide strong evidence for ontogenetic shifts. This highlights the importance of considering ontogenetic processes for marine spatial management. Importantly, predictive hotspot maps were created that identify potential areas that accumulate individuals of similar life stages of multiple species (e.g., multispecies nursery areas). In circumstances where limited resources are available for monitoring and management of fish resources, predictive modelling is a valuable tool for studying previously overlooked processes such as ontogenetic habitat shifts. Predictive modelling provides crucial information that elucidates spatial patterns in community composition across mosaics of benthic habitats. This novel technique can contribute to the spatial management of coastal fish and fisheries by identifying areas that are important for different life history stages of multiple fish species.

Influence of nursery microhabitats on the future abundance of a coral reef fish

Species habitat associations are often complex, making it difficult to assess their influence on populations. Among coral reef fishes, habitat requirements vary among species and with ontogeny, but the relative importance of nursery and adult-preferred habitats on future abundances remain unclear. Moreover, adult populations may be influenced by recruitment of juveniles and assessments of habitat importance should consider relative effects of juvenile abundance. We conducted surveys across 16 sites and 200 km of reef to identify the microhabitat preferences of juveniles, sub-adults and adults of the damselfish Pomacentrus moluccensis Microhabitat preferences at different life-history stages were then combined with 6 years of juvenile abundance and microhabitat availability data to show that the availability of preferred juvenile microhabitat (corymbose corals) at the time of settlement was a strong predictor of future sub-adult and adult abundance. However, the influence of nursery microhabitats on future population size differed spatially and at some locations abundance of juveniles and adult microhabitat (branching corals) were better predictors of local populations. Our results demonstrate that while juvenile microhabitats are important nurseries, the abundance of coral-dependent fishes is not solely dependent on these microhabitats, especially when microhabitats are readily available or following large influxes of juveniles.

Thermal carrying capacity for a thermally-sensitive species at the warmest edge of its range

Anthropogenic environmental change is causing unprecedented rates of population extirpation and altering the setting of range limits for many species. Significant population declines may occur however before any reduction in range is observed. Determining and modelling the factors driving population size and trends is consequently critical to predict trajectories of change and future extinction risk. We tracked during 12 years 51 populations of a cold-water fish species (brown trout Salmo trutta) living along a temperature gradient at the warmest thermal edge of its range. We developed a carrying capacity model in which maximum population size is limited by physical habitat conditions and regulated through territoriality. We first tested whether population numbers were driven by carrying capacity dynamics and then targeted on establishing (1) the temperature thresholds beyond which population numbers switch from being physical habitat- to temperature-limited; and (2) the rate at which carrying capacity declines with temperature within limiting thermal ranges. Carrying capacity along with emergent density-dependent responses explained up to 76% of spatio-temporal density variability of juveniles and adults but only 50% of young-of-the-year's. By contrast, young-of-the-year trout were highly sensitive to thermal conditions, their performance declining with temperature at a higher rate than older life stages, and disruptions being triggered at lower temperature thresholds. Results suggest that limiting temperature effects were progressively stronger with increasing anthropogenic disturbance. There was however a critical threshold, matching the incipient thermal limit for survival, beyond which realized density was always below potential numbers irrespective of disturbance intensity. We additionally found a lower threshold, matching the thermal limit for feeding, beyond which even unaltered populations declined. We predict that most of our study populations may become extinct by 2100, depicting the gloomy fate of thermally-sensitive species occurring at thermal range margins under limited potential for adaptation and dispersal.

The economic efficiency of conservation measures for amphibians in organic farming--results from bio-economic modelling

This paper presents a whole farm bio-economic modelling approach for the assessment and optimisation of amphibian conservation conditions applied at the example of a large scale organic farm in North-Eastern Germany. The assessment focuses mainly on the habitat quality as affected by conservation measures such as through specific adapted crop production activities (CPA) and in-field buffer strips for the European tree frog (Hyla arborea), considering also interrelations with other amphibian species (i.e. common spadefoot toad (Pelobates fuscus), fire-bellied toad (Bombina bombina)). The aim of the approach is to understand, analyse and optimize the relationships between the ecological and economic performance of an organic farming system, based on the expectation that amphibians are differently impacted by different CPAs. The modelling system consists of a set of different sub-models that generate a farm model on the basis of environmentally evaluated CPAs. A crop-rotation sub-model provides a set of agronomically sustainable crop rotations that ensures overall sufficient nitrogen supply and controls weed, pest and disease infestations. An economic sub-model calculates the gross margins for each possible CPA including costs of inputs such as labour and machinery. The conservation effects of the CPAs are assessed with an ecological sub-model evaluates the potential negative or positive effect that each work step of a CPA has on amphibians. A mathematical programming sub-model calculates the optimal farm organization taking into account the limited factors of the farm (e.g. labour, land) as well as ecological improvements. In sequential model runs, the habitat quality is to be improved by the model, while the highest possible gross margin is still to be achieved. The results indicate that the model can be used to show the scope of action that a farmer has to improve habitat quality by reducing damage to amphibian population on its land during agricultural activities. Thereby, depending on the level of habitat quality that is aimed at, different measures may provide the most efficient solution. Lower levels of conservation can be achieved with low-cost adapted CPAs, such as an increased cutting height, reduced sowing density and grubbing instead of ploughing. Higher levels of conservation require e.g. grassland-like managed buffer strips around ponds in sensible areas, which incur much higher on-farm conservation costs.

A piecewise linear modeling approach for testing competing theories of habitat selection: an example with mule deer in northern winter ranges

Habitat selection fundamentally drives the distribution of organisms across landscapes; density-dependent habitat selection (DDHS) is considered a central component of ecological theories explaining habitat use and population regulation. A preponderance of DDHS theories is based on ideal distributions, such that organisms select habitat according to either the ideal free, despotic, or pre-emptive distributions. Models that can be used to simultaneously test competing DDHS theories are desirable to help improve our understanding of habitat selection. We developed hierarchical, piecewise linear models that allow for simultaneous testing of DDHS theories and accommodate densities from multiple habitats and regional populations, environmental covariates, and random effects. We demonstrate the use of these models with data on mule deer (Odocoileus hemionus) abundance and net energy costs in different snow depths within winter ranges of five regional populations in western Idaho, USA. Regional population density explained 40% of the variation in population growth, and we found that deer were ideal free in winter ranges. Deer occupied habitats with lowest net energy costs at higher densities and at a higher rate than compared to habitats with intermediate and high energy costs. The proportion of a regional population in low energy cost habitat the previous year accounted for a significant amount of variation in population growth (17%), demonstrating the importance of winter habitat selection in regulating deer populations. These linear models are most appropriate for empirical data collected from centralized habitat patches within the local range of a species where individuals are either year-round residents or migratory (but have already arrived from migration).

Habitat utilization by coral reef fish: implications for specialists vs. generalists in a changing environment

1. The impact of environmental disturbance and habitat loss on associated species is expected to be dependent on a species' level of specialization. We examined habitat use and specialization of coral reef fish from the diverse and ecologically important family Pomacentridae, and determined which species are susceptible to declines in coral cover due to disturbance induced by crown-of-thorns seastar (COTS, Acanthaster planci L.). 2. A high proportion of pomacentrid species live in association with live coral as adults (40%) or juveniles (53%). Adults of many species had strong affiliations with branching corals, while juveniles favoured plating growth forms, reflecting the sizes of refuge provided by coral types. 3. Juveniles of species that associated with coral had narrower niche breadths than adult conspecifics, due to associations with specific coral types. The especially high coral association and narrower niche breadth of juveniles suggest that the presence of live coral is crucial for many species during early life history, and that disturbance-induced coral loss may have serious flow-on effects on adult abundance. 4. Microhabitat availability was a poor predictor of fish species abundance. Significant correlations between coverage of coral types and abundance of five adults and two juvenile species were detected; however, these relationships explained <35% and <10% of the variation in abundance of adult and juvenile species, respectively. 5. Niche breadth explained 74% of the variation in species' mean response to coral decline and it is clear that disturbance has a greater impact on resource specialists, suggesting that increasing frequency and intensity of coral loss will cause reef fish communities to become dominated by habitat generalists at the expense of coral-dwelling specialists.

Density dependence in the terrestrial life history stage of two anurans

Populations of species with complex life cycles have the potential to be regulated at multiple life history stages. However, research tends to focus on single stage density-dependence, which can lead to inaccurate conclusions about population regulation and subsequently hinder conservation efforts. In amphibians, many studies have demonstrated strong effects of larval density and have often assumed that populations are regulated at this life history stage. However, studies examining density regulation in the terrestrial stages are rare, and the functional relationships between terrestrial density and vital rates in amphibians are unknown. We determined the effects of population density on survival, growth and reproductive development in the terrestrial stage of two amphibians by raising juvenile wood frogs (Rana sylvatica) and American toads (Bufo americanus) at six densities in terrestrial enclosures. Density had strong negative effects on survival, growth and reproductive development in both species. We fitted a priori recruitment functions to describe the relationship between initial density and the density of survivors after one year, and determined the functional relationship between initial density and mass after one year. Animals raised at the lowest densities experienced growth and survival rates that were over twice as great as those raised at the highest density. All female wood frogs in the lowest density treatment showed signs of reproductive development, compared to only 6% in the highest density treatment. Female American toads reached minimum reproductive size only at low densities, and male wood frogs and American toads reached maturity only in the three lowest density treatments. Our results demonstrate that in the complex life cycle of amphibians, density in the terrestrial stage can reduce growth, survival and reproductive development and may play an important role in amphibian population regulation. We discuss the implications of these results for population regulation in complex life cycles and for amphibian conservation.

Habitat choice, recruitment and the response of coral reef fishes to coral degradation

The global degradation of coral reefs is having profound effects on the structure and species richness of associated reef fish assemblages. Historically, variation in the composition of fish communities has largely been attributed to factors affecting settlement of reef fish larvae. However, the mechanisms that determine how fish settlers respond to different stages of coral stress and the extent of coral loss on fish settlement are poorly understood. Here, we examined the effects of habitat degradation on fish settlement using a two-stage experimental approach. First, we employed laboratory choice experiments to test how settlers responded to early and terminal stages of coral degradation. We then quantified the settlement response of the whole reef fish assemblage in a field perturbation experiment. The laboratory choice experiments tested how juveniles from nine common Indo-Pacific fishes chose among live colonies, partially degraded colonies, and dead colonies with recent algal growth. Many species did not distinguish between live and partially degraded colonies, suggesting settlement patterns are resilient to the early stages of declining coral health. Several species preferred live or degraded corals, and none preferred to associate with dead, algal-covered colonies. In the field experiment, fish recruitment to coral colonies was monitored before and after the introduction of a coral predator (the crown-of-thorns starfish) and compared with undisturbed control colonies. Starfish reduced live coral cover by 95-100%, causing persistent negative effects on the recruitment of coral-associated fishes. Rapid reductions in new recruit abundance, greater numbers of unoccupied colonies and a shift in the recruit community structure from one dominated by coral-associated fishes before degradation to one predominantly composed of algal-associated fish species were observed. Our results suggest that while resistant to coral stress, coral death alters the process of replenishment of coral reef fish communities.

Marine reserve design: optimal size, habitats, species affinities, diversity, and ocean microclimate

The design of marine reserves is complex and fraught with uncertainty. However, protection of critical habitat is of paramount importance for reserve design. We present a case study as an example of a reserve design based on fine-scale habitats, the affinities of exploited species to these habitats, adult mobility, and the physical forcing affecting the dynamics of the habitats. These factors and their interaction are integrated in an algorithm that determines the optimal size and location of a marine reserve for a set of 20 exploited species within five different habitats inside a large kelp forest in southern California. The result is a reserve that encompasses approximately 42% of the kelp forest. Our approach differs fundamentally from many other marine reserve siting methods in which goals of area, diversity, or biomass are targeted a priori. Rather, our method was developed to determine how large a reserve must be within a specific area to protect a self-sustaining assemblage of exploited species. The algorithm is applicable across different ecosystems, spatial scales, and for any number of species. The result is a reserve in which habitat value is optimized for a predetermined set of exploited species against the area left open to exploitation. The importance of fine-scale habitat definitions for the exploited species off La Jolla is exemplified by the spatial pattern of habitats and the stability of these habitats within the kelp forest, both of which appear to be determined by ocean microclimate.