Impacts of urbanisation on biodiversity: the role of species mobility,degree of specialisation and spatial scale

Urbanisation has an important impact on biodiversity, mostly driving changes in species assemblages, through the replacement of specialist with generalist species, thus leading to biotic homogenisation. Mobility is also assumed to greatly affect species’ ability to cope in urban environments. Moreover, specialisation, mobility and their interaction are expected to greatly influence ecological processes such as metacommunity dynamics and assembly processes, and consequently the way and the spatial scale at which organisms respond to urbanisation. Here we investigate urbanisation impacts on distinct characteristics of species assemblages – namely specialisation degree in resource use, mobility and number of species, classified according to both characteristics and their combination – for vascular plants, butterflies and birds, across a range of spatial scales (from 1 × 1 km plots to 5 km‐radius buffers around them). We found that the degree of specialisation, mobility and their interaction, greatly influenced species’ responses to urbanisation, with highly mobile specialist species of all taxonomic groups being affected most. Two different patterns were found: for plants, urbanisation induced trait divergence by favouring highly mobile species with narrow habitat ranges. For birds and butterflies, however, it reduced the number of highly mobile specialist species, thus driving trait convergence. Mobile organisms, across and within taxonomic groups, tended to respond at larger spatial scales than those that are poorly mobile. These findings emphasize the need to take into consideration species’ ecological aspects, as well as a wide range of spatial scales when evaluating the impact of urbanisation on biodiversity. Our results also highlight the harmful impact of widespread urban expansion on organisms such as butterflies, especially highly mobile specialists, which were negatively affected by urban areas even at great distances.     

Resource-based habitat definition, niche overlap and conservation of two sympatric glacial relict butterflies

The precise knowledge of ecological resources and conditions required by species threatened by rapidly changing environmental conditions is of prime importance for conservation biology. Transferability of this knowledge between species with similar ecological requirements is often assumed, but rarely tested. This is especially the case for glacial relict populations confined to climate‐habitat traps from where they cannot move to rejoin areas with suitable environmental conditions. Using two glacial relict butterflies as model organisms, we first quantitatively define larval and adult resource‐based habitat use of each species. Secondly, we test the transferability of ecological profiles (both habitat and ecological niche) between these two species that share both the same biotope and the same host plant. Our results show that both species have markedly different ecological requirements relating to differences in life history and behavioural traits (i.e. egg‐laying strategies and mate‐locating behaviour). Although the two species share many ecological features, they use different functional habitats within our study site. The high degree of interspecific niche overlap should indicate a high interspecific competition. However, we argue that their co‐existence can be explained by the non‐limiting abundance of some resources (e.g. host plants), by the partial separation in time of adult flight periods and by the territorial behaviour of one of the species. We discuss the following general messages: (1) functional habitat of a (threatened) species should be defined in a spatial context corresponding to individual station keeping, and (2) quick diagnosis based on similar ecological requirements may be misleading for the design of reliable conservation and restoration strategies. Detailed mechanistic and quantitative ecological understanding of resource‐use and environmental tolerances across an organism's life cycle is essential for effective conservation in changing environments, like for glacial relict species.     

The use of specialisation indices to predict vulnerability of coral‐feeding butterflyfishes to environmental change

In the absence of detailed assessments of extinction risk, ecological specialisation is often used as a proxy of vulnerability to environmental disturbances and extinction risk. Numerous indices can be used to estimate specialisation; however, the utility of these different indices to predict vulnerability to future environmental change is unknown. Here we compare the performance of specialisation indices using coral‐feeding butterflyfishes as a model group. Our aims were to 1) quantify the dietary preferences of three butterflyfish species across habitats with differing levels of resource availability; 2) investigate how estimates of dietary specialisation vary with the use of different specialisation indices; 3) determine which specialisation indices best inform predictions of vulnerability to environmental change; and 4) assess the utility of resource selection functions to inform predictions of vulnerability to environmental change. The relative level of dietary specialisation estimated for all three species varied when different specialisation indices were used, indicating that the choice of index can have a considerable impact upon estimates of specialisation. Specialisation indices that do not consider resource abundance may fail to distinguish species that primarily use common resources from species that actively target resources disproportionately more than they are available. Resource selection functions provided the greatest insights into the potential response of species to changes in resource availability. Examination of resource selection functions, in addition to specialisation indices, indicated that Chaetodon trifascialis was the most specialised feeder, with highly conserved dietary preferences across all sites, suggesting that this species is highly vulnerable to the impacts of climate‐induced coral loss on reefs. Our results indicate that vulnerability assessments based on some specialisation indices may be misleading and the best estimates of dietary specialisation will be provided by indices which incorporate resource availability measures, as well as assessing responses of species to changes in resource availability.     

Novel tri‐isotope ellipsoid approach reveals dietary variation in sympatric predators

Sympatric species may partition resources to reduce competition and facilitate co‐existence. While spatial variation and specialization in feeding strategies may be prevalent among large marine predators, studies have focussed on sharks, birds, and marine mammals. We consider for the first time the isotopic niche partitioning of co‐occurring, teleost reef predators spanning multiple families. Using a novel tri‐isotope ellipsoid approach, we investigate the feeding strategies of seven of these species across an atoll seascape in the Maldives. We demonstrate substantial spatial variation in resource use of all predator populations. Furthermore, within each area, there was evidence of intraspecific variation in feeding behaviors that could not wholly be attributed to individual body size. Assessing species at the population level will mask these intraspecific differences in resource use. Knowledge of resource use is important for predicting how species will respond to environmental change and spatial variation should be considered when investigating trophic diversity.     

Residency Patterns and Migration Dynamics of Adult Bull Sharks (Carcharhinus leucas) on the East Coast of Southern Africa

Bull sharks (Carcharhinus leucas) are globally distributed top predators that play an important ecological role within coastal marine communities. However, little is known about the spatial and temporal scales of their habitat use and associated ecological role. In this study, we employed passive acoustic telemetry to investigate the residency patterns and migration dynamics of 18 adult bull sharks (195–283 cm total length) tagged in southern Mozambique for a period of between 10 and 22 months. The majority of sharks (n = 16) exhibited temporally and spatially variable residency patterns interspersed with migration events. Ten individuals undertook coastal migrations that ranged between 433 and 709 km (mean  = 533 km) with eight of these sharks returning to the study site. During migration, individuals exhibited rates of movement between 2 and 59 km.d⁻¹ (mean  = 17.58 km.d⁻¹) and were recorded travelling annual distances of between 450 and 3760 km (mean  = 1163 km). Migration towards lower latitudes primarily took place in austral spring and winter and there was a significant negative correlation between residency and mean monthly sea temperature at the study site. This suggested that seasonal change is the primary driver behind migration events but further investigation is required to assess how foraging and reproductive activity may influence residency patterns and migration. Results from this study highlight the need for further understanding of bull shark migration dynamics and suggest that effective conservation strategies for this vulnerable species necessitate the incorporation of congruent trans-boundary policies over large spatial scales.     

Neuroecology and the need for broader synthesis

Neuroecology combines physiological and ecological principles toward understanding behavioral mechanisms and their roles in establishing patterns of organismal abundances and species distributions. This amalgamation of research approaches incorporates the strengths of neuroethology to determine the cellular basis of behavior. It, however, treads where neuroethology does not by establishing critical linkages between neural processes and the population- and community-level consequences of individual behavior. Neuroecology also promotes understanding of nervous systems within a strong environmental context by encouraging use of keystone and foundation species as critical "ecological models" for studies of electrically excitable cells. Previous investigations of environmental stress, metabolism, and energy relations have proven the value of a combined cellular biochemical and biophysical approach toward predicting natural patterns of organismal abundances and species distributions. Borrowing from this approach, neuroecology would coalesce neuroscience with population and community ecology to establish how individual behavior functions, and how such behavior acts to determine higher-order biological processes.     

Using neutral landscapes to identify patterns of aggregation across resource points

Many organisms are aggregated within resource patches and aggregated spatially across landscapes with multiple resources. Such patchy distributions underpin models of population regulation and species coexistence, so ecologists require methods to analyse spatially‐explicit data of resource distribution and use. I describe a method for analysing maps of resources and testing hypotheses about how resource distribution influences the distribution of organisms, where resource patches can be described as points in a landscape and the number of organisms on each resource point is known. Using a mark correlation function and the linearised form of Ripley's K‐function, this version of marked point pattern analysis can characterise and test hypotheses about the spatial distribution of organisms (marks) on resource patches (points). The method extends a version of point pattern analysis that has wide ecological applicability, it can describe patterns over a range of scales, and can detect mixed patterns. Statistically, Monte Carlo permutations are used to estimate the difference between the observed and expected values of the mark correlation function. Hypothesis testing employs a flexible neutral landscape approach in which spatial characteristics of point patterns are preserved to some extent, and marks are randomised across points. I describe the steps required to identify the appropriate neutral landscape and apply the analysis. Simulated data sets illustrate how the choice of neutral landscape can influence ecological interpretations, and how this spatially‐explicit method and traditional dispersion indices can yield different interpretations. Interpretations may be general or context‐sensitive, depending on information available about the underlying point pattern and the neutral landscape. An empirical example of caterpillars exploiting food plants illustrates how this technique might be used to test hypotheses about adult oviposition and larval dispersal. This approach can increase the value of survey data, by making it possible to quantify the distribution of resource points in the landscape and the pattern of resource use by species.     

Body plan of consumed organisms influences ecological range of consumers through neural processing bias

The number of different resources used by an organism to feed, reproduce, and survive (ecological range) is a key determinant of community structure and community response to environmental change. It is known empirically that animals can have strong sensory biases, and here we use artificial neural networks to demonstrate how such biases may influence ecological range. We show that networks have strong biases for resources of a certain shape, producing distinct profiles of "cognitive accuracy" with ecological range. Generally, ecological specialization is tolerated for some resource body plans more than others; however, certain combinations of resources actually promote ecological specialization by producing local maxima in cognitive accuracy. Some of the variation in ecological range across consumers may be explained by these interactions between evolving nervous system and resource shape. Ecological patterns at even the largest of scales may be influenced by the miniscule processes of information exchange within networks of neurons.     

Stable isotope analysis provides new information on winter habitat use of declining avian migrants that is relevant to their conservation

Winter habitat use and the magnitude of migratory connectivity are important parameters when assessing drivers of the marked declines in avian migrants. Such information is unavailable for most species. We use a stable isotope approach to assess these factors for three declining African-Eurasian migrants whose winter ecology is poorly known: wood warbler Phylloscopus sibilatrix, house martin Delichon urbicum and common swift Apus apus. Spatially segregated breeding wood warbler populations (sampled across a 800 km transect), house martins and common swifts (sampled across a 3,500 km transect) exhibited statistically identical intra-specific carbon and nitrogen isotope ratios in winter grown feathers. Such patterns are compatible with a high degree of migratory connectivity, but could arise if species use isotopically similar resources at different locations. Wood warbler carbon isotope ratios are more depleted than typical for African-Eurasian migrants and are compatible with use of moist lowland forest. The very limited variance in these ratios indicates specialisation on isotopically restricted resources, which may drive the similarity in wood warbler populations' stable isotope ratios and increase susceptibility to environmental change within its wintering grounds. House martins were previously considered to primarily use moist montane forest during the winter, but this seems unlikely given the enriched nature of their carbon isotope ratios. House martins use a narrower isotopic range of resources than the common swift, indicative of increased specialisation or a relatively limited wintering range; both factors could increase house martins' vulnerability to environmental change. The marked variance in isotope ratios within each common swift population contributes to the lack of population specific signatures and indicates that the species is less vulnerable to environmental change in sub-Saharan Africa than our other focal species. Our findings demonstrate how stable isotope research can contribute to understanding avian migrants' winter ecology and conservation status.     

Estimation of Shark Home Ranges using Passive Monitoring Techniques

We examined a population of blacktip sharks, Carcharhinus limbatus, within a coastal nursery area to define how individuals use the nursery habitat throughout the summer. We used a series of acoustic hydrophones to passively monitor the movement patterns of sharks for periods up to 167 days. We used passive monitoring data to calculate home range estimates using minimum convex polygon (MCP) and fixed kernel estimators. MCP calculated the extent of an individual's range. Kernel estimates provided information regarding the utilization of space within the home range including core area (50% kernel) and larger excursions outside the core area (95% kernel). Individuals within the nursery area typically used a consistently small core area. All sharks monitored in the study site underwent a home range expansion during the month of July, suggesting a synchronous population-level change in habitat use. This change in habitat use was reflected in all home range calculations. Passive monitoring revealed that young sharks remain within the nursery area for up to 6 months. The long-term use of this nursery area reflects its critical importance to young blacktip sharks.     

Novel model‐based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient

A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome‐based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate‐associated ecotypes in populations of nitrogen‐fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate‐associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.     

Phylogeography: spanning the ecology‐evolution continuum

Synthesis of ecological and evolutionary concepts and tools has led to improved understanding of how diversification, dispersal, community assembly, long‐term coexistence and extinction shape patterns of biological diversity. Phylogeography, with its focus on Quaternary interactions within and between populations, can help elucidate the processes acting between the evolutionary time‐scales on which species arise and the ecological time‐scales on which members of an assemblage interact with each other and their environment. Still, it has yet to be widely incorporated in that synthesis. Here, we highlight three areas where integration of phylogeography with ecological and evolutionary approaches can provide new insights into key questions. First, phylogeography can help clarify the roles of isolation, niche conservatism and environmental stability in generating patterns of alpha‐ and beta‐diversity. Second, phylogeography can help isolate the effects of Quaternary dispersal limitation from other factors driving community assembly and spatial turnover. Third, phylogeography can help identify key processes leading to and resulting from extinction events, including the population dynamics of species range reduction and its effects on the strength and temporal flexibility of networks of species interactions. We conclude with an outlook on the data‐gathering protocols necessary for this collaborative, interdisciplinary research agenda.     

Environmental diel variation, parasite loads, and local population structuring of a mixed-mating mangrove fish

Genetic variation within populations depends on population size, spatial structuring, and environmental variation, but is also influenced by mating system. Mangroves are some of the most productive and threatened ecosystems on earth and harbor a large proportion of species with mixed-mating (self-fertilization and outcrossing). Understanding population structuring in mixed-mating species is critical for conserving and managing these complex ecosystems. Kryptolebias marmoratus is a unique mixed-mating vertebrate inhabiting mangrove swamps under highly variable tidal regimes and environmental conditions. We hypothesized that geographical isolation and ecological pressures influence outcrossing rates and genetic diversity, and ultimately determine the local population structuring of K. marmoratus. By comparing genetic variation at 32 microsatellites, diel fluctuations of environmental parameters, and parasite loads among four locations with different degrees of isolation, we found significant differences in genetic diversity and genotypic composition but little evidence of isolation by distance. Locations also differed in environmental diel fluctuation and parasite composition. Our results suggest that mating system, influenced by environmental instability and parasites, underpins local population structuring of K. marmoratus. More generally, we discuss how the conservation of selfing species inhabiting mangroves and other biodiversity hotspots may benefit from knowledge of mating strategies and population structuring at small spatial scales.     

Patterns of resource use and isotopic niche overlap among three species of sharks occurring within a protected subtropical estuary

Predation is one of the most fundamental and unifying concepts in ecology, and we are beginning to obtain a more complete understanding of how predators drive community structure and ecosystem function through their impacts on prey. We know considerably less about how predators affect each other through intraguild interactions, which is surprising considering predators often occur simultaneously and may compete for resources while avoiding being killed themselves. In the present study, we examined aspects of inter- and intra-specific resource use among three species of large-bodied predatory sharks (blacktip, bull, lemon) co-occurring within a subtropical, protected bay in the southeastern USA. Specifically, we inferred relative trophic position, isotopic niche overlap, and patterns of resource use of sharks using stable isotope analysis of carbon-13 and nitrogen-15 from blood and fin cartilage samples. We also combined these approaches with estimates of abundance and occurrence from empirical shark surveys to consider whether these species may exhibit resource partitioning in space and time. We found that all three species overlapped in space, and there was some isotopic niche overlap between the species. We also found evidence of temporal isotopic niche stability, suggesting that co-occurring shark species may compete for available prey resources, but individuals of those species may have similar patterns of resource use over time. We discuss our findings as they relate to the ecologies of the species in question and how sound conservation and management of ecosystems can allow for predator diversity, sympatry, and stable use of resources at the top of the food chain.     

What's your move? Movement as a link between personality and spatial dynamics in animal populations

Recent studies have established the ecological and evolutionary importance of animal personalities. Individual differences in movement and space‐use, fundamental to many personality traits (e.g. activity, boldness and exploratory behaviour) have been documented across many species and contexts, for instance personality‐dependent dispersal syndromes. Yet, insights from the concurrently developing movement ecology paradigm are rarely considered and recent evidence for other personality‐dependent movements and space‐use lack a general unifying framework. We propose a conceptual framework for personality‐dependent spatial ecology. We link expectations derived from the movement ecology paradigm with behavioural reaction‐norms to offer specific predictions on the interactions between environmental factors, such as resource distribution or landscape structure, and intrinsic behavioural variation. We consider how environmental heterogeneity and individual consistency in movements that carry‐over across spatial scales can lead to personality‐dependent: (1) foraging search performance; (2) habitat preference; (3) home range utilization patterns; (4) social network structure and (5) emergence of assortative population structure with spatial clusters of personalities. We support our conceptual model with spatially explicit simulations of behavioural variation in space‐use, demonstrating the emergence of complex population‐level patterns from differences in simple individual‐level behaviours. Consideration of consistent individual variation in space‐use will facilitate mechanistic understanding of processes that drive social, spatial, ecological and evolutionary dynamics in heterogeneous environments.     

Behavioral response of a mobile marine predator to environmental variables differs across ecoregions

Animal movement and habitat selection are in part a response to landscape heterogeneity. Many studies of movement and habitat selection necessarily use environmental covariates that are readily available over large‐scales, which are assumed representative of functional habitat features such as resource availability. For widely distributed species, response to such covariates may not be consistent across ecosystems, as response to any specific covariate is driven by its biological relevance within the context of each ecosystem. Thus, the study of any widely distributed species within a limited geographic region may provide inferences that are not widely generalizable. Our goal was to evaluate the response of a marine predator to a suite of environmental covariates across a wide ecological gradient. We identified two behavioral states (resident and transient) in the movements of shortfin mako sharks Isurus oxyrinchus tracked via satellite telemetry in two regions of the western North Atlantic Ocean: the tropical Caribbean/Gulf of Mexico marginal sea (CGM), and the temperate waters of the open western Atlantic Ocean (OWA). We compared patterns of resident behavior between regions, and modeled relationships between oceanographic variables and resident behavior. We tracked 39 sharks during 2013–2015. Resident behavior was associated with shallow, continental shelf and slope waters in both regions. In the OWA resident behavior was associated with low sea surface temperature and high primary productivity, however, sharks exhibited no response to either variable in the CGM. There was a negative relationship between sea‐surface height gradient (a proxy for oceanic fronts) and resident behavior in the OWA, and a positive relationship in the CGM. Our observations likely reflect shark responses to regional variability in factors responsible for the distribution and availability of prey. Our study illustrates the importance of studying widely distributed species in a consistent manner over large spatial scales.     

Ecological strategies in stable and disturbed environments depend on species specialisation

Ecological strategies are integral to understanding species survival in different environments. However, how habitat specialisation is involved in such strategies is not fully understood, particularly in heterogeneous and disturbed environments. Here, we studied the trait associations between specialisation, dispersal ability, competitiveness, reproductive investment and survival rate in a spatially explicit metacommunity model under various disturbance rates. Though no unique trait values were associated with specialisation, relationships were uncovered depending on environmental factors. We found strong trait associations mainly for generalist species, while specialist species exhibited a larger range of trait combinations. Trait associations were driven first by the disturbance rate and second by species' dispersal ability and generation overlap. With disturbance, low dispersal ability was strongly selected against, for specialists as well as for generalists. Our results demonstrate that habitat specialisation is critical for the emergence of trait strategies in metacommunities and that disturbance in interaction with dispersal ability limits not only the range of trait values but also the type of possible trait associations.     

Isolation by environmental distance in mobile marine species: molecular ecology of franciscana dolphins at their southern range

The assessment of population structure is a valuable tool for studying the ecology of endangered species and drafting conservation strategies. As we enhance our understanding about the structuring of natural populations, it becomes important that we also understand the processes behind these patterns. However, there are few rigorous assessments of the influence of environmental factors on genetic patterns in mobile marine species. Given their dispersal capabilities and localized habitat preferences, coastal cetaceans are adequate study species for evaluating environmental effects on marine population structure. The franciscana dolphin, a rare coastal cetacean endemic to the Western South Atlantic, was studied to examine these issues. We analysed genetic data from the mitochondrial DNA and 12 microsatellite markers for 275 franciscana samples utilizing frequency‐based, maximum‐likelihood and Bayesian algorithms to assess population structure and migration patterns. This information was combined with 10 years of remote sensing environmental data (chlorophyll concentration, water turbidity and surface temperature). Our analyses show the occurrence of genetically isolated populations within Argentina, in areas that are environmentally distinct. Combined evidence of genetic and environmental structure suggests that isolation by distance and a process here termed isolation by environmental distance can explain the observed correlations. Our approach elucidated important ecological and conservation aspects of franciscana dolphins, and has the potential to increase our understanding of ecological processes influencing genetic patterns in other marine species.     

Capital and income breeding traits differentiate trophic match–mismatch dynamics in large herbivores

For some species, climate change has altered environmental conditions away from those in which life-history strategies evolved. In such cases, if adaptation does not keep pace with these changes, existing life-history strategies may become maladaptive and lead to population declines. We use life-history theory, with a specific emphasis on breeding strategies, in the context of the trophic match–mismatch framework to form generalizable hypotheses about population-level consumer responses to climate-driven perturbations in resource availability. We first characterize the income and breeding traits of sympatric caribou and muskoxen populations in western Greenland, and then test trait-based hypotheses about the expected reproductive performance of each population during a period of high resource variability at that site. The immediate reproductive performance of income breeding caribou decreased with trophic mismatch. In contrast, capital breeding muskoxen were relatively unaffected by current breeding season resource variability, but their reproductive performance was sensitive to resource conditions from previous years. These responses matched our expectations about how capital and income breeding strategies should influence population susceptibility to phenological mismatch. We argue for a taxon-independent assessment of trophic mismatch vulnerability based on a life-history strategy perspective in the context of prevailing environmental conditions.     

Modelling the niche for a marine vertebrate: a case study incorporating behavioural plasticity,proximate threats and climate change

The integration of satellite telemetry, remotely sensed environmental data, and habitat/environmental modelling has provided for a growing understanding of spatial and temporal ecology of species of conservation concern. The Republic of Cape Verde comprises the only substantial rookery for the loggerhead turtle Caretta caretta in the eastern Atlantic. A size related dichotomy in adult foraging patterns has previously been revealed for adult sea turtles from this population with a proportion of adults foraging neritically, whilst the majority forage oceanically. Here we describe observed habitat use and employ ecological niche modelling to identify suitable foraging habitats for animals utilising these two distinct behavioural strategies. We also investigate how these predicted habitat niches may alter under the influence of climate change induced oceanic temperature rises. We further contextualise our niche models with fisheries catch data and knowledge of fisheries ‘hotspots’ to infer threat from fisheries interaction to this population, for animals employing both strategies. Our analysis revealed repeated use of coincident oceanic habitat, over multiple seasons, by all smaller loggerhead turtles, whilst larger neritic foraging turtles occupied continental shelf waters. Modelled habitat niches were spatially distinct, and under the influence of predicted sea surface temperature rises, there was further spatial divergence of suitable habitats. Analysis of fisheries catch data highlighted that the observed and modelled habitats for oceanic and neritic loggerhead turtles could extensively interact with intensive fisheries activity within oceanic and continental shelf waters of northwest Africa. We suggest that the development and enforcement of sustainable management strategies, specifically multi‐national fisheries policy, may begin to address some of these issues; however, these must be flexible and adaptive to accommodate potential range shift for this species.