Estimating historic movement of a climatological variable from a pair of misaligned functional data sets

Environmental and Ecological Statistics - We consider the problem of estimating the mean function from a pair of paleoclimatic functional data sets after one of them has been registered with the...     

Estimating age-specific hazards from wildlife telemetry data

We illustrate 2 techniques for estimating age-specific hazards with wildlife telemetry data: Siler’s (Ecology 60:750–757, 1979) competing risk model fit using maximum likelihood and a penalized likelihood estimate that only assumes the hazard varies smoothly with age. In most telemetry studies, animals enter at different points in time (and at different ages), leading to data that are left-truncated. In addition, death times may only be known to occur within an interval of time (interval-censoring). Observations may also be right-censored (e.g., due to the end of the study, radio-collar failure, or emigration from the study area). It is important to consider the observation process, since the contribution of each individual’s data to the likelihood will depend on whether data are left-truncated or censored. We estimate age-specific hazards using telemetry data collected in two Phases during a 13-year study of white-tailed deer (Odocoileus virginianus) in northern Minnesota. The hazards estimated from the two methods were similar for the full data set that included 302 adults and 76 neonates (followed since or shortly after birth). However, estimated hazards for early-aged individuals differed considerably for subsets of the data that did not include neonates. We discuss the advantages and disadvantages of these two modeling approaches and also compare the estimators using a short simulation study.     

Density dependence and density independence during the early life stages of four marine fish stocks

Recruitment variability caused by density-dependent and density-independent processes is an important area within the study of fish dynamics. These processes can exhibit nonlinearities and nonadditive properties that may have profound dynamic effects. We investigate the importance of population density (i.e., density dependence) and environmental forcing (i.e., density independence) on the age-0 and age-1 abundance of capelin (Mallotus villosus), northeast Arctic cod (Gadus morhua), northeast Arctic haddock (Melanogrammus aeglefinus), and Norwegian spring spawning herring (Clupea harengus) in the Barents Sea. We use statistical methods that explicitly account for nonlinearities and nonadditive interactions between internal and external variables in the abundance of these two pre-recruitment stages. Our results indicate that, during their first five months of life, cod, haddock, and herring experience higher density-dependent survival than capelin. The abundance of age-0 cod depends on the mean age and biomass of the spawning stock, a result which has implications for the management of the entire cod stock. Temperature is another important factor influencing the abundance at age-0 and age-1 of all four species, except herring at age-1. Between age-0 and age-1, there is an attenuation of density-dependent survival for cod and herring, while haddock and capelin experience density dependence at high and low temperatures, respectively. Predation by subadult cod is important for both capelin and cod at age-1. We found strong indications for interactions among the studied species, pointing to the importance of viewing the problem of species recruitment variability as a community, rather than as a population phenomenon.     

Nymphal density, behavioral development, and life history in a field cricket

Population density regulates the strength of intraspecific competition and may thereby be reflected in life-history variables, such as development time, growth rate, or investment in immune defense. However, population density may also affect the fitness payoffs of different behaviors and consequently shape the development of personality. Here we studied if population density during nymphal development (one, four, or ten individuals raised together) affects the level of boldness, measured as the latency time to recover from freezing and emerge from a shelter, aggressiveness towards conspecifics or their correlation at the adult stage in the field crickets, Gryllus integer. In addition, we tested if individuals invest more resources in immune function or speed up their development in response to a high conspecifics density during ontogeny. Nymphal density did not affect adult boldness or aggressiveness towards conspecific males per se, but these variables showed a negative association, i.e., indicated an unconventional behavioral syndrome in the highest density treatment. Supporting the effectiveness of density treatments in inducing plastic responses, individuals reached maturity sooner and invested more resources in immune function in the highest nymphal density group compared to groups consisting of one or four individuals. Our results suggest that population density may play an important role in shaping both the realized life history and development of behavioral syndromes.     

Estimating equations for separable spatial-temporal binary data

For binary data with correlation across space and over time, the literature concerning the estimation of fixed effects in marginal models is limited. In this paper, we model the marginal probability of binary responses in terms of parameters of interest by a logistic function. An estimating equation based on the quasi-likelihood concept is developed to estimate parameters. Under separable correlation models, we show that the quasi-likelihood estimate is asymptotically optimal. A series of simulations is conducted to evaluate how the efficiency varies with the regression coefficients. We also compare the relative efficiency with another estimating equation by simulations. The proposed method is applied to an ecological study of forest decline to test independence of two spatial-temporal binary outcomes.     

The morphology,anatomy and life history of a complanate form of Scytosiphon lomentaria (Scytosiphonales,Phaeophyta) from southern Australia

Complanate Scytosiphon lomentaria (Lyngbye) J. Agardh is characterised and distinguished from the typical cylindrical form by a flattened thallus, plurilocular sporangia having a mucilaginous covering layer, and an autumn-spring seasonal growth pattern. Cultural studies show that zooids from the plurilocular sporangia give rise to an independent ralfsioid stage, to ralfsioid plethysmothalli bearing complanate fronds, and to a cylindrical form of S. lomentaria. In culture, the complanate thalli are initiated only in short-day conditions, cylindrical thalli are initiated in both short- and long-day conditions. Ralfsioid thalli are of two kinds: one developing independently of day length, the other developing only during long days; the alternative short-day thallus form is complanate.     

Estimating age from recapture data: integrating incremental growth measures with ancillary data to infer age-at-length

Estimating the age of individuals in wild populations can be of fundamental importance for answering ecological questions, modeling population demographics, and managing exploited or threatened species. Significant effort has been devoted to determining age through the use of growth annuli, secondary physical characteristics related to age, and growth models. Many species, however, either do not exhibit physical characteristics useful for independent age validation or are too rare to justify sacrificing a large number of individuals to establish the relationship between size and age. Length-at-age models are well represented in the fisheries and other wildlife management literature. Many of these models overlook variation in growth rates of individuals and consider growth parameters as population parameters. More recent models have taken advantage of hierarchical structuring of parameters and Bayesian inference methods to allow for variation among individuals as functions of environmental covariates or individual-specific random effects. Here, we describe hierarchical models in which growth curves vary as individual-specific stochastic processes, and we show how these models can be fit using capture-recapture data for animals of unknown age along with data for animals of known age. We combine these independent data sources in a Bayesian analysis, distinguishing natural variation (among and within individuals) from measurement error. We illustrate using data for African dwarf crocodiles, comparing von Bertalanffy and logistic growth models. The analysis provides the means of predicting crocodile age, given a single measurement of head length. The von Bertalanffy was much better supported than the logistic growth model and predicted that dwarf crocodiles grow from 19.4 cm total length at birth to 32.9 cm in the first year and 45.3 cm by the end of their second year. Based on the minimum size of females observed with hatchlings, reproductive maturity was estimated to be at nine years. These size benchmarks are believed to represent thresholds for important demographic parameters; improved estimates of age, therefore, will increase the precision of population projection models. The modeling approach that we present can be applied to other species and offers significant advantages when multiple sources of data are available and traditional aging techniques are not practical.     

Host-parasitoid dynamics: Effects of the position of density dependence

Four models are presented, two of which have density-dependent regulation in the hosts and two in the parasitoids. Host and parasitoid equilibria are both less with density-dependent regulation in the hosts than in the parasitoids. The percent of hosts parasitized at equilibrium is also less with density dependence in the hosts than in the parasitoids. These results are compared with those from other models.     

Phenotypic variation in shell form in the intertidal acorn barnacle Chthamalus montagui: distribution,response to predators and life history trade-offs

The acorn barnacle Chthamalus montagui can present strong variation in shell morphology, ranging from flat conic to a highly bent form, caused by a substantial overgrowth of the rostrum plate. Shell shape distribution was investigated between January and May 2004 from geographical to microhabitat spatial scales along the western coast of Britain. Populations studied in the north (Scotland and Isle of Man) showed a higher degree of shell variation compared to those in the south (Wales and south-west England). In the north, C. montagui living at lower tidal levels and in proximity to the predatory dogwhelk, Nucella lapillus, were more bent in profile. Laboratory experiments were conducted to examine behavioural responses, and vulnerability of bent and conic barnacles to predation by N. lapillus. Dogwhelks did not attack one morphotype more than the other, but only 15 % of attacks on bent forms were successful compared to 75 % in conic forms. Dogwhelk effluent reduced the time spent feeding by C. montagui (11 %), but there was no significant difference between conic and bent forms. Examination of barnacle morphology indicated a trade-off in investment in shell structure and feeding appendages associated with being bent, but none with egg or somatic tissue mass. These results are consistent with C. montagui showing an induced defence comparable to that found in its congeners Chthamalus anisopoma and Chthamalus fissus on the Pacific coast of North America, but further work to demonstrate inducibility is required.     

Isomorphic chain graphs for modeling spatial dependence in ecological data

Graphical models (alternatively, Bayesian belief networks, path analysis models) are increasingly used for modeling complex ecological systems (e.g., Lee, In: Ferson S, Burgman M(eds) Quantative methods for conservation biology. Springer, Berlin Heilin Heideslperk New York, pp.127–147, 2000; Borsuk et al., J Water Res Plann Manage 129:271–282, 2003). Their implementation in this context leverages their utility in modeling interrelationships in multivariate systems, and in a Bayesian implementation, their intuitive appeal of yielding easily interpretable posterior probability estimates. However, methods for incorporating correlational structure to account for observations collected through time and/or space—features of most ecological data—have not been widely studied; Haas et al. (AI Appl 8:15–27, 1994) is one exception. In this paper, an “isomorphic” chain graph (ICG) model is introduced to account for correlation between samples by linking site-specific Bayes network models. Several results show that the ICG preserves many of the Markov properties (conditional and marginal dependencies) of the site-specific models. The ICG model is compared with a model that does not account for spatial correlation. Data from several stream networks in the Willamette River valley, Oregon (USA) are used. Significant correlation between sites within the same stream network is shown with an ICG model.     

Insights from life history theory for an explicit treatment of trade‐offs in conservation biology

As economic and social contexts become more embedded within biodiversity conservation, it becomes obvious that resources are a limiting factor in conservation. This recognition is leading conservation scientists and practitioners to increasingly frame conservation decisions as trade‐offs between conflicting societal objectives. However, this framing is all too often done in an intuitive way, rather than by addressing trade‐offs explicitly. In contrast, the concept of trade‐off is a keystone in evolutionary biology, where it has been investigated extensively. I argue that insights from evolutionary theory can provide methodological and theoretical support to evaluating and quantifying trade‐offs in biodiversity conservation. I reviewed the diverse ways in which trade‐offs have emerged within the context of conservation and how advances from evolutionary theory can help avoid the main pitfalls of an implicit approach. When studying both evolutionary trade‐offs (e.g., reproduction vs. survival) and conservation trade‐offs (e.g., biodiversity conservation vs. agriculture), it is crucial to correctly identify the limiting resource, hold constant the amount of this resource when comparing different scenarios, and choose appropriate metrics to quantify the extent to which the objectives have been achieved. Insights from studies in evolutionary theory also reveal how an inadequate selection of conservation solutions may result from considering suboptimal rather than optional solutions when examining whether a trade‐off exits between 2 objectives. Furthermore, the shape of a trade‐off curve (i.e., whether the relationship between 2 objectives follows a concave, convex, or linear form) is known to affect crucially the definition of optimal solutions in evolutionary biology and very likely affects decisions in biodiversity conservation planning too. This interface between evolutionary biology and biodiversity conservation can therefore provide methodological guidance to support decision makers in the difficult task of choosing among conservation solutions. Percepciones de la Teoría de Historia de Vida para una Tratamiento Explícito de las Compensaciones en la Biología de la Conservación     

Estimating the extinction date of the thylacine with mixed certainty data

The thylacine (Thylacinus cynocephalus), one of Australia's most characteristic megafauna, was the largest marsupial carnivore until hunting, and potentially disease, drove it to extinction in 1936. Although thylacines were restricted to Tasmania for 2 millennia prior to their extinction, recent so‐called plausible sightings on the Cape York Peninsula in northern Queensland have emerged, leading some to speculate the species may have persisted undetected. We compiled a data set that included physical evidence, expert‐validated sightings, and unconfirmed sightings up to the present day and implemented a range of extinction models (focusing on a Bayesian approach that incorporates all 3 types of data by modeling valid and invalid sightings as independent processes) to evaluate the likelihood of the thylacine's persistence. Although the last captive individual died in September 1936, our results suggested that the most likely extinction date would be 1940. Our other extinction models estimated the thylacine's extinction date between 1936 and 1943, and the most optimistic scenario indicated that the species did not persist beyond 1956. The search for the thylacine, much like similar efforts to rediscover other recently extinct charismatic taxa, is likely to be fruitless, especially given that persistence on Tasmania would have been no guarantee the species could reappear in regions that had been unoccupied for millennia. The search for the thylacine may become a rallying point for conservation and wildlife biology and could indirectly help fund and support critical research in understudied areas such as Cape York. However, our results suggest that attempts to rediscover the thylacine will be unsuccessful and that the continued survival of the thylacine is entirely implausible based on most current mathematical theories of extinction.     

Estimating wildfire growth from noisy and incomplete incident data using a state space model

Wildfire behaviors are complex and are of interest to fire managers and scientists for a variety of reasons. Many of these important behaviors are directly measured from the cumulative burn area time series of individual wildfires; however, estimating cumulative burn area time series is challenging due to the magnitude of measurement errors and missing entries. To resolve this, we introduce two state space models for reconstructing wildfire burn area using repeated observations from multiple data sources that include different levels of measurement error and temporal gaps. The constant growth parameter model uses a few parameters and assumes a burn area time series that follows a logistic growth curve. The non-constant growth parameter model uses a time-varying logistic growth curve to produce detailed estimates of the burn area time series that permit sudden pauses and pulses of growth. We apply both reconstruction models to burn area data from 13 large wildfire incidents to compare the quality of the burn area time series reconstructions and computational requirements. The constant growth parameter model reconstructs burn area time series with minimal computational requirements, but inadequately fits observed data in most cases. The non-constant growth parameter model better describes burn area time series, but can also be highly computationally demanding. Sensitivity analyses suggest that in a typical application, the reconstructed cumulative burn area time series is fairly robust to minor changes in the prior distributions.     

Implications of dispersal and life history strategies for the persistence of Linyphiid spider populations

Linyphiid spiders have evolved the ability to disperse long distances by a process known as ballooning. It has been hypothesized that ballooning may allow populations to persist in the highly disturbed agricultural areas that the spiders prefer. In this study, I develop a stochastic population model to explore how the propensity for this type of long distance dispersal influences long term population persistence in a heterogeneous landscape where catastrophic mortality events are common. Analysis of this model indicates that although some dispersal does indeed decrease the probability of extinction of the population, the frequency of dispersal is only important in certain extremes. Instead, both the mean population birth and death rates, and the landscape composition, are much more important in determining the probability of extinction than the dispersal process. Thus, in order to develop effective conservation strategies for these spiders, better understanding of life history processes should be prioritized over an understanding of dispersal strategies.     

Observations on the life history of the blue-ringed octopus Hapalochlaena maculosa

The life-history of the blue-ringed octopus Hapalochlaena maculosa (Hoyle) was observed in laboratory aquaria. Eggs from a brooding female were bred through to the next generation. The life cycle lasts approximately 7 months–4 months from hatching to maturity, 1 month from copulation to egg-laying, and an estimated 2 months for embryonic development. This venomous octopus has several unique and interesting habits. Eggs are not attached to a substratum but are carried by the mother throughout their embryonic life. She assumes a brooding posture for the greater part of the time and cradles the eggs between her raised skirt and body. However, she can move froely with her clutch of eggs, conveying them individually or in clusters along her arms from one sucker to the next as occasion demands. Embryos reverse position within their capsules 1 week prior to hatching, and hatch at the distal end of the capsule, mantle-first. Development is direct; there is no planktonic stage. The young immediately assume a benthic habit and, within a few hours, consume the remnant of the yolk-sac which they carry with them from the egg. Juveniles begin to feed on pieces of crab within a week of hatching, and to kill and eat live crabs within a month. They pierce the carapace of their prey at the abdominal articulation and with the aid, apparently, of venom from their posterior salivary glands suck out the partially pre-digested tissues. The ink gland is relatively small in size and is mainly used between the second and the fourth week of juvenile life. Chromatophores begin to function during embryonic life. After hatching there is a progressive change in coloration, and the iridescent blue rings which characterize the species appear at the age of about 6 weeks. Mating is a more active process than has been recorded for other octopuses. The male mounts the female and clasps her securely. After a short struggle the female becomes quite passive, almost inert. Copulation lasts about one hour. The unusual life-history of H. maculosa suggests that it is a highly evolved octopus species. Its direct development, simple diet, and rapid rate of growth make the animal relatively easy to cultivate for experimental or pharmacological purposes.     

Strength of evidence for density dependence in abundance time series of 1198 species

Population limitation is a fundamental tenet of ecology, but the relative roles of exogenous and endogenous mechanisms remain unquantified for most species. Here we used multi-model inference (MMI), a form of model averaging, based on information theory (Akaike's Information Criterion) to evaluate the relative strength of evidence for density-dependent and density-independent population dynamical models in long-term abundance time series of 1198 species. We also compared the MMI results to more classic methods for detecting density dependence: Neyman-Pearson hypothesis-testing and best-model selection using the Bayesian Information Criterion or cross-validation. Using MMI on our large database, we show that density dependence is a pervasive feature of population dynamics (median MMI support for density dependence = 74.7-92.2%), and that this holds across widely different taxa. The weight of evidence for density dependence varied among species but increased consistently, with the number of generations monitored. Best-model selection methods yielded similar results to MMI (a density-dependent model was favored in 66.2-93.9% of species time series), while the hypothesis-testing methods detected density dependence less frequently (32.6-49.8%). There were no obvious differences in the prevalence of density dependence across major taxonomic groups under any of the statistical methods used. These results underscore the value of using multiple modes of analysis to quantify the relative empirical support for a set of working hypotheses that encompass a range of realistic population dynamical behaviors.     

Effect of intraspecific density on life history traits and population growth rate of Neanthes arenaceodentata (Polychaeta: Nereidae) in the laboratory

The effects of intraspecific density on life history traits and population dynamics of the nereid polychaete Neanthes arenaceodentata Moore were assessed in a laboratory experiment. Survival, growth, and fecundity were measured for one generation of worms at densities of 40, 80 and 160 worms per 840 cm² (1x, 2x, and 4x treatments, respectively). Density did not affect size (prior to pairing), percentage of worms paired, time to pairing, or size of mature paired males. Density did have a significant negative effect on survival, size of mature paired females, time to spawning, percentage of females that reproduced, and number of eggs per reproducing female. As density increased, mean survival was 90.0, 80.8 and 74.0%; mean size of mature females was 52.2, 49.2 and 48.1 segments; mean time to spawning was 100.6, 102.4 and 109.4 d; and mean fecundity was 881, 622, and 598 eggs per female, for 1x, 2x and 4x treatments, respectively. Increased density reduced the potential population growth rate, ; for a given rate of larval survivorship, was lower in the 2x and 4x treatments than the 1x treatment. Analysis of sensitivity of to changes in survivorship indicated that population growth rate at the highest density was sensitive to both changes in larval survivorship and the probability of producing a successful brood, although at low densities, was sensitive only to changes in larval survivorship. We attribute these density effects to aggressive bahavioral interactions between the worms, primarily the adults. This experiment identifies key life history traits that could be measured in future experiments to test population level responses of N. arenaceodentata populations to pollutants, both in the laboratory and in the field.Contribution No. 820 of the U.S. Environmental Protection Agency, Environmental Research Laboratory and Contribution No. 189 of the Marine Sciences Institute, University of Connecticut     

Stingray life history trade-offs associated with nursery habitat use inferred from a bioenergetics model

Consumption rates of marine predators are vital to assessing their trophic impacts and potential consequences of fisheries removal and habitat alteration, yet are rarely estimated. Standard metabolic rates were estimated for juvenile brown stingrays, Dasyatis lata, and used as input parameters for a bioenergetics model to predict consumption rates. Temperature and mass had significant effects on metabolic rates. The energy budget of juvenile brown stingrays was heavily weighted toward metabolism, accounting for 66 % of consumed energy. Growth accounted for 7 % of the energy budget indicating very slow growth potentially due to limited food resources. Population consumption rates suggest potential for strong top-down effects on prey populations due to stingray predation. This study suggests the use of Kāne‘ohe Bay as a nursery habitat for juvenile brown stingrays is a trade-off between increased juvenile survival through predator avoidance and a late age at first maturity due to slow growth rates resulting from low prey availability.     

Evidence for life history changes in high-altitude populations of three perennial forbs

Relatively little is known about how the life histories of perennial forb species, and especially their lifetime patterns of growth, vary across environmental gradients. We used a post hoc approach (herb-chronology) to determine plant age and previous growth (width of successive annual rings in roots) in three species of perennial forb (two long-lived species [Penstemon venustus, Lupinus laxiflorus] and one short-lived [Rudbeckia occidentalis]) along a 1000-m altitudinal gradient in the Wallowa Mountains (northeast Oregon, USA). Plants from the highest altitude tended to be considerably older and produced up to five times as many flowering shoots as lowland plants. In addition, mean ring widths of high-altitude plants were about half those of lowland plants. In plants from low and intermediate altitudes, ring width either decreased linearly or varied inconsistently during the life of the plant. In contrast, ring widths of high-altitude plants increased at first and later decreased, resulting in curvilinear growth trajectories that were highly consistent among species. Together, these data for three ecologically distinct forb species provide evidence of a consistent shift toward more conservative and strongly constrained life histories at higher altitudes. More generally, the results indicate the possible importance of changes in selection pressures across strong environmental gradients on life history strategies within a single species.