Genomic erosion in a demographically recovered bird species during conservation rescue

The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ex situ population was established from which captive-bred individuals were released into free-living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400–480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993–2008) with restriction site-associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free-living population. However, further genetic rescue with captive-bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.     

Glutathione S-transferase gene polymorphisms in association with susceptibility to lead toxicity in lead- and cadmium-exposed children near an abandoned lead-zinc mining area in Kabwe,Zambia

Environmental Science and Pollution Research - Interindividual genetic variations determine human’s susceptibility to heavy metal-induced toxicity. Thus, we analyzed blood concentrations of...     

Effect of thallium on phototactic behaviour in Daphnia magna

Environmental Science and Pollution Research - Thallium (Tl) is a trace metal enriched in wastewaters associated with mining and smelting of base metals. The toxicity of Tl to aquatic biota is...     

Consumptive and nonconsumptive effects of predators on metacommunities of competing prey

Although predators affect prey both via consumption and by changing prey migration behavior, the interplay between these two effects is rarely incorporated into spatial models of predator-prey dynamics and competition among prey. We develop a model where generalist predators have consumptive effects (i.e., altering the likelihood of local prey extinction) as well as nonconsumptive effects (altering the likelihood of colonization) on spatially separated prey populations (metapopulations). We then extend this model to explore the effects of predators on competition among prey. We find that generalist predators can promote persistence of prey metapopulations by promoting prey colonization, but predators can also hasten system-wide extinction by either increasing local extinction or reducing prey migration. By altering rates of prey migration, predators in one location can exert remote control over prey dynamics in another location via predator-mediated changes in prey flux. Thus, the effect of predators may extend well beyond the proportion of patches they visit. In the context of prey metacommunities, predator-mediated shifts in prey migration and mortality can shift the competition-colonization trade-off among competing prey, leading to changes in the prey community as well as changes in the susceptibility of prey species to habitat loss. Consequently, native prey communities may be susceptible to invasion not only by exotic prey species that experience reduced amounts of mortality from resident predators, but also by exotic prey species that exhibit strong dispersal in response to generalist native predators. Ultimately, our work suggests that the consumptive and nonconsumptive effects of generalist predators may have strong, yet potentially cryptic, effects on competing prey capable of mediating coexistence, fostering invasion, and interacting with anthropogenic habitat alteration.     

A hierarchical model for spatial capture-recapture data

Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates because the effective sample area is unknown. A number of methods involving the adjustment of estimates based on heuristic considerations are in widespread use. In this paper, a hierarchical model of spatially indexed capture-recapture data is proposed for sampling based on area searches of spatial sample units subject to uniform sampling intensity. The hierarchical model contains explicit models for the distribution of individuals and their movements, in addition to an observation model that is conditional on the location of individuals during sampling. Bayesian analysis of the hierarchical model is achieved by the use of data augmentation, which allows for a straightforward implementation in the freely available software WinBUGS. We present results of a simulation study that was carried out to evaluate the operating characteristics of the Bayesian estimator under variable densities and movement patterns of individuals. An application of the model is presented for survey data on the flat-tailed horned lizard (Phrynosoma mcallii) in Arizona, USA.     

New expansions in old clades: population genetics and phylogeny of Gnatholepis species (Teleostei: Gobioidei) in the Pacific

Species of the reef goby genus Gnatholepis exhibit enormous geographic ranges with little evidence of population segregation detectable based on mitochondrial DNA. To determine if genetic differentiation is evident with more rapidly evolving markers, seven microsatellite loci were screened from the species Gnatholepis anjerensis and G. scapulostigma and population segregation was tested among fish from across the South Pacific. Both AMOVA and pairwise F _ST analyses showed that, in concordance with previous mitochondrial results, most genetic variance occurs within individual populations, as population differentiation is evident only over the largest distances (>3,700 km). This result is contrasted with previous studies demonstrating that despite their relatively long larval periods, some gobiid fishes exhibit population differentiation on small (<100 km) geographic scales. Coalescence analysis showed that current Pacific populations of these species originated in the Pleistocene, presumably related to sea level fluctuations associated with episodes of glaciation. However, rate analysis based on a phylogeny of Gnatholepis species indicates that the species themselves are much older, consistent with a complex history of rapid, short-term population contractions and expansions, with corresponding rapid dispersal.     

Net primary production, growth, and standing crop of Macrocystis pyrifera in Southern California

Marine macroalgae are believed to be among the most productive autotrophs in the world. However, relatively little information exists about spatial and temporal variation in net primary production (NPP) by these organisms. The data presented here are being collected to investigate patterns and causes of variation in NPP by the giant kelp, Macrocystis pyrifera, which is believed to be one of the fastest growing autotrophs on earth. The standing crop and loss rates of M. pyrifera have been measured monthly in permanent plots at three sites in the Santa Barbara Channel, USA. Collection of these data began in June 2002 and is ongoing. Seasonal estimates of NPP and growth rate are made by combining the field data with a model of kelp dynamics. The purpose of this Data Paper is to make available a time series of M. pyrifera NPP, growth, and standing crop that is appropriate for examining seasonal and interannual patterns across multiple sites. Data on plant density in each plot and censuses of fronds on tagged plants at each site are also made available here. NPP, mass-specific growth rate, and standing crop are presented in four different metrics (wet mass, dry mass, carbon mass, and nitrogen mass) to facilitate comparisons with previous studies of M. pyrifera and with NPP measured in other ecosystems. Analyses of these data reveal seasonal cycles in growth and standing crop as well as substantial differences in M. pyrifera NPP among sites and years.     

Individual boldness affects interspecific interactions in sticklebacks

Within populations of many species, individuals that are otherwise similar to one another in age, size or sex can differ markedly in behaviours such as resource use, risk taking and competitive ability. There has been much research into the implications of such variation for intraspecific interactions, yet little investigation into its role in influencing interspecific interactions outside of a predator–prey context. In this study, we investigated the role of individual-level behavioural variation in determining the outcomes of interactions between two ecologically similar fishes, the threespine and ninespine sticklebacks (Gasterosteus aculeatus and Pungitius pungitius). Experiment 1 asked whether individuals of both species were consistent in their expression of two behaviours: activity in novel surroundings and latency to attack prey. For each behaviour, focal individuals were assayed twice, 10 days apart. Performances were positively correlated between exposures, suggesting behavioural consistency within individuals, at least over this timescale. Experiment 2 revealed not only differences in habitat use described both by species-level variation, with ninespines spending more time in vegetated areas, but also by individual differences, with more active individuals of both species spending more time in open water than in vegetation. Experiment 3 revealed that when heterospecific pairs competed for prey, bolder individuals consumed a greater share, irrespective of species. These findings suggest that individual-level variation can facilitate overlap in habitat use between heterospecifics and also determine the outcomes of resource contests when they meet. We discuss how this might vary between populations as a function of prevailing selection pressures and suggest approaches for testing our predictions.     

Does the risk of encountering lions influence African herbivore behaviour at waterholes?

A central question in the study of predator–prey relationships is to what extent prey behaviour is determined by avoidance of predators. Here, we test whether the long-term risk of encountering lions and the presence of lions in the vicinity influence the behaviour of large African herbivores at waterholes through avoidance of high-risk areas, increases in group size, changes in temporal niche or changes in the time spent in waterhole areas. In Hwange National Park, Zimbabwe, we monitored waterholes to study the behaviour of nine herbivore species under different risks of encountering lions. We radio-collared 26 lions in the study area which provided the opportunity to monitor whether lions were present during observation sessions and to map longer-term seasonal landscapes of risk of encountering lions. Our results show that the preferred prey species for lions (buffalo, kudu and giraffe) avoided risky waterholes. Group size increased as encounter risk increased for only two species (wildebeest and zebra), but this effect was not strong. Interestingly, buffalo avoided the hours of the day which are dangerous when the long-term and short-term risks of encountering lions were high, and all species showed avoidance of waterhole use at night times when lions were in the vicinity. This illustrates well how prey can make temporal adjustments to avoid dangerous periods coinciding with predator hunting. Additionally, many herbivores spent more time accessing water to drink when the long- and short-term risks of encountering lions were high, and they showed longer potential drinking time when the long-term risk of encountering lions was high, suggesting higher levels of vigilance. This study illustrates the diversity of behavioural adjustments to the risk of encountering a predator and how prey respond differently to temporal variations in this risk.     

Probabilistic movement model with emigration simulates movements of deer in Nebraska, 1990–2006

Movements of deer can affect population dynamics, spatial redistribution, and transmission and spread of diseases. Our goal was to model the movement of deer in Nebraska in an attempt to predict the potential for spread of chronic wasting disease (CWD) into eastern Nebraska. We collared and radio-tracked >600 white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) in Nebraska during 1990–2006. We observed large displacements (>10 km) for both species and sexes of deer, including migrations up to 100 km and dispersals up to 50 km. Average distance traveled between successive daily locations was 166 m for male and 173 for female deer in eastern Nebraska, and 427 m for male and 459 for female deer in western Nebraska. Average daily displacement from initial capture point was 10 m for male and 14 m for female deer in eastern Nebraska, and 27 m for male and 28 m for female deer in western Nebraska. We used these data on naturally occurring movements to create and test 6 individual-based models of movement for white-tailed deer and mule deer in Nebraska, including models that incorporated sampling from empirical distributions of movement lengths and turn angles (DIST), correlated random walks (CRW), home point fidelity (FOCUS), shifting home point (SHIFT), probabilistic movement acceptance (MOVE), and probabilistic movement with emigration (MOVEwEMI). We created models in sequence in an attempt to account for the shortcomings of the previous model(s). We used the Kolmogrov–Smirnov goodness-of-fit test to verify improvement of simulated annual displacement distributions to empirical displacement distributions. The best-fit model (D = 0.07 and 0.08 for eastern and western Nebraska, respectively) included a probabilistic movement chance with emigration (MOVEwEMI) and resulted in an optimal daily movement length of 350 m (maximum daily movement length of 2800 m for emigrators) for eastern Nebraska and 370 m (maximum of 2960 m) for western Nebraska. The proportion of deer that moved as emigrators was 0.10 and 0.13 for eastern and western Nebraska, respectively. We propose that the observed spread of CWD may be driven by large movements of a small proportion of deer that help to establish a low prevalence of the disease in areas east of the current endemic area. Our movement models will be used in a larger individual-based simulation of movement, survival, and transmission of CWD to help determine future surveillance and management actions.