Freshwater zooplankton metapopulations and metacommunities respond differently to environmental and spatial variation

Theory predicts that population genetic structure and metacommunity structure are linked by the common processes of drift and migration, but how population genetic structure and metacommunity structure are related in nature is still unknown. Deeper understanding of the processes influencing both genetic and community diversity is vital for better predicting how environmental change will impact biodiversity patterns. We examined how crustacean zooplankton and rotifer species' metapopulation genetic structure and metacommunities respond to environmental and spatial variation both within and across four regions of boreal Canada. Metapopulation and metacommunity variation partitioning results were compared within and across the four regions. Metapopulations and metacommunities responded differently to environmental variation and spatial structure both within and across regions, as metapopulations were influenced by different environmental variables compared to metacommunities. At larger spatial scales both metapopulations and metacommunities exhibited greater spatial and environmental structuring, again responding to a different subset of environmental variables. Our findings suggest that even though both genetic and species diversity are linked by the same processes, regional variation in environmental characteristics and spatial structure influence resulting biodiversity patterns differently. To date, no other empirical research has explored relationships between entire metapopulation and metacommunity assemblages at large regional spatial scales.

The Spread of Rabies Among Dogs in Pranburi District, Thailand: A Metapopulation Modeling Approach

Rabies, a deadly zoonotic disease, is causing serious public health problems worldwide. Dogs are considered the main reservoir for rabies infection in humans. A better understanding of the dissemination of rabies in the dog population is crucial. The present study, therefore, aimed to explore the subpopulation of dogs roaming around rabies-outbreak areas and the model of its possible spread. We used a Cross-K function to investigate the spatial clustering between the locations of dog rabies cases and the feeding points of a stray dog feeder. We then observed the social interaction of dogs in a community using a metapopulation analysis and further simulated the possible spread of rabies within this population. We found that the reported rabies cases were spatially clustered with the routes of the dog feeder. Therefore, more sustainable stray dog management is required. Based on our community dog observations, we found 20 groups comprising 222 dogs with an average of 11 dogs per group. In our infectious model, we suggested that 47.7% of dogs are likely to be infected in a year if no interventions are implemented. Therefore, the veterinary authorities should rigorously strengthen their rabies prevention and control strategies to protect both animal and human health.

Pan-regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures

Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to characterize the critical yet frequently overlooked biodiversity patterns of marine benthic organisms. In order to disentangle the relevance of environmental factors in benthic patterns, here, through standardized metabarcoding protocols, we analyse sessile and mobile (<2 mm) organisms collected using ARMS deployed across six regions with different environmental conditions (3 sites × 3 replicates per region): Baltic, Western Mediterranean, Adriatic, Black and Red Seas, and the Bay of Biscay. A total of 27,473 Amplicon Sequence Variants (ASVs) were observed ranging from 1,404 in the Black Sea to 9,958 in the Red Sea. No ASVs were shared among all regions. The highest number of shared ASVs was between the Western Mediterranean and the Adriatic Sea (116) and Bay of Biscay (115). Relatively high numbers of ASVs (103), mostly associated with the genus Amphibalanus, were also shared between the lower salinity seas (Baltic and Black Seas). We found that compositional differences in spatial patterns of rocky-shore benthos are determined slightly more by dispersal limitation than environmental filtering. Dispersal limitation was similar between sessile and mobile groups, while the sessile group had a larger environmental niche breadth than the mobile group. Further, our study can provide a foundation for future evaluations of biodiversity patterns in the cryptobiome, which can contribute up to 70% of the local biodiversity.

Dynamical Ising model of spatially coupled ecological oscillators

Long-range synchrony from short-range interactions is a familiar pattern in biological and physical systems, many of which share a common set of 'universal' properties at the point of synchronization. Common biological systems of coupled oscillators have been shown to be members of the Ising universality class, meaning that the very simple Ising model replicates certain spatial statistics of these systems at stationarity. This observation is useful because it reveals which aspects of spatial pattern arise independently of the details governing local dynamics, resulting in both deeper understanding of and a simpler baseline model for biological synchrony. However, in many situations a system's dynamics are of greater interest than their static spatial properties. Here, we ask whether a dynamical Ising model can replicate universal and non-universal features of ecological systems, using noisy coupled metapopulation models with two-cycle dynamics as a case study. The standard Ising model makes unrealistic dynamical predictions, but the Ising model with memory corrects this by using an additional parameter to reflect the tendency for local dynamics to maintain their phase of oscillation. By fitting the two parameters of the Ising model with memory to simulated ecological dynamics, we assess the correspondence between the Ising and ecological models in several of their features (location of the critical boundary in parameter space between synchronous and asynchronous dynamics, probability of local phase changes and ability to predict future dynamics). We find that the Ising model with memory is reasonably good at representing these properties of ecological metapopulations. The correspondence between these models creates the potential for the simple and well-known Ising class of models to become a valuable tool for understanding complex biological systems.

Intersexual differences in density-dependent dispersal and their evolutionary drivers

Dispersal is well recognized as a major driver of evolutionary processes in local populations. Nevertheless, dispersal abilities should also be perceived as a life-history trait, being subject to evolutionary changes in response to various drivers. Empirical studies investigating these drivers rarely consider that they may influence male and female dispersal differently. The purpose of our study was to document intersexual differences in density-dependent emigration from local habitat patches. As a model system, we used a metapopulation of Maculinea (Phengaris) teleius butterfly, in which densities of both sexes vary greatly throughout the flying season. Following intensive mark-release-recapture surveys, the parameters and predictors of dispersal were analysed with the Virtual Migration model and the multi-state recapture model. The emigration rate in males was substantially higher in the early season, especially at smaller habitat patches. With the proportion of females increasing with the season progression, males became reluctant to emigrate from their natal patches. In turn, higher female emigration in the later part of the season was most strongly associated with female tendency to reduce intraspecific competition experienced by their offspring. Our findings provide evidence for the impact of reproductive strategies on dispersal in both sexes. The difference in reproductive strategies of males and females explains sex-biased dispersal in different parts of the season, which carries important implications for metapopulation functioning.

Optimal spatial prioritization of control resources for elimination of invasive species under demographic uncertainty

Populations of invasive species often spread heterogeneously across a landscape, consisting of local populations that cluster in space but are connected by dispersal. A fundamental dilemma for invasive species control is how to optimally allocate limited fiscal resources across local populations. Theoretical work based on perfect knowledge of demographic connectivity suggests that targeting local populations from which migrants originate (sources) can be optimal. However, demographic processes such as abundance and dispersal can be highly uncertain, and the relationship between local population density and damage costs (damage function) is rarely known. We used a metapopulation model to understand how budget and uncertainty in abundance, connectivity, and the damage function, together impact return on investment (ROI) for optimal control strategies. Budget, observational uncertainty, and the damage function had strong effects on the optimal resource allocation strategy. Uncertainty in dispersal probability was the least important determinant of ROI. The damage function determined which resource prioritization strategy was optimal when connectivity was symmetric but not when it was asymmetric. When connectivity was asymmetric, prioritizing source populations had a higher ROI than allocating effort equally across local populations, regardless of the damage function, but uncertainty in connectivity structure and abundance reduced ROI of the optimal prioritization strategy by 57% on average depending on the control budget. With low budgets (monthly removal rate of 6.7% of population), there was little advantage to prioritizing resources, especially when connectivity was high or symmetric, and observational uncertainty had only minor effects on ROI. Allotting funding for improved monitoring appeared to be most important when budgets were moderate (monthly removal of 13-20% of the population). Our result showed that multiple sources of observational uncertainty should be considered concurrently for optimizing ROI. Accurate estimates of connectivity direction and abundance were more important than accurate estimates of dispersal rates. Developing cost-effective surveillance methods to reduce observational uncertainties, and quantitative frameworks for determining how resources should be spatially apportioned to multiple monitoring and control activities are important and challenging future directions for optimizing ROI for invasive species control programs.

Comparison of genomic diversity and structure of sable antelope (Hippotragus niger) in zoos, conservation centers, and private ranches in North America

As we enter the sixth mass extinction, many species that are no longer self-sustaining in their natural habitat will require ex situ management. Zoos have finite resources for ex situ management, and there is a need for holistic conservation programs between the public and private sector. Ex situ populations of sable antelope, Hippotragus niger, have existed in zoos and privately owned ranches in North America since the 1910s. Unknown founder representation and relatedness has made the genetic management of this species challenging within zoos, while populations on privately owned ranches are managed independently and retain minimal-to-no pedigree history. Consequences of such challenges include an increased risk of inbreeding and a loss of genetic diversity. Here, we developed and applied a customized targeted sequence capture panel based on 5,000 genomewide single-nucleotide polymorphisms to investigate the genomic diversity present in these uniquely managed populations. We genotyped 111 sable antelope: 23 from zoos, 43 from a single conservation center, and 45 from ranches. We found significantly higher genetic diversity and significantly lower inbreeding in herds housed in zoos and conservation centers, when compared to those in privately owned ranches, likely due to genetic-based breeding recommendations implemented in the former populations. Genetic clustering was strong among all three populations, possibly as a result of genetic drift. We propose that the North American ex situ population of sable antelope would benefit from a metapopulation management system, to halt genetic drift, reduce the occurrence of inbreeding, and enable sustainable population sizes to be managed ex situ.

Disease in Invasive Plant Populations

Non-native invasive plants can establish in natural areas, where they can be ecologically damaging and costly to manage. Like cultivated plants, invasive plants can experience a relatively disease-free period upon introduction and accumulate pathogens over time. Diseases of invasive plant populations are infrequently studied compared to diseases of agriculture, forestry, and even native plant populations. We evaluated similarities and differences in the processes that are likely to affect pathogen accumulation and disease in invasive plants compared to cultivated plants, which are the dominant focus of the field of plant pathology. Invasive plants experience more genetic, biotic, and abiotic variation across space and over time than cultivated plants, which is expected to stabilize the ecological and evolutionary dynamics of interactions with pathogens and possibly weaken the efficacy of infectious disease in their control. Although disease is expected to be context dependent, the widespread distribution of invasive plants makes them important pathogen reservoirs. Research on invasive plant diseases can both protect crops and help manage invasive plant populations.

Investigating persistent measles dynamics in Niger and associations with rainfall

Measles is a major cause of child mortality in sub-Saharan Africa. Current immunization strategies achieve low coverage in areas where transmission drivers differ substantially from those in high-income countries. A better understanding of measles transmission in areas with measles persistence will increase vaccination coverage and reduce ongoing transmission. We analysed weekly reported measles cases at the district level in Niger from 1995 to 2004 to identify underlying transmission mechanisms. We identified dominant periodicities and the associated spatial clustering patterns. We also investigated associations between reported measles cases and environmental drivers associated with human activities, particularly rainfall. The annual and 2-3-year periodicities dominated the reporting data spectrum. The annual periodicity was strong with contiguous spatial clustering, consistent with the latitudinal gradient of population density, and stable over time. The 2-3-year periodicities were weaker, unstable over time and had spatially fragmented clustering. The rainy season was associated with a lower risk of measles case reporting. The annual periodicity likely reflects seasonal agricultural labour migration, whereas the 2-3-year periodicity potentially results from multiple mechanisms such as reintroductions and vaccine coverage heterogeneity. Our findings suggest that improving vaccine coverage in seasonally mobile populations could reduce strong measles seasonality in Niger and across similar settings.

The loss of self-incompatibility in a range expansion

It is commonly observed that plant species' range margins are enriched for increased selfing rates and, in otherwise self-incompatible species, for self-compatibility (SC). This has often been attributed to a response to selection under mate and/or pollinator limitation. However, range expansion can also cause reduced inbreeding depression, and this could facilitate the evolution of selfing in the absence of mate or pollinator limitation. Here, we explore this idea using spatially explicit individual-based simulations of a range expansion, in which inbreeding depression, variation in self-incompatibility (SI), and mate availability evolve. Under a wide range of conditions, the simulated range expansion brought about the evolution of selfing after the loss of SI in range-marginal populations. Under conditions of high recombination between the self-incompatibility locus (S-locus) and viability loci, SC remained marginal in the expanded metapopulation and could not invade the range core, which remained self-incompatible. In contrast, under low recombination and migration rates, SC was frequently able to displace SI in the range core by maintaining its association with a genomic background with purged genetic load. We conclude that the evolution of inbreeding depression during a range expansion promotes the evolution of SC at range margins, especially under high rates of recombination.‬.

Incorporating the Connectivity Timescale in Metapopulation Partitioning

The often complex spatial patterns of propagule dispersal across a metapopulation present a challenge for species management, motivating efforts to represent the connectivity in simpler but meaningful ways. The reduction of complexity may be achieved by partitioning the metapopulation into groups of highly connected patches called "subpopulations." To have relevance for management, these subunits must be defined from ecological or evolutionary principles. The probabilities of dispersal-mediated propagule interchange between sites, commonly organized into a connectivity matrix, entail a timescale that is usually ignored in subpopulation analyses, limiting their utility and possibly leading to misinterpretation and wrong management decisions. Recognition of the essentially dynamical role played by metapopulation connectivity naturally leads to the incorporation of the generational timescale into the partitioning analysis. An algorithm is proposed to determine the subpopulations-both their cardinality and their composition-as a function of the generational timescale and of a limiting probability of connection, illustrated with a novel empirical estimate of mesopelagic connectivity. The proposed framework allows the unambiguous determination of the timescales corresponding to dispersal barriers and the identification of effective ecological units across the spectrum of management-relevant time horizons.

Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation

Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition, characteristics that can affect the severity of inbreeding depression. We utilized extensive long-term data on more than 3,100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realized inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than noninbred individuals. Inbreeding depression, measured as the decline in fitness-related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.

Estimating the potential for coral adaptation to global warming across the Indo-West Pacific

The potential of reef-building corals to adapt to increasing sea-surface temperatures is often debated but has rarely been comprehensively modeled on a region-wide scale. We used individual-based simulations to model adaptation to warming in a coral metapopulation comprising 680 reefs and representing the whole of the Central Indo-West Pacific. Encouragingly, some reefs-most notably Vietnam, Japan, Taiwan, New Caledonia and the southern half of the Great Barrier Reef-exhibited high capacity for adaptation and, in our model, maintained coral cover even under a rapid "business-as-usual" warming scenario throughout the modeled period (200 years). Higher resilience of these reefs was observed under all tested parameter settings except the models prohibiting selection and/or migration during warming. At the same time, the majority of reefs in the region tended to collapse within the first 100 years of warming. The adaptive potential (odds of maintaining high coral cover) of a given reef could be predicted based on two metrics: the reef's present-day temperature, and the proportion of recruits immigrating from warmer locations. The latter metric explains the most variation in adaptive potential, and significantly correlates with actual coral cover changes observed throughout the region between the 1970s and the early 2000s. These findings will help prioritize coral conservation efforts and plan assisted gene flow interventions to boost the adaptive potential of specific coral populations.

Contrasting demographic trends and asymmetric migration rates in a spatially structured amphibian population

Natural populations often persist at the landscape scale as metapopulations, with breeding units (subpopulations) experiencing temporal extinction and recolonization events. Important parameters to forecast population viability in these systems include the ratio of the effective number of breeders (N_b ) to the total number of adults (N_a ) and migration rates among subpopulations. Here, we present the results of a 10-year integrative monitoring program of a metapopulation of the Iberian green frog (Pelophylax perezi) in central Spain. We characterized population dynamics at two main breeding ponds (Gravera and Laguna) using capture-mark-recapture data to estimate N_a in each breeding season, and multilocus genotypes to estimate the effective population size (N_e ), N_b , individual breeding success, and migration rates. Both ponds experienced population decline after a dry season, with Gravera subsequently recovering and Laguna suffering a bottleneck associated with genetic impoverishment. In this subpopulation, average allelic richness and private alleles decreased from 2010 (10.87 and 1.67, respectively) to 2018 (8.0 and 0.20). The N_b /N_a ratio in Laguna in 2018 was twice as high (0.95) than in Gravera (0.41) or in pre-bottleneck Laguna (0.50), suggesting plasticity or genetic compensation through increased individual breeding success. Migration rates were asymmetric between ponds, with a stronger contribution from Gravera to Laguna (29.9% vs. 16.2% in the opposite direction) that may result in a rescue effect. This study emphasizes the importance of integrative demographic approaches for the monitoring of natural populations based on a better understanding of their spatio-temporal dynamics, which provides valuable information for conservation actions.

Disentangling local, metapopulation, and cross-community sources of stabilization and asynchrony in metacommunities

Asynchronous fluctuations of populations are essential for maintaining stable levels of bio-mass and ecosystem function in landscapes. Yet, understanding the stabilization of metacommunities by asynchrony is complicated by the existence of multiple forms of asynchrony that are typically studied independently: Community ecologists, for instance, focus on asynchrony within and among local communities, while population ecologists emphasize asynchrony of populations in metapopulations. Still, other forms of asynchrony, such as that which underlies the spatial insurance effect, are not captured by any existing analytical frameworks. We therefore developed a framework that would in one analysis unmask the stabilizing roles of local communities and metapopulations and so unify these perspectives. Our framework shows that metacommunity stabilization arises from one local and two regional forms of asynchrony: (1) asynchrony among species of a local community, (2) asynchrony among populations of a metapopulation, and (3) cross-community asynchrony, which is between different species in different local communities and underlies spatial insurance. For each type of stabilization, we derived links to diversity indices and associated diversity-stability relationships. We deployed this framework in a set of rock pool invertebrate metacommunities in Discovery Bay, Jamaica, to partition sources of stabilization and test their dependence on diversity. Cross-community asynchrony was the dominant form of stabilization, accounting for >60% of total metacommunity stabilization despite being undetectable with existing frameworks. Environmental variation influenced types of stabilization through different mechanisms. pH and dissolved oxygen, for example, increased asynchrony by decorrelating local species, while salinity did so by changing the abundance structure of metapopulations. Lastly, all types of asynchrony depended strongly on different types of diversity (alpha, metapopulation, and beta diversity drove local, metapopulation, and cross-community asynchrony, respectively) to produce multiple diversity-stability relationships within metacommunities. Our new partition of metacommunity dynamics highlights how different elements—from local communities to metapopulations—combine to stabilize metacommunities and depend critically on contrasting environmental regimes and diversities. Understanding and balancing these sources of stability in dynamic landscapes is a looming challenge for the future. We suggest that synthetic frameworks which merge ecological perspectives will be essential for grasping and safeguarding the stability of natural systems.

Spatial variation in exploited metapopulations obscures risk of collapse

Unanticipated declines among exploited species have commonly occurred despite harvests that appeared sustainable prior to collapse. This is particularly true in the oceans where spatial scales of management are often mismatched with spatially complex metapopulations. We explore causes, consequences, and potential solutions for spatial mismatches in harvested metapopulations in three ways. First, we generate novel theory illustrating when and how harvesting metapopulations increases spatial variability and in turn masks local-scale volatility. Second, we illustrate why spatial variability in harvested metapopulations leads to negative consequences using an empirical example of a Pacific herring metapopulation. Finally, we construct a numerical management strategy evaluation model to identify and highlight potential solutions for mismatches in spatial scale and spatial variability. Our results highlight that spatial complexity can promote stability at large scales, however, ignoring spatial complexity produces cryptic and negative consequences for people and animals that interact with resources at small scales. Harvesting metapopulations magnifies spatial variability, which creates discrepancies between regional and local trends while increasing risk of local population collapses. Such effects asymmetrically impact locally constrained fishers and predators, which are more exposed to risks of localized collapses. Importantly, we show that dynamically optimizing harvest can minimize local risk without sacrificing yield. Thus, multiple nested scales of management may be necessary to avoid cryptic collapses in metapopulations and the ensuing ecological, social, and economic consequences.

Mating System and Genetic Structure Across All Known Populations of Dyckia brevifolia: A Clonal, Endemic, and Endangered Rheophyte Bromeliad

Dyckia brevifolia is an endemic rheophyte bromeliad that occurs exclusively in patches on rocky banks of the Itajaí-Açu River in southern Brazil. The genetic diversity of all known populations was carried out using allozyme markers and the total numbers of rosettes, reproductive rosettes, and clumps per population were characterized. The mating system was also investigated. Most rosettes were aggregated in groups, and the populations differed significantly in number of rosettes and reproductive rosettes per population. The outcrossing rate obtained was 8.2%, with predominant selfing. The populations presented an average of 1.4 alleles per locus and 27% of polymorphisms. The mean expected genetic diversity was 0.067. Downstream populations showed the highest genetic diversity which could be attributed to hydrochory (unidirectional river flow). Most genetic diversity is distributed among populations (F^ST = 0.402). Natural habitats of D. brevifolia are not recommended for the construction of hydroelectric plants given that it would seriously complicate in situ conservation of this species. Based on the results of this study, it can be concluded that between 35 and 161 reproductive rosettes must be collected for effective ex situ conservation, depending on the targeted population, or seeds collected from 157 seed-rosettes per population.

Using metapopulation theory for practical conservation of mangrove endemic birds

As a landscape becomes increasingly fragmented through habitat loss, the individual patches become smaller and more isolated and thus less likely to sustain a local population. Metapopulation theory is appropriate for analyzing fragmented landscapes because it combines empirical landscape features with species-specific information to produce direct information on population extinction risks. This approach contrasts with descriptions of habitat fragments, which provide only indirect information on risk. Combining a spatially explicit metapopulation model with empirical data on endemic species' ranges and maps of habitat cover, we calculated the metapopulation capacity-a measure of a landscape's ability to sustain a metapopulation. Mangroves provide an ideal model landscape because they are of conservation concern and their patch boundaries are easily delineated. For 2000-20015, we calculated global metapopulation capacity for 99 metapopulations of 32 different bird species endemic to mangroves. Northern Australia and Southeast Asia had the highest richness of mangrove endemic birds. The Caribbean, Pacific coast of Central America, Madagascar, Borneo, and isolated patches in Southeast Asia in Myanmar and Malaysia had the highest metapopulation losses. Regions with the highest loss of habitat area were not necessarily those with the highest loss of metapopulation capacity. Often, it was not a matter of how much, but how the habitat was lost. Our method can be used by managers to evaluate and prioritize a landscape for metapopulation persistence.

The rescue effect and inference from isolation-extinction relationships

The rescue effect in metapopulations hypothesises that less isolated patches are unlikely to go extinct because recolonisation may occur between breeding seasons ('recolonisation rescue'), or immigrants may sufficiently bolster population size to prevent extinction altogether ('demographic rescue'). These mechanisms have rarely been demonstrated directly, and most evidence of the rescue effect is from relationships between isolation and extinction. We determined the frequency of recolonisation rescue for metapopulations of black rails (Laterallus jamaicensis) and Virginia rails (Rallus limicola) from occupancy surveys conducted during and between breeding seasons, and assessed the reliability of inferences about the occurrence of rescue drawn from isolation-extinction relationships, including autologistic isolation measures that corrected for unsurveyed patches and imperfect detection. Recolonisation rescue occurred at expected rates, but was elevated during periods of disturbance that resulted in non-equilibrium metapopulation dynamics. Inferences from extinction-isolation relationships were unreliable, particularly for autologistic measures and for the more vagile Virginia rail.

Quantifying resistance and resilience to local extinction for conservation prioritization

Species-focused conservation planning is often based on reducing local extinction risk at key sites. However, with increasing levels of habitat fragmentation and pressures from climate change and overexploitation, surrounding landscapes also influence the persistence of species populations, and their effects are increasingly incorporated in conservation planning and management for both species and communities. Here, we present a framework based on metapopulation dynamics in fragmented landscapes, for quantifying the survival (resistance) and reestablishment of species populations following localized extinction events (resilience). We explore the application of this framework to guide the conservation of a group of threatened bird species endemic to papyrus (Cyperus papyrus) swamps in East and Central Africa. Using occupancy data for five species collected over two years from a network of wetlands in Uganda, we determine the local and landscape factors that influence local extinction and colonization, and map expected rates of population turnover across the network to draw inferences about the locations that contribute most to regional resistance and resilience for all species combined. Slight variation in the factors driving extinction and colonization between individual papyrus birds led to species-specific differences in the spatial patterns of site-level resistance and resilience. However, despite this, locations with the highest resistance and/or resilience overlapped for most species and reveal where resources could be invested for multispecies persistence. This novel simplified framework can aid decision making associated with conservation planning and prioritization for multiple species residing in overlapping, fragmented habitats; helping to identify key sites that warrant urgent conservation protection, with consideration of the need to adapt and respond to future change.

Parasite-mediated selection in a natural metapopulation of Daphnia magna

Parasite-mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease-related traits. However, nonadaptive processes like migration and extinction-(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life-history and disease-related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite-mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life-history and disease traits in common garden experiments. Combining phenotypic and genotypic data a Q_ST -F_ST -like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction-(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.

Dispersing male Parnassius smintheus butterflies are more strongly affected by forest matrix than are females

Dispersal is a central aspect of the ecology, evolution, and conservation of species. Predicting how species will respond to changing environmental conditions requires understanding factors that produce variation in dispersal. We explore one source of variation, differences between sexes within a spatial population network. Here, we compare the dispersal patterns of male and female Parnassius smintheus among 18 subpopulations over 8 years using the Virtual Migration Model. Estimated dispersal parameters differed between males and females, particularly with respect to movement through meadow and forest matrix habitat. The estimated dispersal distances of males through forest were much less than for females. Observations of female movement showed that, unlike males, females do not avoid forest nor does forest exert an edge effect. We explored whether further forest encroachment in this system would have different effects for males and females by fitting mean parameter estimates to the landscape configuration seen in 1993 and 2012. Despite differences in their dispersal due presumably to both habitat and physiological differences, males and females are predicted to respond in similar ways to reduced meadow area and increased forest isolation.

Lessons from a Life in Time and Space

A research career investigating epidemiological and evolutionary patterns in both natural and crop host-pathogen systems emphasizes the need for flexibility in thinking and a willingness to adopt ideas from a wide diversity of subdisciplines. Here, I reflect on the pivotal issues, research areas, and interactions, including the role of science management, that shaped my career in the hope of demonstrating that career paths and collaborations in science can be as diverse and unpredictable as the natural world in which we study our organisms of choice.

Sporadic Genetic Connectivity among Small Insular Populations of the Rare Geoendemic Plant Caulanthus amplexicaulis var. barbarae (Santa Barbara Jewelflower)

Globally, a small number of plants have adapted to terrestrial outcroppings of serpentine geology, which are characterized by soils with low levels of essential mineral nutrients (N, P, K, Ca, Mo) and toxic levels of heavy metals (Ni, Cr, Co). Paradoxically, many of these plants are restricted to this harsh environment. Caulanthus ampexlicaulis var. barbarae (Brassicaceae) is a rare annual plant that is strictly endemic to a small set of isolated serpentine outcrops in the coastal mountains of central California. The goals of the work presented here were to 1) determine the patterns of genetic connectivity among all known populations of C. ampexlicaulis var. barbarae, and 2) estimate contemporary effective population sizes (Ne), to inform ongoing genomic analyses of the evolutionary history of this taxon, and to provide a foundation upon which to model its future evolutionary potential and long-term viability in a changing environment. Eleven populations of this taxon were sampled, and population-genetic parameters were estimated using 11 nuclear microsatellite markers. Contemporary effective population sizes were estimated using multiple methods and found to be strikingly small (typically Ne < 10). Further, our data showed that a substantial component of genetic connectivity of this taxon is not at equilibrium, and instead showed sporadic gene flow. Several lines of evidence indicate that gene flow between isolated populations is maintained through long-distance seed dispersal (e.g., >1 km), possibly via zoochory.

The effect of multiple natural enemies on a shared herbivore prey

Natural enemy diversity is thought to be important for effective suppression of herbivores in production systems. Studies investigating the importance of the diversity and composition of the natural enemy complex often use within-year empirical studies or experimental exclusion setups.However, within-year population suppression might not translate in long-term population regulation. Therefore, I used a combination of long-term data collection and an exclusion experiment to investigate mechanisms behind year-to-year population changes and potential effects of disturbance of the natural enemy complex.Using the holly leaf miner study system in Wytham Woods, I find that the dominant predator in the system does not necessarily contribute the most to the reduction in year-to-year changes in mine density or within-patch fluctuations. Using the exclusion experiment, it becomes clear that parasitism later in the prey life cycle can to a certain level compensate for disruption of mortality in the earlier life stage of the prey.Thus, for host suppression in perennial systems the mortality pressure over the whole life cycle is important and disturbance during one part of the life cycle might not necessarily be buffered by mortality in other parts of the life cycle, especially if the natural enemy complex consists of multiple predator guilds.

Colonization and extinction dynamics among the plant species at tree bases in Paris (France)

In cities, trees planted along streets could play an important ecological role for spontaneous plants growing at their bases. For example, these trees could represent corridors by potentially connecting large green spaces (e.g., parks, gardens), which allow species to move within the urban matrix. We considered sets of urban trees in 15 streets in Paris, France, as metapopulations for 15 plant species. Our objective was to determine the factors influencing the dynamics of colonization and extinction of populations based on the distance of the streets to green spaces and biological traits of each species.Plant species in 1,324 tree bases of the Bercy District of Paris were surveyed annually from 2009 to 2015. For each species and each street, we used SPOMSIM software to identify the best-fit metapopulation model between four models with different colonization and extinction functions: propagule rain model (PRM) and Levins' model with or without rescue effect.Results demonstrated that species more often conformed to the PRM in streets near green spaces, which suggested that green spaces could act as sources for the populations in those streets. Species with seeds with long-term persistence more often conformed to the PRM, indicating that a soil seed bank helps species invade entire streets. Finally, a higher percentage of species with a short height conformed to models with a rescue effect, which indicated that those small species resisted the effects of weeding by the city technical services better than taller species.Synthesis and applications. This study showed how biological traits of species and geography of the district determine the dynamics of plants in the streets, and these results may provide important information for biodiversity management in cities.

Phenotype-environment mismatch in metapopulations-Implications for the maintenance of maladaptation at the regional scale

Maladaptation is widespread in natural populations. However, maladaptation has most often been associated with absolute population decline in local habitats rather than on a spectrum of relative fitness variation that can assist natural populations in their persistence at larger regional scales. We report results from a field experiment that tested for relative maladaptation between-pond habitats with spatial heterogeneity and (a)symmetric selection in pH. In the experiment, we quantified relative maladaptation in a copepod metapopulation as a mismatch between the mean population phenotype and the optimal trait value that would maximize mean population fitness under either stable or fluctuating pH environmental conditions. To complement the field experiment, we constructed a metapopulation model that addressed both relative (distance from the optimum) and absolute (negative population growth) maladaptation, with the aim of forecasting maladaptation to pH at the regional scale in relation to spatial structure (environmental heterogeneity and connectivity) and temporal environmental fluctuations. The results from our experiment indicated that maladaptation to pH at the regional scale depended on the asymmetry of the fitness surface at the local level. The results from our metapopulation model revealed how dispersal and (a)symmetric selection can operate on the fitness surface to maintain maladaptive phenotype-environment mismatch at local and regional scales in a metapopulation. Environmental stochasticity resulted in the maintenance of maladaptation that was robust to dispersal, but also revealed an interaction between the asymmetry in selection and environmental correlation. Our findings emphasize the importance of maladaptation for planning conservation strategies that can support adaptive potential in fragmented and changing landscapes.

From individual movement behaviour to landscape-scale invasion dynamics and management: a case study of lionfish metapopulations

Modelling the dynamics of small, interconnected populations, or metapopulations, can help pinpoint habitat patches that are critical for population persistence in patchy habitats. For conservation purposes, these patches are typically earmarked for protection, but for invasive species management, these patches could be targeted to hasten the populations' demise. Here, we show how metapopulation modelling, coupled with an understanding of size-dependent dispersal behaviour, can be used to help optimize the distribution of limited resources for culling specific populations of invasive Indo-Pacific lionfish (Pterois volitans) in the western Atlantic. Through simulation using fitted model parameters, we derive three insights that can inform management. First, culling lionfish from target patches reduces the probability of lionfish occupancy at surrounding patches. Second, this effect depends on patch size and connectivity, but is strongest at the local scale and decays with distance. Finally, size-dependent dispersal in lionfish means that size-selective culling can change both a population's size distribution and dispersal potential, with cascading effects on network connectivity, population dynamics and management outcomes. By explicitly considering seascape structure and movement behaviour when allocating effort to the management of invasive species, managers can optimize resource use to improve management outcomes. This article is part of the theme issue 'Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation'.

Scaling up the effects of inbreeding depression from individuals to metapopulations

Inbreeding is common in nature, and many laboratory studies have documented that inbreeding depression can reduce the fitness of individuals. Demonstrating the consequences of inbreeding depression on the growth and persistence of populations is more challenging because populations are often regulated by density- or frequency-dependent selection and influenced by demographic and environmental stochasticity. A few empirical studies have shown that inbreeding depression can increase extinction risk of local populations. The importance of inbreeding depression at the metapopulation level has been conjectured based on population-level studies but has not been evaluated. We quantified the impact of inbreeding depression affecting the fitness of individuals on metapopulation persistence in heterogeneous habitat networks of different sizes and habitat configuration in a context of natural butterfly metapopulations. We developed a spatial individual-based simulation model of metapopulations with explicit genetics. We used Approximate Bayesian Computation to fit the model to extensive demographic, genetic and life-history data available for the well-studied Glanville fritillary butterfly (Melitaea cinxia) metapopulations in the Åland islands in SW Finland. We compared 18 semi-independent habitat networks differing in size and fragmentation. The results show that inbreeding is more frequent in small habitat networks, and consequently, inbreeding depression elevates extinction risks in small metapopulations. Metapopulation persistence and neutral genetic diversity maintained in the metapopulations increase with the total habitat amount in and mean patch size of habitat networks. Dispersal and mating behaviour interact with landscape structure to determine how likely it is to encounter kin while looking for mates. Inbreeding depression can decrease the viability of small metapopulations even when they are strongly influenced by stochastic extinction-colonization dynamics and density-dependent selection. The findings from this study support that genetic factors, in addition to demographic factors, can contribute to extinctions of small local populations and also of metapopulations.

Phylogenetic analysis of Fasciola spp. isolated from slaughtered cattle in KwaZulu-Natal and Mpumalanga provinces of South Africa based on the cytochrome c oxidase subunit I mitochondrial marker

Fasciola spp. are the causative agents of fascioliasis in humans and livestock. Before the development of control and management measures, the geographical distribution of the species and patterns of infection must be considered. Because of difficulties in the phenotypic differentiation and morphometric classification of Fasciola spp., DNA molecular markers have become more useful for fluke differentiation and description of phylogenetic patterns. This study aimed to differentiate and describe the phylogenetic background of Fasciola spp. isolated from cattle slaughtered at three abattoirs in the Mpumalanga and KwaZulu-Natal provinces of South Africa. The cytochrome c oxidase I (COI) - FHCO1 (forward: 5'-TTGGTTTTTTGGGCATCCT-3') and FHCO1 (reverse: 5' -AGGCCACCACCAAATAAAAGA3') - marker was sequenced from 55 Fasciola flukes that were collected from abattoirs in catchment areas of the KwaZulu-Natal and Mpumalanga provinces. Fasciola hepatica was demonstrated to have 100% prevalence in KwaZulu-Natal and Mpumalanga (highveld), respectively, and 76% prevalence in the lowveld (Belfast area) of Mpumalanga. Two animals from the Belfast metapopulation were co-infected with both Fasciola gigantica and F. hepatica. DNA sequence analysis of all the isolates demonstrated a sequence conservation of 0.472, nucleotide diversity of 0.082 and Tajima's D of -1.100; however, it was not statistically significant (p > 0.05). Twenty-two haplotypes were identified, with 18 novel haplotypes being unique to the isolates from South Africa. Within the study samples, 12 haplotypes were isolated to a few individuals, with a haplotype diversity of 0.8957 indicating high genetic diversity. Principal coordinate analysis supported the clustering and distribution of the haplotypes, with 11.38% of the variation being attributed to coordinate 2 and 55.52% to coordinate 1. The distribution of Fasciola spp. has been demonstrated to be related to the distribution of the freshwater intermediate host snails, Lymnaea spp., as well as the relative altitude of the localities in South Africa. Information provided by this study serves as preliminary evidence for further studies on the mapping of the distribution of F. gigantica and F. hepatica in South Africa, which is key in designing control programmes for fascioliasis in humans and livestock.

Genetic diversity and metapopulation structures of two intertidal species along the coast of Zhejiang, China: implications for conservation

To priority areas for conservation in the coast of Zhejiang, this study attempts to map the spatial patterns of the intra-specific genetic diversity of two intertidal species, Septifer virgatus and Tetraclita japonica, using the sequences of mitochondrial DNA cytochrome oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA) genes. In total, 129 and 112 specimens were collected from 12 and 11 populations for S. virgatus and T. japonica, respectively. These two species revealed congruent population historical signals, including (1) high levels of haplotype diversity and low values of nucleotide diversity, (2) post-LGM expansion, (3) the lack of population genetic structure, sharing haplotypes over all sampling populations, (4) gene flow connections, and (5) migration directions. Largely, all results supported that all sampling populations could be divided into two main metapopulations, exhibiting a northern and southern distribution. The north metapopulation could be considered as a marine protected area. The genetic patterns of the two species should be considered in the management and conservation in the islands along the Zhejiang, China.

Non-native species spread in a complex network: the interaction of global transport and local population dynamics determines invasion success

The number of released individuals, which is a component of propagule pressure, is considered to be a major driver for the establishment success of non-native species. However, propagule pressure is often assumed to result from single or few release events, which does not necessarily apply to the frequent releases of invertebrates or other taxa through global transport. For instance, the high intensity of global shipping may result in frequent releases of large numbers of individuals, and the complexity of shipping dynamics impedes predictions of invasion dynamics. Here, we present a mathematical model for the spread of planktonic organisms by global shipping, using the history of movements by 33 566 ships among 1477 ports to simulate population dynamics for the comb jelly Mnemiopsis leidyi as a case study. The degree of propagule pressure at one site resulted from the coincident arrival of individuals from other sites with native or non-native populations. Key to sequential spread in European waters was a readily available source of propagules and a suitable recipient environment. These propagules were derived from previously introduced 'bridgehead' populations supplemented with those from native sources. Invasion success is therefore determined by the complex interaction of global shipping and local population dynamics. The general findings probably hold true for the spread of species in other complex systems, such as insects or plant seeds exchanged via commercial trade or transport.

Proximity of restored hedgerows interacts with local floral diversity and species' traits to shape long-term pollinator metacommunity dynamics

Disconnected habitat fragments are poor at supporting population and community persistence; restoration ecologists, therefore, advocate for the establishment of habitat networks across landscapes. Few empirical studies, however, have considered how networks of restored habitat patches affect metacommunity dynamics. Here, using a 10-year study on restored hedgerows and unrestored field margins within an intensive agricultural landscape, we integrate occupancy modelling with network theory to examine the interaction between local and landscape characteristics, habitat selection and dispersal in shaping pollinator metacommunity dynamics. We show that surrounding hedgerows and remnant habitat patches interact with the local floral diversity, bee diet breadth and bee body size to influence site occupancy, via colonisation and persistence dynamics. Florally diverse sites and generalist, small-bodied species are most important for maintaining metacommunity connectivity. By providing the first in-depth assessment of how a network of restored habitat influences long-term population dynamics, we confirm the conservation benefit of hedgerows for pollinator populations and demonstrate the importance of restoring and maintaining habitat networks within an inhospitable matrix.

Dispersal syndromes can impact ecosystem functioning in spatially structured freshwater populations

Dispersal can strongly influence ecological and evolutionary dynamics. Besides the direct contribution of dispersal to population dynamics, dispersers often differ in their phenotypic attributes from non-dispersers, which leads to dispersal syndromes. The consequences of such dispersal syndromes have been widely explored at the population and community level; however, to date, ecosystem-level effects remain unclear. Here, we examine whether dispersing and resident individuals of two different aquatic keystone invertebrate species have different contributions to detrital processing, a key function in freshwater ecosystems. Using experimental two-patch systems, we found no difference in leaf consumption rates with dispersal status of the common native species Gammarus fossarum. In Dikerogammarus villosus, however, a Ponto-Caspian species now expanding throughout Europe, dispersers consumed leaf litter at roughly three times the rate of non-dispersers. Furthermore, this put the contribution of dispersing D. villosus to leaf litter processing on par with native G. fossarum, after adjusting for differences in organismal size. Given that leaf litter decomposition is a key function in aquatic ecosystems, and the rapid species turnover in freshwater habitats with range expansions of non-native species, this finding suggests that dispersal syndromes may have important consequences for ecosystem functioning.

The application of self-limiting transgenic insects in managing resistance in experimental metapopulations

The mass release of transgenic insects carrying female lethal self-limiting genes can reduce pest insect populations. Substantial releases are also a novel resistance management tool, since wild type alleles conferring susceptibility to pesticides can dilute resistance alleles in target populations. However, a potential barrier is the need for large-scale area-wide releases. Here, we address whether localized releases of transgenic insects could provide an alternative means of population suppression and resistance management, without serious loss of efficacy.We used experimental mesocosms constituting insect metapopulations to explore the evolution of resistance to the Bacillus thuringiensis toxin Cry1Ac in a high-dose/refugia landscape in the insect Plutella xylostella. We ran two selection experiments, the first compared the efficacy of "everywhere" releases and negative controls to a spatially density-dependent or "whack-a-mole" strategy that concentrated release of transgenic insects in subpopulations with elevated resistance. The second experiment tested the relative efficacy of whack-a-mole and everywhere releases under spatially homogenous and heterogeneous selection pressure.The whack-a-mole releases were less effective than everywhere releases in terms of slowing the evolution of resistance, which, in the first experiment, largely prevented the evolution of resistance. In contrast to predictions, heterogeneous whack-a-mole releases were no more effective under heterogeneous selection pressure. Heterogeneous selection pressure did, however, reduce total insect population sizes.Whack-a-mole releases provided early population suppression, indistinguishable from homogeneous everywhere releases. However, insect population densities tracked the evolution of resistance in this system, as phenotypic resistance provides access to additional diet containing the toxin Cry1Ac. Thus, as resistance levels diverged between treatments, carrying capacities and population sizes increased under the whack-a-mole approach. Synthesis and applications. Spatially density-dependent releases of transgenic insects, particularly those targeting source populations at a landscape level, could suppress pest populations in the absence of blanket area-wide releases. The benefits of self-limiting transgenic insects were reduced in spatially localized releases, suggesting that they are not ideal for "spot" treatment of resistance problems. Nevertheless, spatially homogeneous or heterogeneous releases could be used to support other resistance management interventions.

Prioritization of landscape connectivity for the conservation of Peary caribou

Adequate connectivity between discontinuous habitat patches is crucial for the persistence of metapopulations across space and time. Loss of landscape connectivity is often a direct result of fragmentation caused by human activities but also can be caused indirectly through anthropogenic climate change. Peary caribou (Rangifer tarandus pearyi) are widely dispersed across the islands of the Canadian Arctic Archipelago and rely on sea ice to move seasonally between island habitats throughout their range. Seasonal connectivity provided by sea ice is necessary to maintain genetic diversity and to facilitate dispersal and recolonization of areas from which caribou have been extirpated. We used least-cost path analysis and circuit theory to model connectivity across Peary caribou range, and future climate projections to investigate how this connectivity might be affected by a warming climate. Further, we used measures of current flow centrality to estimate the role of High Arctic islands in maintaining connectivity between Peary caribou populations and to identify and prioritize those islands and linkages most important for conservation. Our results suggest that the Bathurst Island complex plays a critical role in facilitating connectivity between Peary caribou populations. Large islands, including Banks, Victoria, and Ellesmere have limited roles in connecting Peary caribou. Without rigorous greenhouse gas emission reductions our projections indicate that by 2100 all connectivity between the more southern Peary caribou populations will be lost for important spring and early-winter movement periods. Continued connectivity across the Canadian Arctic Archipelago, and possibly Peary caribou persistence, ultimately hinges on global commitments to limit climate change. Our research highlights priority areas where, in addition to emission reductions, conservation efforts to maintain connectivity would be most effective.

The three regimes of spatial recovery

An enduring challenge for ecology is identifying the drivers of ecosystem and population stability. In a spatially explicit context, key features to consider are landscape spatial structure, local interactions, and dispersal. Substantial work has been done on each of these features as a driver of stability, but little is known on the interplay between them. Missing has been a more integrative approach, able to map and identify different dynamical regimes, predicting a system's response to perturbations. Here we first consider a simple scenario, i.e., the recovery of a homogeneous metapopulation from a single localized pulse disturbance. The analysis of this scenario reveals three fundamental recovery regimes: Isolated Regime when dispersal is not significant, Rescue Regime when dispersal mediates recovery, and Mixing Regime when perturbations spread throughout the system. Despite its simplicity, our approach leads to remarkably general predictions. These include the qualitatively different outcomes of various scenarios of habitat fragmentation, the surprising benefits of local extinctions on population persistence at the transition between regimes, and the productivity shifts of metacommunities in a changing environment. This study thus provides context to known results and insight into future directions of research.

Strategies in scheduling marine protected area establishment in a network system

Instantaneous implementation of systematic conservation plans at regional scales is rare. More typically, planned actions are applied incrementally over periods of years or decades. During protracted implementation, the character of the connected ecological system will change as a function of external anthropogenic pressures, local metapopulation processes, and environmental fluctuations. For heavily exploited systems, habitat quality will deteriorate as the plan is implemented, potentially influencing the schedule of protected area implementation necessary to achieve conservation objectives. Understanding the best strategy to adopt for applying management within a connected environment is desirable, especially given limited conservation resources. Here, we model the sequential application of no-take marine protected areas (MPAs) in the central Philippines within a metapopulation framework, using a range of network-based decision rules. The model was based on selecting 33 sites for protection from 101 possible sites over a 35-yr period. The graph-theoretic network criteria to select sites for protection included PageRank, maximum degree, closeness centrality, betweenness centrality, minimum degree, random, and historical events. We also included a dynamic strategy called colonization-extinction rate that was updated every year based on the changing capacity of each site to produce and absorb larvae. Each rule was evaluated in the context of achieving the maximum metapopulation mean lifetime at the conclusion of the implementation phase. MPAs were designated through the alteration of the extinction risk parameter. The highest ranked criteria were PageRank while the actual implementation from historical records ranked lowest. Our results indicate that protecting the sites ranked highest with regard to larval supply is likely to yield the highest benefit for fish abundance and fish metapopulation persistence. Model results highlighted the benefits of including network processes in conservation planning.

Asymmetrical gene flow of the recently delisted passerine black-capped vireo (Vireo atricapilla) indicates source-sink dynamics in central Texas

Habitat fragmentation can produce metapopulations or source-sink systems in which dispersal in crucial for population maintenance. Our objective was to investigate connectivity among black-capped vireo (Vireo atricapilla) populations in tandem with a demographic study (Biological Conservation, 2016, 203, 108-118) to elucidate if central Texas populations act as a source-sink system. We genotyped 343 individuals at 12 microsatellite loci to elucidate the movement ecology of the black-capped vireo in central Texas surrounding Fort Hood; the largest and most stable breeding population of black-capped vireos inhabit Fort Hood. To gain insight into gene flow among populations, we analyzed genetic differentiation, migration rates, number of migrants, and parentage. We found statistically significant, but low levels of genetic differentiation among several populations, suggesting some limited restriction to gene flow. Across approaches to estimate migration, we found consistent evidence for asymmetrical movement from Fort Hood to the other central Texas sites consistent with source-sink dynamics. Our results are complementary to black-capped vireo demographic studies done in tandem showing that portions of Fort Hood are acting as a source population to smaller central Texas populations.

Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly

There is now clear evidence that species across a broad range of taxa harbor extensive heritable variation in dispersal. While studies suggest that this variation can facilitate demographic outcomes such as range expansion and invasions, few have considered the consequences of intraspecific variation in dispersal for the maintenance and distribution of genetic variation across fragmented landscapes. Here, we examine how landscape characteristics and individual variation in dispersal combine to predict genetic structure using genomic and spatial data from the Glanville fritillary butterfly. We used linear and latent factor mixed models to identify the landscape features that best predict spatial sorting of alleles in the dispersal-related gene phosphoglucose isomerase (Pgi). We next used structural equation modeling to test if variation in Pgi mediated gene flow as measured by Fst at putatively neutral loci. In a year when the population was recovering following a large decline, individuals with a genotype associated with greater dispersal ability were found at significantly higher frequencies in populations isolated by water and forest, and these populations showed lower levels of genetic differentiation at neutral loci. These relationships disappeared in the next year when metapopulation density was high, suggesting that the effects of individual variation are context dependent. Together our results highlight that (1) more complex aspects of landscape structure beyond just the configuration of habitat can be important for maintaining spatial variation in dispersal traits and (2) that individual variation in dispersal plays a key role in maintaining genetic variation across fragmented landscapes.

The role of spatial structure in the collapse of regional metapopulations

Many wildlife populations are either naturally, or as a result of human land use, patchily distributed in space. The degree of fragmentation-specifically the remaining patch sizes and habitat configuration-is an important part of population dynamics. Demographic stochasticity is also likely to play an important role in patchy habitats that host small local populations. We develop a simulation model to evaluate the significance of demographic stochasticity and the role fragmentation plays in the determination of population dynamics and the risk of extinction of populations on habitat patches. Our model is formulated as a Markov-chain stochastic process on a finite, spatially explicit array of patches in which probability of successful dispersal is a function of interpatch distance. Unlike past work, we explicitly model local population dynamics and examine how these scale up to the entire population. As a test case, we apply the model to the American pika (Ochotona princeps) population living on the ore dumps in the ghost mining town of Bodie, California. This population has been studied nearly continuously for over four decades and has been of conservation concern as the southern half of the population declined precipitously beginning in 1989. Our model suggests that both the specific configuration of habitat and landscape heterogeneity are necessary and sufficient predictors of the eventual extinction of the southern constellation of patches. This example has important implications, as it suggests that fragmentation alone can lead to regional extinctions within metapopulations.

Population Dynamics of Anopheles albimanus (Diptera: Culicidae) at Ipetí-Guna, a Village in a Region Targeted for Malaria Elimination in Panamá

Anopheles albimanus Wiedemann is a major malaria vector in Mesoamerica and the Caribbean whose population dynamics, in response to changing environments, has been relatively poorly studied. Here, we present monthly adult and larvae data collected from May 2016 to December 2017 in Ipetí-Guna, a village within an area targeted for malaria elimination in the República de Panamá. During the study period we collected a total of 1678 Anopheles spp. mosquitoes (1602 adults and 76 larvae). Over 95% of the collected Anopheles spp. mosquitoes were An. albimanus. Using time series analysis techniques, we found that population dynamics of larvae and adults were not significantly correlated with each other at any time lag, though correlations were highest at one month lag between larvae and adults and four months lag between adults and larvae. Larvae population dynamics had cycles of three months and were sensitive to changes in temperature with 5 months lag, while adult abundance was correlated with itself (1 month lag) and with the normalized difference vegetation index (NDVI) with three months lag. A key observation from our study is the absence of both larvae and adults of An. albimanus between January and April from environments associated with Guna population’s daily activities, which suggests this time window could be the best time to implement elimination campaigns aimed at clearing Plasmodium spp. parasites from Guna populations using, for example, mass drug administration.

Island biogeography and ecological modeling of the amblypygid Phrynus marginemaculatus in the Florida Keys archipelago

AIM

The biogeography of terrestrial organisms across the Florida Keys archipelago is poorly understood. We used population genetics and spatioecological modeling of the Amblypygi Phrynus marginemaculatus to understand the genetic structure and metapopulation dynamics of Keys populations that are otherwise isolated by human development and ocean.

LOCATION

The Florida Keys archipelago and mainland Florida.

METHODS

We sequenced a 1,238 bp fragment of mtDNA for 103 individuals of P. marginemaculatus from 13 sites in the Florida Keys and South Florida, binned into four regions. We used population genetic analyses to understand the population structure of the species throughout its US range. Furthermore, we used ecological modeling with climate, habitat, and human development data to develop habitat suitability estimates for the species.

RESULTS

We found clear genetic structure between localities. The Lower Keys, in particular, support populations separate from those in other regions studied. Ecological modeling and genetic analyses showed the highest habitat suitability and genetic isolation in the Lower Keys, but urban development across the species range has resulted in the loss of most historical habitat.

MAIN CONCLUSIONS

A mainland-metapopulation model best fits P. marginemaculatus gene flow patterns in the Florida Keys and mainland. Ocean currents likely play a role in metapopulation dynamics and gene flow for terrestrial Keys species like P. marginemaculatus, and genetic patterns also matched patterns consistent with geologic history. Suitable habitat, however, is limited and under threat of human destruction. The few remaining pockets of the most suitable habitat tend to occur in parks and protected areas. We argue that conservation efforts for this species and others in the terrestrial Florida Keys would benefit from a deeper understanding of the population genetic structure and ecology of the archipelago.

Climate change accelerates local disease extinction rates in a long-term wild host-pathogen association

Pathogens are a significant component of all plant communities. In recent years, the potential for existing and emerging pathogens of agricultural crops to cause increased yield losses as a consequence of changing climatic patterns has raised considerable concern. In contrast, the response of naturally occurring, endemic pathogens to a warming climate has received little attention. Here, we report on the impact of a signature variable of global climate change - increasing temperature - on the long-term epidemiology of a natural host-pathogen association involving the rust pathogen Triphragmium ulmariae and its host plant Filipendula ulmaria. In a host-pathogen metapopulation involving approximately 230 host populations growing on an archipelago of islands in the Gulf of Bothnia we assessed changes in host population size and pathogen epidemiological measures over a 25-year period. We show how the incidence of disease and its severity declines over that period and most importantly demonstrate a positive association between a long-term trend of increasing extinction rates in individual pathogen populations of the metapopulation and increasing temperature. Our results are highly suggestive that changing climatic patterns, particularly mean monthly growing season (April-November) temperature, are markedly influencing the epidemiology of plant disease in this host-pathogen association. Given the important role plant pathogens have in shaping the structure of communities, changes in the epidemiology of pathogens have potentially far-reaching impacts on ecological and evolutionary processes. For these reasons, it is essential to increase understanding of pathogen epidemiology, its response to warming, and to invoke these responses in forecasts for the future.

Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird

Anthropogenic alterations to landscape structure and composition can have significant impacts on biodiversity, potentially leading to species extinctions. Population‐level impacts of landscape change are mediated by animal behaviors, in particular dispersal behavior. Little is known about the dispersal habits of rails (Rallidae) due to their cryptic behavior and tendency to occupy densely vegetated habitats. The effects of landscape structure on the movement behavior of waterbirds in general are poorly studied due to their reputation for having high dispersal abilities. We used a landscape genetic approach to test hypotheses of landscape effects on dispersal behavior of the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered subspecies endemic to the Hawaiian Islands. We created a suite of alternative resistance surfaces representing biologically plausible a priori hypotheses of how gallinules might navigate the landscape matrix and ranked these surfaces by their ability to explain observed patterns in genetic distance among 12 populations on the island of O`ahu. We modeled effective distance among wetland locations on all surfaces using both cumulative least‐cost‐path and resistance‐distance approaches and evaluated relative model performance using Mantel tests, a causal modeling approach, and the mixed‐model maximum‐likelihood population‐effects framework. Across all genetic markers, simulation methods, and model comparison metrics, surfaces that treated linear water features like streams, ditches, and canals as corridors for gallinule movement outperformed all other models. This is the first landscape genetic study on the movement behavior of any waterbird species to our knowledge. Our results indicate that lotic water features, including drainage infrastructure previously thought to be of minimal habitat value, contribute to habitat connectivity in this listed subspecies.

Reserve design to optimize the long-term persistence of multiple species

Protected areas form the cornerstone of global efforts to conserve biodiversity. Most current methods for designing reserve networks focus on maximizing the representation of species, but with no assurance that those species will persist in the protected landscapes into the future. We present a new strategy for reserve design that combines metapopulation theory with spatial conservation prioritization to estimate conservation solutions that minimize extinction risk across numerous species simultaneously. Our framework optimizes the spatial configuration of reserves to maximize metapopulation persistence for an entire assemblage of species by accounting for both species representation and landscape connectivity. As a case study, we design a reserve network for 114 terrestrial mammal species in Indonesian New Guinea. Our approach builds on Marxan, the flagship representation-based reserve design tool, improving estimated persistence (metapopulation capacity) by an average of 4.6-fold across species, without increasing the socioeconomic cost. We suggest that enhancing species persistence, rather than protecting arbitrary proportions of species' ranges, should be the ultimate objective of conservation planning.

A general method for estimating seed dormancy and colonisation in annual plants from the observation of existing flora

In plant ecology, characterising colonisation and extinction in plant metapopulations is challenging due to the non-detectable seed bank that allows plants to emerge after several years of absence. In this study, we used a Hidden Markov Model to characterise seed dormancy, colonisation and germination solely from the presence-absence of standing flora. Applying the model to data from a long-term survey of 38 annual weeds across France, we identified three homogeneous functional groups: (1) species persisting preferentially through spatial colonisation, (2) species persisting preferentially through seed dormancy and (3) a mix of both strategies. These groups are consistent with existing ecological knowledge, demonstrating that ecologically meaningful parameters can be estimated from simple presence-absence observations. These results indicate that such studies could contribute to the design of weed management strategies. They also open the possibility of testing life-history theories such as the dormancy/colonisation trade-off in natura.

Effect of the anther-smut fungus Microbotryum on the juvenile growth of its host Silene latifolia

PREMISE OF THE STUDY

Plant pathogens that form persistent systemic infections within plants have the potential to affect multiple plant life history traits, yet we tend to focus only on visible symptoms. Anther smut of Silene latifolia caused by the fungus Microbotryum lychnidis-dioicae induces the anthers of its host to support fungal spore production instead of pollen, and the pathogen is primarily transmitted among flowering plants by pollinators. Nevertheless, most of its life cycle is spent in the asymptomatic vegetative phase, and spores falling on seedlings or nonflowering plants can also infect the host. The purpose of this study was to ask whether the fungus also had an effect on its host plant in the juvenile vegetative phase before flowering as this is important for the disease dynamics in species where infection of seedlings is commonplace.

METHODS

Leaf length and leaf number of inoculated and uninoculated juvenile plants were compared in greenhouse experiments, and in one experiment, disease status of the plants at flowering was determined.

KEY RESULTS

Inoculated plants had shorter but more leaves, and reduced root mass at the early juvenile (preflowering) stage. Some of these effects were detectable in plants that were inoculated but showed no disease symptoms at flowering.

CONCLUSIONS

These results show that pathogenic fungi can have endophyte-like effects even in the total absence of their typical and more charismatic symptoms, and conversely that the assessment of endophyte effects on the fitness of their hosts should include all stages of the host life cycle.

Stormwater wetlands can function as ecological traps for urban frogs

Around cities, natural wetlands are rapidly being destroyed and replaced with wetlands constructed to treat stormwater. Although the intended purpose of these wetlands is to manage urban stormwater, they are inhabited by wildlife that might be exposed to contaminants. These effects will be exacerbated if animals are unable to differentiate between stormwater treatment wetlands of varying quality and some function as "ecological traps" (i.e., habitats that animals prefer despite fitness being lower than in other habitats). To examine if urban stormwater wetlands can be ecological traps for frogs, we tested if survival, metamorphosis-related measures, and predator avoidance behaviors of frogs differed within mesocosms that simulated stormwater wetlands with different contaminant levels, and paired this with a natural oviposition experiment to assess breeding-site preferences. We provide the first empirical evidence that these wetlands can function as ecological traps for frogs. Tadpoles had lower survival and were less responsive to predator olfactory cues when raised in more polluted stormwater wetlands, but also reached metamorphosis earlier and at a larger size. A greater size at metamorphosis was likely a result of increased per capita food availability due to higher mortality combined with eutrophication, although other compensatory effects such as selective-mortality removing smaller individuals from low-quality mesocosms may also explain these results. Breeding adults laid comparable numbers of eggs across wetlands with high and low contaminant levels, indicating no avoidance of the former. Since stormwater treatment wetlands are often the only available aquatic habitat in urban landscapes we need to better understand how they perform as habitats to guide management decisions that mitigate their potential ecological costs. This may include improving wetland quality so that fitness is no longer compromised, preventing colonization by animals, altering the cues animals use when selecting habitats, pretreating contaminated water prior to release, providing off-line wetlands nearby, or simply not constructing stormwater treatment wetlands in sensitive areas. Our study confirms the potential for urban stormwater treatment wetlands to function as ecological traps and highlights the need for greater awareness of their prevalence and impact at landscape scales.

Human movement, cooperation and the effectiveness of coordinated vector control strategies

Vector-borne disease transmission is often typified by highly focal transmission and influenced by movement of hosts and vectors across different scales. The ecological and environmental conditions (including those created by humans through vector control programmes) that result in metapopulation dynamics remain poorly understood. The development of control strategies that would most effectively limit outbreaks given such dynamics is particularly urgent given the recent epidemics of dengue, chikungunya and Zika viruses. We developed a stochastic, spatial model of vector-borne disease transmission, allowing for movement of hosts between patches. Our model is applicable to arbovirus transmission by Aedes aegypti in urban settings and was parametrized to capture Zika virus transmission in particular. Using simulations, we investigated the extent to which two aspects of vector control strategies are affected by human commuting patterns: the extent of coordination and cooperation between neighbouring communities. We find that transmission intensity is highest at intermediate levels of host movement. The extent to which coordination of control activities among neighbouring patches decreases the prevalence of infection is affected by both how frequently humans commute and the proportion of neighbouring patches that commits to vector surveillance and control activities. At high levels of host movement, patches that do not contribute to vector control may act as sources of infection in the landscape, yet have comparable levels of prevalence as patches that do cooperate. This result suggests that real cooperation among neighbours will be critical to the development of effective pro-active strategies for vector-borne disease control in today's commuter-linked communities.