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USGS2000

Microsatellites: Evolutionary and methodological background and empirical applications at individual, population, and phylogenetic levels

The recent proliferation and greater accessibility of molecular genetic markers has led to a growing appreciation of the ecological and evolutionary inferences that can be drawn from molecular characterizations of individuals and populations (Burke et al. 1992, Avise 1994). Different techniques have the ability to target DNA sequences which have different patterns of inheritance, different modes and rates of evolution and, concomitantly, different levels of variation. In the quest for 'the right marker for the right job', microsatellites have been widely embraced as the marker of choice for many empirical genetic studies. The proliferation of microsatellite loci for various species and the voluminous literature compiled in very few years associated with their evolution and use in various research applications, exemplifies their growing importance as a research tool in the biological sciences. The ability to define allelic states based on variation at the nucleotide level has afforded unparalleled opportunities to document the actual mutational process and rates of evolution at individual microsatellite loci. The scrutiny to which these loci have been subjected has resulted in data that raise issues pertaining to assumptions formerly stated, but largely untestable for other marker classes. Indeed this is an active arena for theoretical and empirical work. Given the extensive and ever-increasing literature on various statistical methodologies and cautionary notes regarding the uses of microsatellites, some consideration should be given to the unique characteristics of these loci when determining how and under what conditions they can be employed.

Book chapter↗

USGS2022

Informing surveillance through the characterization of outbreak potential of chronic wasting disease in white-tailed deer

Understanding the role that an environmental prion reservoir plays in the outbreak dynamics of chronic wasting disease (CWD) in free ranging white-tailed deer ( Odocoileus virginianus ) is critical for the allocation of disease surveillance resources by state and provincial wildlife agencies. We hypothesized that demographic, ecological, and epidemiological configurations naturally attenuate epidemic risk despite the introduction of infectious prions into a susceptible population of deer, but the magnitude of infectious prions in the environmental prion reservoir complicate outbreak expectations. We developed a Susceptible-Latent-Exposed-Infective (SLEI) compartment model to represent the dynamics of CWD epidemics in free-ranging white-tailed deer, then used the basic reproductive ratio ( R 0 "> R0 ) to pinpoint counties under which pathogenic introduction (transport of infectious bodily fluids, tissues, and carcasses through natural or anthropogenic means) naturally produced (or failed to produce) an epidemic. We found that the outlook for an epidemic hinged on transmission rates, the magnitude of environmental contamination, and system type (density-, frequency-, or density/frequency-dependent). CWD can persistently infect individuals living in a contaminated environment even if direct transmission is insufficient to sustain circulation. Theoretical results show that transmission of CWD cannot be exclusively density dependent, and must behave as either a mix between frequency and density dependent, or strictly frequency dependent. While the compartment model is a simplistic representation of reality and did not contain many complicating biological considerations, it was immediately useful in hypothesis generation, motivating the collection of additional data for use in more biologically detailed models, and in the allocation of finite surveillance resources to place emphasis on data collection in areas where an introduction of infectious prions is comparatively more likely to result in an epidemic.

Ecological Modelling↗

USGS2017

Climate change as a long-term stressor for the fisheries of the Laurentian Great Lakes of North America

The Laurentian Great Lakes of North America provide valuable ecosystem services, including fisheries, to the surrounding population. Given the prevalence of other anthropogenic stressors that have historically affected the fisheries of the Great Lakes (e.g., eutrophication, invasive species, overfishing), climate change is often viewed as a long-term stressor and, subsequently, may not always be prioritized by managers and researchers. However, climate change has the potential to negatively affect fish and fisheries in the Great Lakes through its influence on habitat. In this paper, we (1) summarize projected changes in climate and fish habitat in the Great Lakes; (2) summarize fish responses to climate change in the Great Lakes; (3) describe key interactions between climate change and other stressors relevant to Great Lakes fish, and (4) summarize how climate change can be incorporated into fisheries management. In general, fish habitat is projected to be characterized by warmer temperatures throughout the water column, less ice cover, longer periods of stratification, and more frequent and widespread periods of bottom hypoxia in productive areas of the Great Lakes. Based solely on thermal habitat, fish populations theoretically could experience prolonged optimal growth environment within a changing climate, however, models that assess physical habitat influences at specific life stages convey a more complex picture. Looking at specific interactions with other stressors, climate change may exacerbate the negative impacts of both eutrophication and invasive species for fish habitat in the Great Lakes. Although expanding monitoring and research to consider climate change interactions with currently studied stressors, may offer managers the best opportunity to keep the valuable Great Lakes fisheries sustainable, this expansion is globally applicable for large lake ecosystem dealing with multiple stressors in the face of continued human-driven changes.

Great Lakes↗

USGS2016

Ecological requirements for pallid sturgeon reproduction and recruitment in the Missouri River—A synthesis of science, 2005 to 2012

This report is intended to synthesize the state of the scientific understanding of pallid sturgeon ecological requirements to provide recommendations for future science directions and context for Missouri River restoration and management decisions. Recruitment of pallid sturgeon has been low to non-existent throughout its range. Emerging understanding of the genetic structure of pallid sturgeon populations sets a broad framework for species and river management decisions, including decisions about managing the future genetic diversity of the species, but also decisions about where and what type of river restoration actions will be effective for subpopulations of this highly migratory species. Adult pallid sturgeon may migrate hundreds of kilometers (km) to spawn and their progeny may disperse even greater distances downstream as drifting free embryos. As a result of their complex life history pallid sturgeon naturally exploit a wide range of habitats during their life cycles. The construction of dams and reservoirs has fragmented habitats and may have shifted Missouri River subpopulations downstream. Research has not identified one primary biological or ecological constraint that appears to limit populations of the pallid sturgeon. With the present (2013) state of knowledge many life stages and life-stage transitions cannot be ruled out as contributing to recruitment failure. Biological opinions in 2000 (and amended in 2003) presented the dominant hypotheses for recruitment failure that existed at that time. Emphasis was on the role of the flow regime, specifically spring flow pulses (“spring rises”), to condition spawning substrate and cue reproductive aggregations and migrations, and on low flows and additional slow, shallow-water area to serve as rearing habitat for age-0 to juvenile pallid sturgeon. Studies on spawning habitat dynamics have documented that habitat patches selected for spawning by fish in the Lower Missouri River (Missouri River downstream from Gavins Point Dam to the confluence with the Mississippi River) are dominantly on outside, revetted bends in the deepest, fastest, and most turbulent water. Studies in more natural habitat on the Yellowstone River have documented spawning in convergent flow in the middle of the channel on discrete patches of gravel within a sand-dominated channel, an arrangement that may be more effective in attracting aggregations of reproductive fish compared to the nearly continuous revetment on the Lower Missouri River. Pallid sturgeon spawn in the spring and early summer during periods of increasing day length. Water temperature consistently exerts a threshold effect for spawning at 16–18 °C. In addition, the role of water temperature is indicated by pauses and reversals in upstream migrations that have been associated with cold weather fronts that create a transient decrease in water temperature. From 2005 to 2012 on the Lower Missouri River, no obvious relations between flow pulses and fish movements and spawning behaviors have been apparent. However, pallid sturgeon tracking at the Upper Missouri–Yellowstone confluence indicates that in most years, most telemetered pallid sturgeon migrate out of the Missouri River and into the Yellowstone River in the June–July timeframe in association with the spring pulse. This pattern was disrupted in 2011 when a high flow pulse with warm temperatures and high turbidity emanated from the Milk River, followed by record releases from Fort Peck Dam, and 36–39 percent of the telemetered population migrated up the Upper Missouri. This result supports the hypothesis that sufficiently large flow pulses may trigger migration and aggregation but it is not clear that functional pulses are within reservoir management authorities. Notably, a pallid sturgeon free embryo was captured on the Upper Missouri River in 2011 and another single, genetically confirmed embryo was captured on the Yellowstone River in 2012. Research on free-embryo drift has indicated the potential for hundreds of miles of downstream dispersal. Lack of distance to accommodate the extended downstream dispersal period of free embryos on the Upper Missouri and Yellowstone Rivers is the predominant hypothesis for recruitment failure in the upper basin. Long drift distances in the Lower Missouri River may be responsible for shifting Lower Missouri River sub-populations further into the Middle Mississippi River. Physical understanding of drift processes indicates that mean velocities could be slowed through decreased discharges or increased channel hydraulic radius (width and topographic diversity) to reduce free-embryo dispersal distances. In addition, the probability that free embryos are transported into and retained in channel-margin habitats is theoretically amenable to channel re-engineering that would increase cross-channel secondary currents in bends or channel expansions. Considerable uncertainty persists, however, about whether extended drift of Lower Missouri River larvae is responsible for recruitment failure. If drift distance is limiting, it is important to discern whether it would be advisable to retain larvae within the Missouri River, and where along the river restoration projects should be placed to optimize survival and growth of age-0 and juvenile sturgeon. Longitudinal differences in female pallid sturgeon fecundity lend support to the hypothesis that recruitment failure may be due, in part, to fish having insufficient nutrition to produce the numbers of gametes needed for the population to grow, perhaps because of simultaneous declines in prey-fish populations and their habitats. Establishing a chain of causality from habitat decline, to prey-fish populations, to sturgeon diets, to sturgeon fecundity, and to pallid sturgeon population growth presents a considerable scientific challenge. In addition to the dominant hypotheses relating pallid sturgeon populations to changes in flow regime and channel morphology, other factors have been identified that might be sources of stress and contribute to recruitment failure. Among these are water quality and contaminants. Ambient water-quality monitoring on the Missouri River has demonstrated summer episodes when dissolved oxygen dips below 5 milligrams per liter, a threshold that may be stressful especially to age-0 and juvenile sturgeon. Documented cases of intersex in shovelnose and pallid sturgeon indicate that agricultural and municipal sources of endocrine disrupting chemicals also may have a role in pallid sturgeon recruitment failure. Scientific understanding of the ecological requirements of pallid sturgeon has increased almost exponentially in the last two decades, and efforts are now turning from understanding fundamental biology of the species to quantifying how population dynamics relate to potential management actions. Progress in developing the science needed to inform management actions on the Missouri River may benefit from continuation of monitoring of reproductive cycles, reproductive movements, growth, and survival of telemetry tagged adults, increased emphasis on focused, complementary field and laboratory studies of factors influencing early life history, implementation of studies to resolve the role of food limitations in growth, survival, and reproductive condition, and implementation of studies designed specifically to parameterize models linking management to populations.

Missouri River↗

USGS2005

Life-history variation of a neotropical thrush challenges food limitation theory

Since David Lack first proposed that birds rear as many young as they can nourish, food limitation has been accepted as the primary explanation for variation in clutch size and other life-history traits in birds. The importance of food limitation in life-history variation, however, was recently questioned on theoretical grounds. Here, we show that clutch size differences between two populations of a neotropical thrush were contrary to expectations under Lack's food limitation hypothesis. Larger clutch sizes were found in a population with higher nestling starvation rate (i.e. greater food limitation). We experimentally equalized clutches between populations to verify this difference in food limitation. Our experiment confirmed greater food limitation in the population with larger mean clutch size. In addition, incubation bout length and nestling growth rate were also contrary to predictions of food limitation theory. Our results demonstrate the inability of food limitation to explain differences in several life-history traits: clutch size, incubation behaviour, parental feeding rate and nestling growth rate. These life-history traits were better explained by inter-population differences in nest predation rates. Food limitation may be less important to life history evolution in birds than suggested by traditional theory. ?? 2005 The Royal Society.

Proceedings of the Royal Society B: Biological Sci↗

USGS1992

Biological diversity of a temporary pond herpetofauna in north Florida sandhills

From 1985 through 1990, the herpetofauna of a temporary pond in an uplands longleaf pine sandhills community in north-central Florida was monitored. A drift fence completely encircled the pond. Animals were captured in pitfall traps and marked as they entered and exited the pond basin. I captured 16 155 individuals of 42 species (16 amphibians, 26 reptiles). The species richness, diversity (using Margalef's Diversity Index) and dominance (using the Berger-Parker Index) varied among years. Between 62.5% and 87.5% of the amphibian species and 65% to 81% of the reptile species were captured in any one year. Daily amphibian capture was positively correlated with rainfall, whereas reptile capture was either not correlated or weakly negatively correlated with rainfall. Hydroperiod duration was not correlated with the numbers of either amphibians or reptiles captured. Neither the amphibian nor the reptile community showed any trends in diversity or dominance indices during the course of the study, although both communities were dominated by a few species. However, the species responsible for community dominance changed somewhat as the study progressed. Assessing the results of this study is hampered by the lack of comparable studies elsewhere, expected natural fluctuations of amphibian populations, and a prolonged drought, especially during the latter stages of the study. The herpetological community at Breezeway Pond does not appear to follow theoretical predictions of community response to stress. Temporary ponds are important centres of herpetofaunal biodiversity in uplands sandhills communities. Long-term studies are needed to monitor the composition, structure, and functional interactions of their resident species.

Biodiversity and Conservation↗

USGS2017

Potential influence of wildfire in modulating climate-induced forest redistribution in a central Rocky Mountain landscape

Introduction Climate change is expected to impose significant tension on the geographic distribution of tree species. Yet, tree species range shifts may be delayed by their long life spans, capacity to withstand long periods of physiological stress, and dispersal limitations. Wildfire could theoretically break this biological inertia by killing forest canopies and facilitating species redistribution under changing climate. We investigated the capacity of wildfire to modulate climate-induced tree redistribution across a montane landscape in the central Rocky Mountains under three climate scenarios (contemporary and two warmer future climates) and three wildfire scenarios (representing historical, suppressed, and future fire regimes). Methods Distributions of four common tree species were projected over 90 years by pairing a climate niche model with a forest landscape simulation model that simulates species dispersal, establishment, and mortality under alternative disturbance regimes and climate scenarios. Results Three species (Douglas-fir, lodgepole pine, subalpine fir) declined in abundance over time, due to climate-driven contraction in area suitable for establishment, while one species (ponderosa pine) was unable to exploit climate-driven expansion of area suitable for establishment. Increased fire frequency accelerated declines in area occupied by Douglas-fir, lodgepole pine, and subalpine fir, and it maintained local abundance but not range expansion of ponderosa pine. Conclusions Wildfire may play a larger role in eliminating these conifer species along trailing edges of their distributions than facilitating establishment along leading edges, in part due to dispersal limitations and interspecific competition, and future populations may increasingly depend on persistence in locations unfavorable for their establishment.

Idaho↗

USGS2024

Flooding-induced failure of an invasive Burmese Python nest in southern Florida

It is important to understand the factors affecting the reproductive success of an invasive species to estimate population size and develop management plans. There remains much we do not understand about the reproductive biology of invasive Burmese Pythons in both their native and invasive range. Oviposition site selection is an important factor in determining reproductive success as nesting is a vulnerable period in the life of reptiles. Flooding can be particularly influential for nesting outcomes and success of developing embryos in habitats that experience periods of heavy rainfall or seasonal flooding. It is not clear how seasonal flooding may impact oviposition site selection by females or hatchling survival of Burmese Pythons in Florida. On 10 May 2023, a radio-transmitted female python oviposited in a hollow log and during incubation all eggs were completely submerged for variable amounts of time. All eggs were collected (n = 78) and dissected to confirm fertilization and assess the stage of embryo development. Two eggs were found to be infertile, while the remaining fertile eggs contained embryos that died at various stages of development. The observed failure of this python nest was a direct result of oviposition site selection by the female. The frequency at which females lay eggs in suboptimal locations in southern Florida is currently unknown. This maladaptive behavior would suggest Burmese Pythons have fitness levels below theoretical optima.

Florida↗

USGS2016

Considering transient population dynamics in the conservation of slow life-history species: An application to the sandhill crane

The importance of transient dynamics of structured populations is increasingly recognized in ecology, yet these implications are not largely considered in conservation practices. We investigate transient and long-term population dynamics to demonstrate the process and utility of incorporating transient dynamics into conservation research and to better understand the population management of slow life-history species; these species can be theoretically highly sensitive to short- and long-term transient effects. We are specifically interested in the effects of anthropogenic removal of individuals from populations, such as caused by harvest, poaching, translocation, or incidental take. We use the sandhill crane ( Grus canadensis ) as an exemplar species; it is long-lived, has low reproduction, late maturity, and multiple populations are subject to sport harvest. We found sandhill cranes to have extremely high potential, but low likelihood for transient dynamics, even when the population is being harvested. The typically low population growth rate of slow life-history species appears to buffer against many perturbations causing large transient effects. Transient dynamics will dominate population trajectories of these species when stage structures are highly biased towards the younger and non-reproducing individuals, a situation that may be rare in established populations of long-lived animals. However, short-term transient population growth can be highly sensitive to vital rates that are relatively insensitive under equilibrium, suggesting that stage structure should be known if perturbation analysis is used to identify effective conservation strategies. For populations of slow life-history species that are not prone to large perturbations to their most productive individuals, population growth may be approximated by equilibrium dynamics.

Biological Conservation↗

USGS2010

Estimating migratory game-bird productivity by integrating age ratio and banding data

Context: Reproduction is a critical component of fitness, and understanding factors that influence temporal and spatial dynamics in reproductive output is important for effective management and conservation. Although several indices of reproductive output for wide-ranging species, such as migratory birds, exist, there has been no theoretical justification for their estimators or associated measures of variance. Aims: The aims of our research were to develop statistical justification for an estimator of reproduction and associated variances on the basis of an existing national wing-collection survey and banding data, and to demonstrate the applicability of this estimator to a migratory game bird. Methods: We used a Bayesian hierarchical modelling approach to integrate wing-collection data, which provides information on population age ratios, and band-recovery data, which provides information on recovery probabilities of various age classes, for American woodcock ( Scolopax minor ) to estimate productivity and associated measures of variance. We present two models of relative vulnerability between age classes: one model assumed that adult recovery probabilities were higher, but that annual fluctuations were synchronous between the two age classes (i.e. an additive effect of age and year). The second model assumed that adults, on average, had higher recovery probabilities than did juveniles and that annual fluctuations were asynchronous through time (i.e. an interaction between age and year). Key results: Fitting our models within a hierarchical Bayesian framework efficiently incorporates the two data types into a single estimator and derives appropriate variances for the productivity estimator. Further, use of Bayesian methods enabled us to derive credible intervals that avoid the reliance on asymptotic assumptions. When applied to American woodcock data, the additive model resulted in biologically realistic and more precise age-ratio estimates each year and is adequate when the relative vulnerability to sampling only slightly varies or does not vary among components of a population (e.g. age, sex class) among years. Therefore, we recommend using woodcock indices from our analysis based on this model. Conclusions: We provide a flexible modelling framework for estimating productivity and associated variances that can incorporate ecological covariates to explore various factors that could drive annual dynamics in productivity. Applying our model to the American woodcock data indicated that assumptions about the variability in relative recovery probabilities could greatly influence the precision of our productivity estimator. Therefore, researchers should carefully consider the assumption of temporally variable relative recovery probabilities (i.e. ratio of juvenile to adults' recovery probability) for different age classes when applying this estimator. Implications: Several national and international management strategies for migratory game birds in North America rely on measures of productivity from harvest survey parts collections, without a justification of the estimator or providing estimates of precision. We derive an estimator of productivity with realistic measures of uncertainty that can be directly incorporated into management plans or ecological studies across large spatial scales.

Wildlife Research↗

USGS2018

What it is to be established: policy and management implications for non-native and invasive species

Management of invasive species, whether prevention, population reduction, or eradication, requires assessment of the invasive species’ population status and an assessment of the probability of success of management options. Perceptions of a species’ permanence in an environment or lack thereof frequently drives how limited time, financial, and personnel resources are allocated to such efforts. Language we use to describe a non-native species’ status largely defines these perceptions and sets boundaries, real or perceived, to potential management actions. Here we discuss the use of a particular term – “established” – when confronting management decisions for invasive species. Our objective is to contribute to bridging the gap between the realms of conceptual development and management with respect to use of the term “established”. We find that although there are benefits of polysemy and synonymy to conceptual development they present an additional challenge to managers who must weigh the costs, benefits, and potential for success of particular management actions. We also examine how existing conceptual frameworks might be augmented to bridge the theoretical-practical gap, such as more precisely defining potential management actions and explicitly including assessment of risk.

Management of Biological Invasions↗

USGS2020

Highly variable rates of survival to metamorphosis in wild boreal toads (Anaxyrus boreas boreas)

Life history theory suggests that long‐lived, pond‐breeding amphibians should have low and highly variable early life‐stage survival rates, but this theoretical expectation is often untested and the causes of variation are usually unknown. We evaluated the impact of hydroperiod, presence of a pathogen ( Batrachochytrium dendrobatidis [Bd]), presence of a potential predator (cutthroat trout Oncorhychus clarki stomias) , and whether animals had been reintroduced into a site on survival of early life stages of boreal toads ( Anaxyrus boreas boreas ). We used a multistate mark‐recapture framework to estimate survival of boreal toad embryos from egg to metamorphosis at four sites over 5 years. We found substantial spatial and temporal variation in survival to metamorphosis and documented some evidence that monthly tadpole survival was lower in sites with Bd, without trout, and at permanent sites. Our results support theories of amphibian life history, aid in the management of this species of conservation concern, and contribute to our knowledge of the ecology of the species. Additionally, we present methodology that allows practitioners to account for different lengths of time between sampling periods when estimating survival probabilities which is especially applicable to organisms with distinct biological stages.

Population Ecology↗

USGS1998

Estimator selection for closed-population capture: recapture

For valid statistical inference, it is important to select an appropriate statistical model. In the analysis of capture-recapture data under the closed-population models of Otis et al. (1978), information theoretic and hypothesis testing approaches to model selection are not practical, because some of the models have likelihoods with nonidenti- fiable parameters. A further problem is that, for some of the Otis et al. models, multiple estimators exist but there is no objective basis for deciding which estimator to use for a particular dataset. In CAPTURE, a computer program for estimating parameters un- der the closed models of Otis et al., a linear discriminant classifier is used to select an appropriate model. This classifier frequently selects the incorrect generating model in simulation studies, and it provides no guidance on which estimator to use once a model has been selected. In this study, we develop new classifiers for selecting the best esti- mator (as opposed to the generating model) and evaluate their performance. In addition, we investigate an estimator averaging approach to estimation that is a modification of the model averaging approach described by Buckland et al. (1997). We found that, in general, the overall performance of the new classifiers was unimpressive. In contrast, the estimator averaging approach we investigated performed well.

Journal of Agricultural, Biological, and Environme↗

USGS2021

Evaluating establishment success of non-native fishes introduced to inland aquatic habitats of tropical Pacific islands

An information-theoretic approach was used to evaluate non-native freshwater fish species introduced to insular habitats of Hawaii and Guam comparing successful establishments vs. failures. Since the late 1800s, as many as 81 non-native freshwater fish species have been recorded as introduced to Hawaii and Guam (combined) and 50 (62%) of these are documented as having one or more established populations. We examined eleven independent variables to investigate establishment success by creating 21 a priori logistic regression models ranked using Akaike's Information Criterion adjusted for small sample size. An additional eight post-hoc models were included that comprised the best a priori model and various combinations of individual variables. The best overall model of establishment probability included effects of taxonomic affinity (family membership), prior establishment success on other tropical islands, and hypoxia tolerance. Establishment success in Hawaii and Guam was highest for those species established on many other islands, and according to our best model air-breathing fishes were more likely to become established. Six fish families, each with from three to 18 species introduced to Pacific islands, were highly successful at establishment: Cichlidae (16 established of 18 species introduced), Poeciliidae (seven of eight), Cyprinidae (four of seven), Centrarchidae (four of four), Clariidae (three of three), and Loricariidae (three of four). Those that successfully established include both small and moderately large-bodied taxa, while representing a diverse array of other morphological and life-history traits. Pathways and motives associated with fish introductions in the Pacific have been linked to desires to develop aquaculture, enhance wild stocks of food, sport, and bait fishes, for use as biological control agents, or are linked to the ornamental fish trade. We found that many established species were introduced via multiple pathways (up to eight) and our analyses suggest that the combination of prior establishment success on other tropical islands and presence of non-native fishes in multiple pathways was indicative of high propagule pressure. Our study results and conclusions on Pacific tropical island introductions are in general agreement with previous studies on non-native freshwater fishes in other regions of the world and similar to observations in continental ecosystems and temperate zones.

Hawaii↗

USGS2016

Fishing diseased abalone to promote yield and conservation

Past theoretical models suggest fishing disease-impacted stocks can reduce parasite transmission, but this is a good management strategy only when the exploitation required to reduce transmission does not overfish the stock. We applied this concept to a red abalone fishery so impacted by an infectious disease (withering syndrome) that stock densities plummeted and managers closed the fishery. In addition to the non-selective fishing strategy considered by past disease-fishing models, we modelled targeting (culling) infected individuals, which is plausible in red abalone because modern diagnostic tools can determine infection without harming landed abalone and the diagnostic cost is minor relative to the catch value. The non-selective abalone fishing required to eradicate parasites exceeded thresholds for abalone sustainability, but targeting infected abalone allowed the fishery to generate yield and reduce parasite prevalence while maintaining stock densities at or above the densities attainable if the population was closed to fishing. The effect was strong enough that stock and yield increased even when the catch was one-third uninfected abalone. These results could apply to other fisheries as the diagnostic costs decline relative to catch value.

Philosophical Transactions of the Royal Society B:↗

USGS2009

Does mobility explain variation in colonisation and population recovery among stream fishes?

1. Colonisation and population recovery are crucial to species persistence in environmentally variable ecosystems, but are poorly understood processes. After documenting movement rates for several species of stream fish, we predicted that this variable would influence colonisation rates more strongly than local abundance, per cent occupancy, body size and taxonomic family. We also predicted that populations of species with higher movement rates would recover more rapidly than species with lower movement rates and that assemblage structure would change accordingly. 2. To test these predictions, we removed fishes from a headwater and a mainstem creek in southwest Virginia and monitored colonisation over a 2-year period. Using an information–theoretic approach, we evaluated the relative plausibility of 15 alternative models containing different combinations of our predictor variables. Our best-supported model contained movement rate and abundance and was 41 times more likely to account for observed patterns in colonisation rates than the next-best model. Movement rate and abundance were both positively related to colonisation rates and explained 88% of the variation in colonisation rates among species. 3. Population recovery, measured as the per cent of initial abundance restored, was also positively associated with movement rate. One species recovered within 3 months, most recovered within 2 years, but two species still had not recovered after 2 years. Despite high variation in recovery, the removal had only a slight impact on assemblage structure because species that were abundant in pre-removal samples were also abundant in post-removal samples. 4. The significance of interspecific variation in colonisation and recovery rates has been underappreciated because of the widely documented recovery of stream fish assemblages following fish kills and small-scale experimental defaunations. Our results indicate that recovery of the overall assemblage does not imply recovery of each component species. Populations of species that are rare and less mobile will recover more slowly and will be more vulnerable to extinction in systems where chemical spills, hydrological alteration, extreme droughts and other impacts are frequent.

Virginia↗

USGS2018

A parasitism-mutualism-predation model consisting of crows, cuckoos and cats with stage-structure and maturation delays on crows and cuckoos

In this paper, a parasitism-mutualism-predation model is proposed to investigate the dynamics of multi-interactions among cuckoos, crows and cats with stage-structure and maturation time delays on cuckoos and crows. The crows permit the cuckoos to parasitize their nestlings (eggs) on the crow chicks (eggs). In return, the cuckoo nestlings produce a malodorous cloacal secretion to protect the crow chicks from predation by the cats, which is apparently beneficial to both the crow and cuckoo population. The multi-interactions, i.e., parasitism and mutualism between the cuckoos (nestlings) and crows (chicks), predation between the cats and crow chicks are modeled both by Holling-type II and Beddington-DeAngelis-type functional responses. The existence of positive equilibria of three subsystems of the model are discussed. The criteria for the global stability of the trivial equilibrium are established by the Krein-Rutman Theorem and other analysis methods. Moreover, the threshold dynamics for the coexistence and weak persistence of the model are obtained, and we show, both analytically and numerically, that the stabilities of the interior equilibria may change with the increasing maturation time delays. We find there exists an evident difference in the dynamical properties of the parasitism-mutualism-predation model based on whether or not we consider the effects of stage-structure and maturation time delays on cuckoos and crows. Inclusion of stage structure results in many varied dynamical complexities which are difficult to encompass without this inclusion.

Journal of Theoretical Biology↗

USGS2015

Assessing the components of adaptive capacity to improve conservation and management efforts under global change

Natural-resource managers and other conservation practitioners are under unprecedented pressure to categorize and quantify the vulnerability of natural systems based on assessment of the exposure, sensitivity, and adaptive capacity of species to climate change. Despite the urgent need for these assessments, neither the theoretical basis of adaptive capacity nor the practical issues underlying its quantification has been articulated in a manner that is directly applicable to natural-resource management. Both are critical for researchers, managers, and other conservation practitioners to develop reliable strategies for assessing adaptive capacity. Drawing from principles of classical and contemporary research and examples from terrestrial, marine, plant, and animal systems, we examined broadly the theory behind the concept of adaptive capacity. We then considered how interdisciplinary, trait- and triage-based approaches encompassing the oft-overlooked interactions among components of adaptive capacity can be used to identify species and populations likely to have higher (or lower) adaptive capacity. We identified the challenges and value of such endeavors and argue for a concerted interdisciplinary research approach that combines ecology, ecological genetics, and eco-physiology to reflect the interacting components of adaptive capacity. We aimed to provide a basis for constructive discussion between natural-resource managers and researchers, discussions urgently needed to identify research directions that will deliver answers to real-world questions facing resource managers, other conservation practitioners, and policy makers. Directing research to both seek general patterns and identify ways to facilitate adaptive capacity of key species and populations within species, will enable conservation ecologists and resource managers to maximize returns on research and management investment and arrive at novel and dynamic management and policy decisions.

Conservation Biology↗