Analysis of capture-recapture models with individual covariates using data augmentation

Summary .  I consider the analysis of capture–recapture models with individual covariates that influence detection probability. Bayesian analysis of the joint likelihood is carried out using a flexible data augmentation scheme that facilitates analysis by Markov chain Monte Carlo methods, and a simple and straightforward implementation in freely available software. This approach is applied to a study of meadow voles ( Microtus pennsylvanicus ) in which auxiliary data on a continuous covariate (body mass) are recorded, and it is thought that detection probability is related to body mass. In a second example, the model is applied to an aerial waterfowl survey in which a double-observer protocol is used. The fundamental unit of observation is the cluster of individual birds, and the size of the cluster (a discrete covariate) is used as a covariate on detection probability.     

Effects of UV-B radiation on ingestion, fecundity, population dynamics and antioxidant enzyme activities of Schmackeria inopinus (Copepoda Calanoida)

Effects of enhanced ultraviolet B (UV-B, 280-320 nm) on copepods have gained particular attention in recent years. In this study, we investigated the effects of UV-B radiation on ingestion, fecundity, population dynamics and antioxidant enzyme activities of copepod Schmackeria inopinus exposed to varying doses of UV-B irradiance. Artificial UV-B radiation resulted in an increased mortality of nauplii, copepodites and adults with increasing UV-B doses. Nauplii and copepodites were more sensitive to UV-B radiation than adults, and adult males had a higher UV-B radiation susceptivity in comparison with adult females. Both ingestion rates and proportion of gravid females decreased with the increase of UV-B doses; and at the same time, we also observed that adult females had higher ingestion rates as compared with adult males. In comparison with the control, the abundance of the treatment significantly decreased. Antioxidant enzyme (GPx and GR) activities attained a significant increase at lower UV-B radiation doses when compared to the control, but declined at higher UV-B doses. These results suggested that enhanced UV-B radiation might change the species composition of copepods. Our study also showed that antioxidant enzymes might protect S. inopinus against UV-induced oxidative damage.     

The role of epistasis on the evolution of recombination in host-parasite coevolution

Antagonistic coevolution between hosts and parasites is known to affect selection on recombination in hosts. The Red Queen Hypothesis (RQH) posits that genetic shuffling is beneficial for hosts because it quickly creates resistant genotypes. Indeed, a large body of theoretical studies have shown that for many models of the genetic interaction between host and parasite, the coevolutionary dynamics of hosts and parasites generate selection for recombination or sexual reproduction. Here we investigate models in which the effect of the host on the parasite (and vice versa) depend approximately multiplicatively on the number of matched alleles. Contrary to expectation, these models generate a dynamical behavior that strongly selects against recombination/sex. We investigate this atypical behavior analytically and numerically. Specifically we show that two complementary equilibria are responsible for generating strong linkage disequilibria of opposite sign, which in turn causes strong selection against sex. The biological relevance of this finding stems from the fact that these phenomena can also be observed if hosts are attacked by two parasites that affect host fitness independently. Hence the role of the Red Queen Hypothesis in natural host parasite systems where infection by multiple parasites is the rule rather than the exception needs to be reevaluated.     

Density dependent growth in adult brown frogs Rana arvalis and Rana temporaria – A field experiment

In species with complex life cycles, density regulation can operate on any of the stages. In frogs there are almost no studies of density effects on the performance of adult frogs in the terrestrial habitat. We therefore studied the effect of summer density on the growth rate of adult frogs during four years. Four 30 by 30 m plots in a moist meadow were used. In early summer, when settled after post-breeding migration, frogs (Rana arvalis and Rana temporaria that have a very similar ecology and potentially compete) were enclosed by erecting a fence around the plots. Frogs were captured, measured, marked and partly relocated to create two high density and two low density plots. In early autumn the frogs were again captured and their individual summer growth determined. Growth effects were evaluated in relation to two density measures: density by design (high/low manipulation), and actual (numerical) density. R. arvalis in plots with low density by design grew faster than those in high density plots. No such effect was found for R. temporaria. For none of the species was growth related to actual summer density, determined by the Lincoln index and including the density manipulation. The result suggests that R. arvalis initially settled according to an ideal free distribution and that density had a regulatory effect (mediated through growth). The fact that there were no density effects on R. temporaria (and a significant difference in its response to that of R. arvalis) suggests it is a superior competitor to R. arvalis during the terrestrial phase. There were no density effects on frog condition index, suggesting that the growth rate modifications may actually be an adaptive trait of R. arvalis. The study demonstrates that density regulation may be dependent on resources in frogs' summer habitat.     

Carnivore population trends in Spanish agrosystems after the reduction in food availability due to rabbit decline by rabbit haemorrhagic disease and improved waste management

We conducted spotlight counts from 1992 to 2006 in 59 localities to describe carnivore presence, distribution and relative abundance in open agriculture lands in Aragon, northeastern Spain. During the study period, urban waste and carcases of domestic livestock became less available to wild animals, and rabbit (Oryctolagus cuniculus) abundance was low after rabbit haemorragic disease. We calculated a kilometric abundance index (KAI, individuals seen per 100 km surveyed) and the ratio between the number of positive localities in which a species was detected and the total of localities surveyed in a year. Indices to abundance and presence included: red fox (Vulpes vulpes), KAI per 100 km 10.70 and 100.0% localities per year; stray dog (Canis familiaris), KAI 0.48 and 22.6% localities; wildcat (Felis silvestris), KAI 0.10 and 19.1% localities; domestic cat (Felis catus), KAI 0.21 and 20.6% localities; polecat (Mustela putorius), KAI 0.02 and 2.0% localities; badger (Meles meles), KAI 0.16 and 23.6% localities; stone marten (Martes foina), KAI 0.11 and 19.6% localities; weasel (Mustela nivalis), KAI 0.002 and 0.6% localities; and genet (Genetta genetta), KAI 0.06 and 10.0% localities. Indices of badger abundance increased significantly, whereas indices of stray dogs decreased significantly over the study period. Abundance indices of red fox, the most important predator of small game, were stable throughout the study period. No significant trend was observed to other studied species. This study concludes that Aragon region maintains a diverse and rather stable carnivore community and shows that large scale data may help to identify trends of the more abundant wild and feral carnivores.     

Tracing the invasion history of mealy plum aphid, Hyalopterus pruni (Hemiptera: Aphididae), in North America: a population genetics approach

Biological invasions are typically the outcome of complex patterns of introduction, establishment, and spread, and genetic methods are excellent tools to resolve such histories for non-native organisms. The mealy plum aphid, Hyalopterus pruni, is an invasive pest of dried plum in California. We examined nine microsatellite loci and DNA sequences from three mitochondrial genes (1,148 bp) in populations throughout the native and invaded ranges of H. pruni to assess key invasion parameters, including geographic origins of invasive populations, number of introductions, and levels of genetic diversity and gene flow. Our results provide evidence for multiple invasions of H. pruni into North America, suggesting that aphids in California may have been introduced from Spain, and aphids in the eastern United States and Vancouver, Canada were likely introduced from central or northern Europe. H. pruni populations in California were characterized by low genetic diversity relative to native populations, while the two other North American populations were less genetically impoverished. Gene flow among introduced populations was low, but does appear to occur with some regularity. These findings provide a framework for more detailed studies of H. pruni, but also represent a model for how population genetics approaches can be used to study invasion biology and aid the development of optimized management methods for agricultural pests. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Population genetics of an invasive riparian species,<Emphasis Type="Italic"> Impatiens glandulifera</Emphasis>

We assess the population genetic structure of the invasive riparian weed Impatiens glandulifera, and where possible, determine whether natural or anthropogenic dispersal best explains the observed patterns. Results are compared with a similar contemporary analysis for Heracleum mantegazzianum undertaken in the same catchments, and we suggest that some of the observed differences in genetic structure could be because of life history differences between these species. Our results confirm the importance of at least occasional dispersal events mediated by human activity in the colonisation and subsequent spread of invasive plants in river catchments. However, processes related to river structure, dispersal range and genetic drift also appear to be structuring these populations over short temporal scales. The implication is that local populations can be established as small founders, and therefore eradication programs need to be thorough and undertaken at the catchment scale. Effective management needs to consider the natural spread of riparian species along rivers, but also prevent long-distance dispersal from sources outside the catchment. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Accelerated failure time (AFT) modeling for the development and survival of Russian wheat aphid, <Emphasis Type="Italic">Diuraphis noxia</Emphasis> (Mordvilko)

Accelerated failure time model (AFT) and Cox’s proportional hazards model (PHM) are considered the two most significant models in survival analysis, which has become a de facto standard for biomedical data analysis and modeling. AFT not only plays an extremely significant role in survival analysis but also finds extensive applications in engineering reliability. Survival analysis studies a special type of random variables: time-to-event (also known as failure time, lifetime or survival time) random variables. Examples of time-to-event random variables include survival times of patients in a clinical trial and failure times of machine components. Since molting and death times of insect individuals are also perfect examples of time-to-event random variables, we argue that survival analysis including AFT modeling is ideal for analyzing insect development and survival data, and further for building dynamic models of insect development and survival. Here we demonstrate such an application with data collected by observing stage-to-stage development and survival of 1,800 Russian wheat aphids (RWA), Diuraphis noxia, reared in laboratory growth chambers arranged in 25 treatments (each with 72 individuals). The main advantages of survival analysis, including the unified modeling of survival and development as well as handling of information censoring, are also discussed.     

Estimating abundance with sparse data: tigers in northern Myanmar

As part of a national strategy for recovering tiger populations, the Myanmar Government recently proposed its first and the world’s largest tiger reserve in the Hukaung Valley, Kachin State. During November 2002–June 2004, camera-traps were used to record tigers, identify individuals, and, using capture–recapture approaches, estimate density in the reserve. Despite extensive (203 trap locations, 275–558 km² sample plots) and intensive (>4,500 trap nights, 9 months of sampling) survey efforts, only 12 independent detections of six individual tigers were made across three study sites. Due to the sparse data, estimates of tiger abundance generated by Program CAPTURE could not be made for all survey sites. Other approaches to estimating density, based on numbers of tigers caught, or derived from borrowed estimates of detection probability, offer an alternative to capture–recapture analysis. Tiger densities fall in the range of 0.2–2.2 tigers/100 km², with 7–71 tigers inside a 3,250 km² area of prime tiger habitat, where efforts to protect tigers are currently focused. Tiger numbers might be stabilized if strict measures are taken to protect tigers and their prey from seasonal hunting and to suppress illegal trade in wildlife. Efforts to monitor abundance trends in the tiger population will be expensive given the difficulty with which tiger data can be obtained and the lack of available surrogate indices of tiger density. Monitoring occupancy patterns, the subject of a separate ongoing study, may be more efficient.