Capture-Recapture Smooth Estimation of Age-Specific Survival Probabilities in Animal Populations

Yielding sound estimates of survival according to age in wild populations where senescence or other age-related variations may occur is very important to management decision makers, and remains challenging. This paper proposes to use penalized maximum likelihood to obtain smooth estimates of annual survival probabilities across age in populations of wild animals followed by capture–recapture. We propose to use two different types of smoothing penalties, and we use ν-fold cross-validation to select the best value of the tuning parameter for the intensity of smoothing. We then assess the accuracy of the method by a simulation study with two different shapes of the relationship between age and survival, and we conclude that a careful use of this method provides reliable noise-free estimates of age-specific annual survival. We apply this procedure to the motivating data from a population of roe deer known to exhibit a marked decrease of survival with age, and we compare our results with those previously published on this population.     

Impacts of urbanization on Florida Key deer behavior and population dynamics

Rapid human population growth and urbanization have had a negative impact on species biodiversity. As competition for resources between man and wildlife continues, it is important to understand the effects of urbanization on species. Endangered Key deer (Odocoileus virginianus clavium) are endemic to the Florida Keys which have undergone rapid human population growth and development over the past 30 years. Our study objectives were to evaluate the impacts of urban development on Key deer habitat use, population dynamics, behavior, and body mass. We used data from two comprehensive studies on Key deer spanning 30 years to evaluate these changes. Our results suggest that Key deer have become more urbanized, using urban areas more today than they did 30 years ago. Contrary to our predictions, survival was higher for more urban deer than for less urban deer. Problems still exist with mortality factors heavily impacting some portions of the deer population including lower survival associated with less urban male deer. Analysis of Key deer body mass also was converse to our predictions as deer weights appear to have increased over time. Collectively, our results suggest that over the past 30 years Key deer have become more urbanized and that deer plasticity has allowed them to adapt and persist in an urbanizing environment. However, the future ability of Key deer to persist in an environment with continued urban development is unknown. At some threshold, urban development would become unsustainable and unlike other forms of habitat change or environmental disturbances, urban development is in most cases irreversible requiring careful planning in habitat conservation strategies.     

Survival and spatial fidelity of mouflons: The effect of location,age, and sex

This article is motivated by a series of data on a population of mouflons (Ovisgmelini) in the Caroux-Espinouse massif and focuses upon discriminating between competing biological hypotheses corresponding to the dependence of any or all of the population parameters upon either sex, location, or age. We show how we can analyze the data using a Bayesian approach, where we are able to take into account prior information obtained via a previous radio-tagging study. We consider the Arnason-Schwarz model together with its submodels to describe the data. Efficiently exploring model space using reversible jump Markov chain Monte Carlo methodology, we are able to calculate model-averaged estimates of parameters of interest, which incorporate both parameter and model uncertainty. In addition, we quantitatively compare different biological hypotheses by calculating their corresponding posterior probabilities. In particular, we show that survival rates tend to remain constant with some evidence to suggest a slight senescent decline. We also provide evidence to suggest that movement around the habitat is largely the same for both sexes up until age 4, when the males appear to extend their migration range, venturing further from the main flock in search of better grazing.     

Sex matters: Modeling male and female habitat differences for jaguar conservation

Competition for mates, cub rearing, and other behaviors differ between males and females in large carnivores. Although these differences can be reflected in patterns of habitat use, gender has rarely been incorporated into habitat models. We evaluated differences in habitat use between male and female jaguars in the Mayan Forest of the Yucatan Peninsula by modeling occupancy as a function of land cover type, distance to roads, and sex. Nested models were fitted to high-spatiotemporal resolution satellite (GPS) telemetry, controlled for temporal autocorrelation, and eliminated selection bias of pseudo-absences using a semi-non-parametric bootstrap. Although both male and female jaguars prefer tall forest, short forest was also preferred by females but avoided by males. Whereas females significantly avoided roads, males didn’t and ventured into low-intensity cattle ranching and agriculture. Females’ preference for intact forests and against roads led to their habitat being fragmented to a greater degree than that of males. Models that ignored sexual differences failed to capture the effect of roads and agriculture on jaguar habitat use, blurred the distinction of use between short and tall forest, and underestimated fragmentation of female jaguar habitat; but incorporating these differences increased precision of habitat maps and allowed the identification of potential jaguar-human conflict areas associated with male’s use of cattle and agricultural lands. Specifying sex differences increases the power of habitat models to understand landscape occupancy by large carnivores, and so greater attention should be paid to these differences in their modeling and conservation.     

橘小实蝇雄性不育技术应用过程中混入雌虫活力的研究

取羽化前1、2和3d(即-1d、-2d和-3d)来自橘小实蝇遗传性别品系的雌蛹,分别经过90、100和105Gy的60Co辐照后,检测成虫的羽化率、飞行能力和耐压存活率;辐照处理的雌蛹羽化后再分别与普通雄虫和来自遗传性别品系的不育雄虫杂交,在羽化后的第10天、第17天分别采卵,记录产卵量和卵孵化率。结果表明,雌虫羽化率、飞行能力和耐压存活率等变化与雄虫接受辐照后的质量监测结果相同;经过辐照的雌、雄虫相互交配不产卵;辐照处理过的雌虫与普通雄虫交配,成虫的产卵量明显减少,而且剂量越大,蛹龄越小,产卵量越少。     

Effects of immunocontraception on a suburban population of white-tailed deer Odocoileus virginianus

Abundant populations of white-tailed deer (Odocoileus virginianus) in North America have altered the structure of some forest communities and caused serious conflicts with farmers, gardeners, and motorists, encouraging the search for novel techniques to control populations of deer and other wildlife. We administered the porcine zona pellucida (PZP) immunocontraceptive vaccine to female white-tailed deer living on the 233-ha campus of the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, USA. Although some tested PZP preparations proved more effective than others, the number of fawns produced per female was significantly lower in treated than untreated females. Following the onset of contraceptive treatments, the population declined by an average of 7.9% per year, and population declines were larger following years when a higher proportion of females was treated. High mortality due largely to deer-vehicle collisions and low population fertility associated with high deer densities facilitated the observed population decline.     

An Integrated Population Model From Constant Effort Bird-Ringing Data

Data from annual bird-ringing programs, in which catch effort is standardized, are routinely used to index abundance, productivity, and adult survival. Efficient models have been developed for each. Such monitoring schemes, based on ringing across a number of sites, are perhaps unique in providing this combination of demographic information and make the data particularly amenable to an integrated approach to population modeling. We develop a Bayesian approach and a deterministic population model uniting abundance, productivity, and survival. The method is applied to sedge warbler Acrocephalus schoenobaenus data from the British Trust for Ornithology’s Constant Effort Sites scheme. The possibility of “transient” birds needs to be incorporated within this analysis. We demonstrate how current methodology can efficiently be extended to use additional data from multiple within year recaptures when controlling for transience. Supplemental materials for this article are available online.     

Modelling the effects of persecution on the population dynamics of golden eagles in Scotland

We used observations of the age structure and breeding productivity of the Scottish population of golden eagles Aquila chrysaetos together with the classic theory of population dynamics to derive current `unmanipulated' estimates of life history parameters. We then used regional differences in age structure associated with differences in persecution intensity to derive estimates of prospective `persecution-free' life history parameters. The different parameter combinations were entered into a population model to simulate their effects on the number of occupied territories over time. Most simulations suggested that with unmanipulated demographic parameters the population should decline. The disparity between these predictions and the observed apparent stability in occupied territories was ascribed to the buffering effect of a lowering in age of breeding in areas where persecution is most intense and that more favourable parameter estimates within the estimated limits may be more realistic. The results indicated, nevertheless, that currently the population is vulnerable to decline as also suggested by the apparent lack of adults to occupy vacant territories. In the absence of the estimated 3-5% annual adult mortality through persecution, modelling suggested the population would increase. Removing estimated effects of persecution on reproductive rate and preadult survival were on their own insufficient to reverse the declines predicted from unmanipulated parameters, although the effect of persecution on preadult survival may be more severe than we estimated. In the absence of persecution we conclude that the population could expand to fill currently vacant but apparently suitable habitat and have a more secure long-term status.     

Protecting more than the wetland: The importance of biased sex ratios and habitat segregation for conservation of the Hine’s emerald dragonfly, Somatochlora hineana Williamson

Within species habitat use may depend on age, season or sex of an individual. The distribution of males and females may vary both temporally and spatially due to differences in the costs of reproduction and the distribution of critical resources. Conservation of a species requires knowledge of the habitat use of both sexes in order to predict the population size and protect all habitats that a species requires. Adult dragonfly populations often have highly male-biased sex ratios at the breeding habitat. This bias has been attributed to females using alternative habitats to avoid male harassment, or to high female mortality. We monitored adult Hine’s emerald dragonfly (Somatochlora hineana Williamson) populations, in breeding and non-breeding habitats in Door County, Wisconsin and found significant differences in habitat use between males and females. Males primarily used wetland habitats, while females primarily used dry meadows and marginal breeding habitats, only coming into wetlands to lay-eggs or find mates. We assessed food resources in the different habitats and found that high quality insect prey (primarily adult Diptera) were more available in the wetland habitat, indicating that these areas were likely a more productive foraging area for adult dragonflies. The fact that females appear to avoid the wetland habitat is consistent with the hypothesis that male harassment alters female distribution patterns. Consideration of the patterns of habitat use by S. hineana indicates the need to develop a broader understanding of the importance of non-wetland areas in the conservation of wetland species.     

Effects of sika deer on vegetation in Japan: A review

The Japanese sika deer Cervus nippon has expanded its range by nearly 70% during the last two decades. Browsing by sika deer affects vegetation in both agricultural and forested habitats. Effects of sika deer on vegetation are conspicuous on deer-inhabited islands: forest structure and composition are altered by deer grazing and browsing, and consequently regeneration is prevented. By felling of old trees, forest gaps are formed, but since sapling recruitment is prevented, shade intolerant plants invade. Unpalatable forbs like ragwort Senecio cannabifolius and ferns like bracken Pteridium aquilinum (Dennstaedtiaceae) become dominants in open habitats. At the places of highest deer density, the Zoysia japonica community, a low growing grass mat, develops. Sika deer function as a seed dispersal agent of this grass. Indirect effects of sika deer are not well studied, but some studies have shown reduction of understory bamboo cover, which in turn improves the survival of tree seedlings and declines of wood mice Apodemus spp. Japanese forests in lower mountainous areas were widely logged during the 1940s and 1950s. These areas were not well planted during the war and until 1950, but thereafter intensively planted to alter to conifer plantation as a nationwide campaign. For several decades after the war, rodents and hares grazed planted trees. According to growth of the planted trees to form canopy, which is unfavorable for rodents and hares, their damage declined. After the 1960s, old-growth forests in high mountainous areas were logged, and conifers were planted. Animals causing forestry damage were replaced by sika deer during the 1980s. Sika deer eat a wide variety of foods, and are gregarious, which causes heavy impacts on vegetation. Effects of sika deer are expanding to natural forests, alpine vegetation, and marshes. To reduce damages on forestry and natural vegetation, as many as 100,000 sika deer are culled every year. However, the hunter population is rapidly declining, and it is expected population control by culling will be insufficient. Although sika deer are an important component of Japanese forests, current population densities exceed the capacity of many ecosystems to tolerate herbivory.     

Sex differences in population genetics, home range size and habitat use of the parti-colored bat (Vespertilio murinus, Linnaeus 1758) in Switzerland and their consequences for conservation

When habitats are declining, niche segregation by demographic groups, such as the two sexes, can have a profound impact on the extinction risk of a species as a whole. Thus, differences in the requirements of demographic groups are of importance in conservation. We combined behavioural and genetic data to investigate whether the sexually segregated parti-colored bat (Vespertilio murinus) exhibits sex-specific niche partitioning. We use our data to evaluate implications for conservation of this potentially vulnerable species in Switzerland, the western boundary of its range. Using radio-telemetry, we found sex-specific differences in habitat use. Foraging females strongly relied on lakes while foraging males displayed more flexibility in their habitat use. Moreover, males covered significantly larger foraging areas than females. Sequencing 341 base pairs of the mitochondrial D-loop of 247 individuals revealed sex-specific differences in the genetic structure of colonies, but no such difference was observed for three nuclear micro-satellite markers. We found high mtDNA diversity in two Swiss male colonies and one German female colony, but low mtDNA diversity in two Swiss female colonies. Our genetic data suggest that considerable gene flow occurs via male dispersal and mating. At the same time immigration of females into the existing female colonies in Switzerland is rare compared to the immigration of new males into male colonies. Since we found the sexes in Vespertilio murinus to differ markedly in their ecology, population genetics, and behaviour, we conclude that sex-specific conservation plans are required to protect this species efficiently.     

Assessing the sustainability of brocket deer hunting in the Tamshiyacu-Tahuayo Communal Reserve, northeastern Peru

Since the 1800s, brocket deer have been an important source of meat and income for subsistence and professional hunters in the Peruvian Amazon. Today, local people continue to hunt brocket deer for subsistence meat and for sale in local meat markets. Although brocket deer are not hunted as frequently as peccaries, they make a significant contribution to rural household economies. This study assessed the sustainability of hunting of brocket deer by local communities in the Tamshiyacu Tahuayo Communal Reserve (TTCR), northeastern Peru. We analyzed data from 1991 to 1999 using density comparisons, hunting pressures, an age structure model, and a harvest model comparing results between heavily hunted, slightly hunted, and non-hunted sites. The four approaches agreed that brocket deer are harvested sustainably. The sustainability of brocket deer hunting will depend on the continued presence of other valuable wildlife species (e.g. peccaries and large rodents), which are more preferred due to their ease of hunting and higher rates of encounters. Gross productivity indicates that brocket deer are showing resilience in the form of density dependent reproductive adjustments in the TTCR, but they may still be vulnerable to overhunting. Consequently, current levels of harvesting may be continued until further ecological and biological information on the species' population trends assist in defining more reliable sustainable offtake levels.     

A unified capture-recapture framework

This article develops a hierarchical framework for capture-recapture data that separates the capture process from the demographic processes of interest, such as birth and survival. This allows users to parameterize in terms of meaningful demographic parameters. The framework is very flexible with many of the current capture-recapture models included as special cases. The hierarchical nature of the model allows natural expression of relationships, both between parameters and between parameters and the realization of random variables, such as population size. Previously, many of these relationships, such as density dependence have been unable to be explored using capture-recapture data. Density dependence, where survival and birth rates depend on the population size, is an interesting special case. We fit a density-dependent model to male Gonodontis bidentata data and report evidence of negative density dependence in percapita birth rates and weak evidence of negative density dependence in survival.     

Genetic Introgression and the Survival of Florida Panther Kittens

Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982-2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0-1 year). Overall, annual survival of Florida panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F₁ admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.     

~(60)Coγ射线对印度谷螟的辐射遗传效应

用~(60)Coγ射线1、3、5、7、10 krad辐照4～5日龄的印度谷螟雄蛹,当辐照剂量为1～7krad时,被辐照蛹都能羽化,但10krad辐照的,羽化率仅40％。用1、3 krad辐照,成虫畸形率低,且对雄成虫交配能力影响较小,但用7、10 krad辐照,成虫畸形率分别为60％、100％,只有30％～50％的成虫能进行交配。1、3、5 Krad辐照雄蛹,F_1代卵孵化率分别比对照降低25.5％、21.1％、39.4％,F_2代卵的孵化率分别比对照降低56.6％、80.8％、74.0％。这可能是遗传不育现象。1、5、7 krad辐照的,诱导出了成虫翅透明的突变品系(透明型)。该突变品系对研究印度谷螟的部分遗传学及遗传防治有重要意义。     

西花蓟马孤雌产雄生殖繁育的后代种群生命表的建立

孤雌生殖是西花蓟马(Frankliniella occidentalis)繁殖的一种重要方式。前期研究发现,西花蓟马在高温下,雌性的存活率远大于雄性。为探究高温处理后仅有雌性西花蓟马孤雌产雄的情况下其后代建立种群的可能性,试验设定:高温(45℃,2 h)处理西花蓟马单个雌性个体,分别进行孤雌产雄生殖后,雄性子代(F1代)与其母系回交产生F2代;高温(45℃,2 h)处理西花蓟马多个雌性个体,进行孤雌产雄生殖后,雄性子代(F1代)与亲代多个雌性个体共存情况下进行交配产生F2代。两组处理模式下建立F2代实验种群生命表。结果表明,上述两种处理模式,母代雌性个体与子代雄性个体交配后均可产生后代,雄性F1代与其母系回交产生的F2代的雌雄性比为1.05∶1;与亲代多个雌性个体共存下交配产生的F2代性比为1.55∶1。雄性F1代与其母系回交产生的F2代的平均单雌产卵量(F)和内禀增长率(rm)显著小于与亲代多个雌性个体共存下交配产生的F2代(P0.05);各龄期的平均发育历期、平均产卵前期和平均总产卵前期2个繁殖力参数以及净生殖率(R0)、平均世代周期(T)2个种群参数,前者则比后者长(P0.05);另周限增长率(λ)两者之间无显著差异。研究表明西花蓟马在孤雌产雄状态下仍然可以在短期建立种群,具有较强的抗高温能力和繁殖能力,为其成功入侵奠定了生态学基础。     

Mark-recapture with occasion and individual effects: Abundance estimation through Bayesian model selection in a fixed dimensional parameter space

We present a Bayesian mark-recapture method for explicitly communicating uncertainty about the size of a closed population where capture probabilities vary across both individuals and sampling occasions. Heterogeneity is modeled hierarchically using a continuous logistic-Normal model to specify the capture probabilities for both individuals that are captured on at least one occasion and individuals that are never captured and so remain undetected. Inference about how many undetected individuals to include in the model is accomplished through a Bayesian model selection procedure using MCMC, applied to a product space of possible models for different numbers of undetected individuals. Setting the estimation problem in a fixed dimensional parameter space enables the model selection procedure to be performed using the freely available WinBUGS software. The outcome of inference is a full “posterior” probability distribution for the population size parameter. We demonstrate this method through an example involving real mark-recapture data.     

Contrasting measures of fitness to classify habitat quality for the black-throated sparrow (Amphispiza bilineata)

Habitat quality is an important consideration when identifying source and sink habitat and setting priority areas for avian conservation. The problem is that different measures may lead to different conclusions about habitat quality, and may also vary in the resources required to estimate them. Individual level measures, such as nest success, and fecundity, will often identify different high quality habitats than population level measures, such as abundance or the number of fledglings produced per unit area. We tested measures of fitness in the Black-throated Sparrow both at the individual and at the population level for six habitats in the northern Chihuahuan Desert, to explore their value as indicators of habitat quality. We compared clutch size, number of nestlings per nest, number of fledglings per successful nest, nest density, nest success, daily nest survival rate, season-long fecundity, number of fledglings produced per 100 ha, and adult abundance, in each habitat type. We also modeled source-sink dynamics to estimate the scale at which they operate, to infer survival rates, and to ascertain the relative source potential of each habitat. We found that fecundity is the best indicator of individual level habitat quality but a poor indicator of population level habitat quality. Nest success (or fecundity, if resources are available to adequately estimate it) plus nest density provide the most robust indicator of population level habitat quality, which is the level at which priority habitats for conservation should be identified. Mesa grassland and black grama grassland functioned as source habitats most consistently, and mesquite was consistently a sink but also probably a reservoir of individuals available to occupy other habitats.     

Predicting Life-History Traits for Female New Zealand Sea Lions, <Emphasis Type="Italic">Phocarctos hookeri</Emphasis>: Integrating Short-Term Mark-Recapture Data and Population Modeling

The trade-off between survival and reproduction by individuals is central to understanding life-history parameters of a species. Few mammal species have life-history information from long-term research. Instead, demographic models are commonly utilized to investigate an individual’s life-history strategy, species dynamics, and population trends. This research investigates age-related survival and reproductive performance of adult female New Zealand (NZ) sea lions (Phocarctos hookeri), using multi-state mark-recapture data from known-age branded individuals over five years. The mark-recapture analysis was integrated with a population model to predict the lifetime reproductive output of female NZ sea lions. The integration of an analysis of short-term datasets with population modeling allows for the prediction of life-history parameters of long lived animals when long-term information is not available. While such approaches involve some caveats, it provides a framework for investigating population dynamics and is preferential to unsubstantiated assumptions. This technique can lead to better design and implementation of conservation management for long lived species.     

Vital rate sensitivity analysis as a tool for assessing management actions for the desert tortoise

Sensitivity analyses of population growth in desert tortoise (Gopherus agassizii) have shown no consensus on the limiting vital rate. More importantly, the most sensitive vital rate might not be the most readily manipulated by management, so it begs the question of what actions would be most effective. We compared 13 management alternatives using a vital rate sensitivity analysis that is valid regardless of age structure, and is sensitive to initial population size and time frame, to determine the efforts required for equivalent population growth. We evaluated three time frames, each with five initial population sizes and three initial age distributions. To achieve equivalent population growth, mortality of older females needed to be reduced less than did mortality of other age classes. Similarly, fewer adults needed to be introduced to a population to have the same effect as releasing juveniles, but differences among adult age classes were trivial. A single release (headstarting) required fewer total individuals than did annual releases to achieve the same population growth. Also, the same population growth was more easily achieved when the initial age structure was deficient of young animals. Interestingly, because small tortoises are difficult to survey, some management alternatives could result in increased population size but decreased numbers of countable individuals over short to intermediate (25 years) time frames. Our paper demonstrates an approach to determine what constitutes equivalent management actions for population growth, thus allowing managers to more directly compare expected gains toward population recovery achieved by their resource-allocation decisions.