A model of the emergence of infectious pancreatic necrosis virus in Scottish salmon farms 1996–2003

Infectious pancreatic necrosis virus (IPNV) is an increasingly common pathogen in farmed Scottish Atlantic salmon; over 80% of marine sites are now infected, although most do not suffer clinical disease. The increasing prevalence of this pathogen in farms over the period 1996–2003 is modelled using a simple susceptible–infected (SI) epidemic model. Because salmon production approximately doubled over this period, population-dependent and -independent transmission models are compared. The model generates mean R₀ (increase ratio) of 1.41 in fresh and 1.45 in marine water farms at the national level; higher values apply with time under population-dependent transmission (1.58, freshwater, 1.80 marine by 2003). Regional differences in R₀ are mostly moderate, indicating similar regional processes in spite of substantial difference in prevalence. Prevalence of IPNV for marine sites was further increased by the use of smolts (young salmon) from multiple freshwater sources. The model suggests that prevalence is entering dynamic equilibrium and will stabilise or only increase slowly as population increases. Cutting freshwater transmission is the most effective single strategy at reducing IPNV prevalence, but a combination of strategies (including reducing the number of sources of smolts) is better and indeed is required for eradication. Eradication would require cuts in transmission of at least 30–45% and this is unlikely to be practicable.     

Bimodality of the combined removal and signs-of-activities estimator for sampling closed animal populations

The possibility of a bimodal log-likelihood function arises with certain data when the combined removal and signs-of-activities estimator is used. Bimodal log-likelihoods may, in turn, yield disjoint confidence intervals for certain confidence levels. The hypothesis that bimodality is caused by the violation of the equal catchability assumption of the removal model, leading to the combination of contradictory data/models in the combined estimator is set forth. Simulations exploring the effect of the violation of removal model assumptions on estimation and inference showed that the assumption of unequal capture probability influenced the frequency of bimodal likelihoods; similarly, extreme parameter values for probability of capture influenced the number of excessively large confidence intervals produced. A sex-specific combined estimator is developed as a remedial model tailored to the problem. The simulations suggest that both the signs-of-activities estimator and the sex-specific estimator perform equally well over the range of simulations presented, though the signs-of-activities estimator is easier to implement.     

Female choice for complex song in the European starling: a field experiment

Male European starlings Sturnus vulgaris sing long complex songs that appear to be important in the courtship of females but which also influence competitive interactions between males. We tested the hypothesis that females choose mates on the basis of the complexity of their songs, rather than on the quality of the territories the males defended. In order to determine whether certain territories were preferred over others, the first set of birds to settle in the experimental nest-boxes was removed and a second set allowed to settle. Consistent preferences for certain nest-boxes were indicated by correlations between the settlement patterns of the first and second sets of birds. However, males with the most complex song did not necessarily occupy the most preferred nest sites. Males with more complex song acquired mates faster. This relationship remained significant when nest-site preference was statistically controlled, indicating that female starlings chose males with complex song rather than those that defended preferred nest sites. A number of morphological variables were also found to be uncorrelated with female choice. Song complexity in European starlings increases with age, and the evolution of song complexity in this species is consistent with an age-indicator model of sexual selection. Males with larger repertoires were also in better condition, indicating that females obtain high-quality mates by choosing on the basis of male song. Received: 29 April 1995/Accepted after revision: 9 September 1995     

Patch Size and Connectivity Thresholds for Butterfly Habitat Restoration

Abstract:  Recovery of endangered species in highly fragmented habitats often requires habitat restoration. Selection of restoration sites typically involves too many options and too much uncertainty to reach a decision based on existing reserve design methods. The Fender's blue butterfly (  Icaricia icarioides fenderi ) survives in small, isolated patches of remnant prairie in Oregon's Willamette Valley—a habitat for which <0.5% of the original remains. Recovery of this species will require considerable habitat restoration. We investigated the potential of biologically based rules of thumb and more complex models to serve as tools in making land acquisitions. Based on Fender's blue dispersal behavior and demography, we have estimated that restored patches should be <1 km from existing habitat and at least 2 ha. We compared these rules to the results of two modeling approaches: an incidence function model and a spatially explicit simulation of demography and dispersal behavior. Not surprisingly, the simple rules and complex models all conclude that large (>2 ha) connected (<1 km) patches have the highest restoration value. The dispersal model, however, suggests that small, connected patches have more restoration value than large, isolated patches, whereas the incidence function model suggests that size and connectivity are equally important. These differences stem from model assumptions. We used incidence functions to predict long-term, stochastic, steady-state conditions and dispersal simulations to predict short-term (25-year) colonization dynamics. To apply our results in the context of selecting restoration sites on the ground, we recommend selecting nearby sites when short-term colonization dynamics are expected to be an important aspect of a species' biology.     

Demographic Limitations of the Ability of Habitat Restoration to Rescue Declining Populations

Abstract:  Habitat restoration is often recommended in conservation without first evaluating whether populations are in fact habitat limited and thus whether declining populations can be stabilized or recovered through habitat restoration. We used a spatially structured demographic model coupled with a dynamic neutral landscape model to evaluate whether habitat restoration could rescue populations of several generic migratory songbirds that differed in their sensitivity to habitat fragmentation (i.e., severity of edge effects on nesting success). Simulating a best-case scenario, landscapes were instantly restored to 100% habitat before, at, or after habitat loss exceeded the species' vulnerability threshold. The vulnerability threshold is a measure of extinction risk, in which the change in population growth rate ( δλ ) scaled to the rate of habitat loss ( δh ) falls below −1% ( δλ/δh ≤ −0.01). Habitat restoration was most effective for species with low-to-moderate edge sensitivities and in landscapes that had not previously experienced extensive fragmentation. To stabilize populations of species that were highly edge sensitive or any species in heavily fragmented landscapes, restoration needed to be initiated long before the vulnerability threshold was reached. In practice, habitat restoration is generally not initiated until a population is at risk of extinction, but our model results demonstrate that some populations cannot be recovered at this point through habitat restoration alone. At this stage, habitat loss and fragmentation have seriously eroded the species' demographic potential such that halting population declines is limited more by demographic factors than the amount of available habitat. Evidence that populations decline in response to habitat loss is thus not sufficient to conclude that habitat restoration will be sufficient to rescue declining populations.     

Importance of Well-Designed Monitoring Programs for the Conservation of Endangered Species: Case Study of the Snail Kite

Abstract:  Monitoring natural populations is often a necessary step to establish the conservation status of species and to help improve management decisions. Nevertheless, many monitoring programs do not effectively address primary sources of variability in monitoring data, which ultimately may limit the utility of monitoring in identifying declines and improving management. To illustrate the importance of taking into account detectability and spatial variation, we used a recently proposed estimator of abundance (superpopulation estimator) to estimate population size of and number of young produced by the Snail Kite ( Rostrhamus sociabilis plumbeus ) in Florida. During the last decade, primary recovery targets set by the U.S. Fish and Wildlife Service for the Snail Kite that were based on deficient monitoring programs (i.e., uncorrected counts) were close to being met (by simply increasing search effort during count surveys). During that same period, the Snail Kite population declined dramatically (by 55% from 1997 to 2005) and the number of young decreased by 70% between 1992–1998 and 1999–2005. Our results provide a strong practical case in favor of the argument that investing a sufficient amount of time and resources into designing and implementing monitoring programs that carefully address detectability and spatial variation is critical for the conservation of endangered species.     

Social system and reproduction of helpers in a cooperatively breeding cichlid fish (Julidochromis ornatus) in Lake Tanganyika: field observations and parentage analyses

It is suggested that some fish of the genus Julidochromis, substrate-brooding Tanganyikan cichlids with biparental care, breed cooperatively with helpers. We studied the social system of J. ornatus in the wild and analysed genetic parentage using microsatellites. Within the studied population three patterns of social system were identified: monogamous pairs (61%, 44 of 72 groups), pairs with helpers (29%, 21), and polygamous harems with helpers (controlled by either a large female or large male owner; 10%, 7). In cooperatively breeding groups, the number of helpers at each nest ranged from 1 to 6 (median 1), and male helpers were more numerous than female helpers. In both sexes, the body size was different among individuals of different social status (harem owner > breeder > helper). Helpers and harem owners of both sexes exhibited brood defence although its frequency was low. The molecular analysis revealed that (1) the helpers were mostly unrelated to dominant breeders, (2) many helpers of both sexes contributed genetically to the next generations, (3) male helpers had high siring success (41% of young in total), and (4) large young unrelated to group members were detected at 30% of observed nests, which may be due to breeder (or helper) replacements and immigration of young. We discuss the implications of these results for understanding the complex social system of this species, especially the low reproductive skew in comparison with other cooperatively breeding cichlids.     

Spatio-temporal Analysis of Acute Admissions for Ischemic Heart Disease in NSW,Australia

The recently funded Spatial Environmental Epidemiology in New South Wales (SEE NSW) project aims to use routinely collected data in NSW Australia to investigate risk factors for various chronic diseases. In this paper, we present a case study focused on the relationship between social disadvantage and ischemic heart disease to highlight some of the methodological challenges that are likely to arise.     

Dynamic multi-resolution spatial models

Data from remote-sensing platforms play an important role in monitoring environmental processes, such as the distribution of stratospheric ozone. Remote-sense data are typically spatial, temporal, and massive. Existing prediction methods such as kriging are computationally infeasible. The multi-resolution spatial model (MRSM) captures nonstationary spatial dependence and produces fast optimal estimates using a change-of-resolution Kalman filter. However, past data can provide valuable information about the current status of the process being investigated. In this article, we incorporate the temporal dependence into the process by developing a dynamic MRSM. An application of the dynamic MRSM to a month of daily total column ozone data is presented, and on a given day the results of posterior inference are compared to those for the spatial-only MRSM. It is apparent that there are advantages to using the dynamic MRSM in regions where data are missing, such as when a whole swath of satellite data is missing.     

A frontier model for landscape ecology: the tapir in Honduras

We borrow a frontier specification from the econometrics literature to make inferences about the tolerance of the tapir to human settlements. We estimate the width of an invisible band surrounding human settlements which would act as a frontier or exclusion zone to the tapir to be around 290 metres.