Bayesian modeling of age-specific survival in bird nesting studies under irregular visits

In this article, a Bayesian model for age-specific nest survival rates is presented to handle the irregular visit case. Both informative priors and noninformative priors are investigated. The reference prior under this model is derived, and, therefore, the hyperparameter specification problem is solved to some extent. The Bayesian method provides a more accurate estimate of the total survival rate than the standard Mayfield method, if the age-specific hazard rates are not constant. The Bayesian method also lets the biologist look for high- and low-survival rates during the whole nesting period. In practice, it is common for data of several types to be collected in a single study. That is, some nests may be aged, others are not. Some nests are visited regularly; others are visited irregularly. The Bayesian method accommodates any mix of these sampling techniques by assuming that the aging and visiting activities have no effect on the survival rate. The methods are illustrated by an analysis of the Missouri northern bobwhite data set.     

Modeling Age and Nest‐Specific Survival Using a Hierarchical Bayesian Approach

Summary : Recent studies have shown that grassland birds are declining more rapidly than any other group of terrestrial birds. Current methods of estimating avian age‐specific nest survival rates require knowing the ages of nests, assuming homogeneous nests in terms of nest survival rates, or treating the hazard function as a piecewise step function. In this article, we propose a Bayesian hierarchical model with nest‐specific covariates to estimate age‐specific daily survival probabilities without the above requirements. The model provides a smooth estimate of the nest survival curve and identifies the factors that are related to the nest survival. The model can handle irregular visiting schedules and it has the least restrictive assumptions compared to existing methods. Without assuming proportional hazards, we use a multinomial semiparametric logit model to specify a direct relation between age‐specific nest failure probability and nest‐specific covariates. An intrinsic autoregressive prior is employed for the nest age effect. This nonparametric prior provides a more flexible alternative to the parametric assumptions. The Bayesian computation is efficient because the full conditional posterior distributions either have closed forms or are log concave. We use the method to analyze a Missouri dickcissel dataset and find that (1) nest survival is not homogeneous during the nesting period, and it reaches its lowest at the transition from incubation to nestling; and (2) nest survival is related to grass cover and vegetation height in the study area.     

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis

In phylogenetic analyses with combined multigene or multiprotein data sets, accounting for differing evolutionary dynamics at different loci is essential for accurate tree prediction. Existing maximum likelihood (ML) and Bayesian approaches are computationally intensive. We present an alternative approach that is orders of magnitude faster. The method, Distance Rates (DistR), estimates rates based upon distances derived from gene/protein sequence data. Simulation studies indicate that this technique is accurate compared with other methods and robust to missing sequence data. The DistR method was applied to a fungal mitochondrial data set, and the rate estimates compared well to those obtained using existing ML and Bayesian approaches. Inclusion of the protein rates estimated from the DistR method into the ML calculation of trees as a branch length multiplier resulted in a significantly improved fit as measured by the Akaike Information Criterion (AIC). Furthermore, bootstrap support for the ML topology was significantly greater when protein rates were used, and some evident errors in the concatenated ML tree topology (i.e., without protein rates) were corrected. [Bayesian credible intervals; DistR method; multigene phylogeny; PHYML; rate heterogeneity.].     

Comparison of Bayesian and maximum-likelihood inference of population genetic parameters

Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic parameters, such as population sizes and migration rates, using coalescence theory. Both inference methods use the same Markov chain Monte Carlo algorithm and differ from each other in only two aspects: parameter proposal distribution and maximization of the likelihood function. Using simulated datasets, the Bayesian method generally fares better than the ML approach in accuracy and coverage, although for some values the two approaches are equal in performance. MOTIVATION: The Markov chain Monte Carlo-based ML framework can fail on sparse data and can deliver non-conservative support intervals. A Bayesian framework with appropriate prior distribution is able to remedy some of these problems. RESULTS: The program MIGRATE was extended to allow not only for ML(-) maximum likelihood estimation of population genetics parameters but also for using a Bayesian framework. Comparisons between the Bayesian approach and the ML approach are facilitated because both modes estimate the same parameters under the same population model and assumptions.     

Nest survival rates of Red‐crested Cardinals increase with nest age in south‐temperate forests of Argentina

ABSTRACT The main cause of nest mortality for most bird species is predation and nest survival rates often vary in relation to time‐specific variables. Few investigators have examined time‐specific patterns of nest survival in Neotropical birds, and most such studies have focused on tropical and subtropical species. To better understand age‐related patterns of nest survival, we studied nest survival of Red‐crested Cardinals (Paroaria coronata, Thraupidae) in a south‐temperate forest in Argentina. We modeled daily nest survival rates (DSR) using program MARK. We examined the relationship between nest age and nest survival rate, controlling for the effects of physical characteristics of nest sites and progression of the breeding season. We monitored 367 nests for a total of 4018 exposure days. We found that DSR increased with nest age and was higher in small isolated patches than in large continuous patches of forests. The increase of DSR with nest age could be a consequence of more vulnerable nests being predated early in the nesting cycle or a result of parents defending nests more vigorously as nestlings age because of their increasing reproductive value. Open areas of grassland that surrounded the small isolated patches of forests in our study may have been a barrier to predator movements, possibly explaining the lower predation rates. Nest survival rates in our study were lower than those reported for tropical or Nearctic temperate birds, but similar to those reported in other studies of Neotropical temperate birds. Reasons for the low nest survival rates of Neotropical temperate birds remain unclear, and additional studies of predator communities are needed to help elucidate this topic.     

Genome-wide evaluation for quantitative trait loci under the variance component model

The identity-by-descent (IBD) based variance component analysis is an important method for mapping quantitative trait loci (QTL) in outbred populations. The interval-mapping approach and various modified versions of it may have limited use in evaluating the genetic variances of the entire genome because they require evaluation of multiple models and model selection. In this study, we developed a multiple variance component model for genome-wide evaluation using both the maximum likelihood (ML) method and the MCMC implemented Bayesian method. We placed one QTL in every few cM on the entire genome and estimated the QTL variances and positions simultaneously in a single model. Genomic regions that have no QTL usually showed no evidence of QTL while regions with large QTL always showed strong evidence of QTL. While the Bayesian method produced the optimal result, the ML method is computationally more efficient than the Bayesian method. Simulation experiments were conducted to demonstrate the efficacy of the new methods.     

分子系统进化关系分析的一种新方法--贝叶斯法在硬蜱属中的应用

距离矩阵邻接法、最大简约法和最大似然法是重建生物系统关系的3种主要方法。普遍认为最大似然法在原理上优于前二种方法，但其计算复杂费时。由于现行计算机的能力尚达不到其要求而实用性差，特别是在处理大数据集样本(即大于25个分类单元)时，用此方法几乎不可能。新近提出的贝叶斯法(Bayesianmethod)既保留了最大似然法的基本原理，又引进了马尔科夫链的蒙特卡洛方法，并使计算时间大大缩短。本文用贝叶斯法对硬蜱属(Ixodes)19个种的线粒体16S rDNA片段进行了系统进化分析。从总体上看，分析结果与现有的基于形态学的分类体系基本吻合。但与现存的假说相反，莱姆病的主要宿主蓖籽硬蜱复合种组并非单系。通过比较贝叶斯法与其它三种方法的结果，我们认为贝叶斯法是一种系统进化分析的好方法，它既能根据分子进化的现有理论和各种模型用概率重建系统进化关系，又克服了最大似然法计算速度慢、不适用于大数据集样本的缺陷。贝叶斯法根据后验概率直观地表示系统进化关系的分析结果，不需要用自引导法进行检验。可以预料，贝叶斯法将会被广泛地应用到系统进化分析上[动物学报49(3)：380—388，2003]。     

Multipoint mapping of viability and segregation distorting loci using molecular markers

In line-crossing experiments, deviations from Mendelian segregation ratios are usually observed for some markers. We hypothesize that these deviations are caused by one or more segregation-distorting loci (SDL) linked to the markers. We develop both a maximum-likelihood (ML) method and a Bayesian method to map SDL using molecular markers. The ML mapping is implemented via an EM algorithm and the Bayesian method is performed via the Markov chain Monte Carlo (MCMC). The Bayesian mapping is computationally more intensive than the ML mapping but can handle more complicated models such as multiple SDL and variable number of SDL. Both methods are applied to a set of simulated data and real data from a cross of two Scots pine trees.     

Effects of leg flags on nest survival of four species of Arctic‐breeding shorebirds

Marking wild birds is an integral part of many field studies. However, if marks affect the vital rates or behavior of marked individuals, any conclusions reached by a study might be biased relative to the general population. Leg bands have rarely been found to have negative effects on birds and are frequently used to mark individuals. Leg flags, which are larger, heavier, and might produce more drag than bands, are commonly used on shorebirds and can help improve resighting rates. However, no one to date has assessed the possible effects of leg flags on the demographic performance of shorebirds. At seven sites in Arctic Alaska and western Canada, we marked individuals and monitored nest survival of four species of Arctic‐breeding shorebirds, including Semipalmated Sandpipers (Calidris pusilla), Western Sandpipers (C. mauri), Red‐necked Phalaropes (Phalaropus lobatus), and Red Phalaropes (P. fulicarius). We used a daily nest survival model in a Bayesian framework to test for effects of leg flags, relative to birds with only bands, on daily survival rates of 1952 nests. We found no evidence of a difference in nest survival between birds with flags and those with only bands. Our results suggest, therefore, that leg flags have little effect on the nest success of Arctic‐breeding sandpipers and phalaropes. Additional studies are needed, however, to evaluate the possible effects of flags on shorebirds that use other habitats and on survival rates of adults and chicks.     

Immigration stabilizes a population of threatened cavity‐nesting raptors despite possibility of nest box imprinting

Nest box provisioning is a common management tool intended to increase population size or stability of threatened birds, but its effectiveness is rarely assessed. The provisioning of nest boxes may lead to unexpected results if nest type imprinting prevents naïve adult birds from immigrating into the nest box population, or limiting the ability of juveniles reared in nest boxes to emigrate to areas with only natural nesting substrates. We analyzed the population trends from 2008 to 2010 of southeastern American kestrels Falco sparverius paulus associated with a network of nest boxes in north‐central Florida, USA, with Bayesian integrated population models (IPMs) that simultaneously considered mark–recapture data sets, fledgling production, and population surveys. We evaluated the demography of the nest box population by comparing population growth rates, apparent survival probabilities, and recapture probabilities between an IPM that explicitly modeled immigration and one that did not. Overall population growth rates suggested that the population was stable, and that immigration was apparently important in maintaining this stability, with approximately 0.3 and 0.5 female immigrants per resident female kestrel each year. Explicitly modeling immigration resulted in lower estimates of juvenile kestrel apparent survival probability, suggesting that a large proportion of locally produced juveniles emigrated rather than recruited locally. We concluded that neither preference for natural cavities nor imprinting on artificial nest boxes appeared to prevent immigration from maintaining the stability of the local population. Natal habitat preference imprinting on nest sites may occur to some degree, but it did not preclude the adoption of nest boxes by most breeding kestrels. We also found additional indications that many juvenile kestrels fledged from nest boxes emigrated to the surrounding natural areas.     

The Role of Wildfire,Prescribed Fire,and Mountain Pine Beetle Infestations on the Population Dynamics of Black-Backed Woodpeckers in the Black Hills,South Dakota

Wildfire and mountain pine beetle infestations are naturally occurring disturbances in western North American forests. Black-backed woodpeckers (Picoides arcticus) are emblematic of the role these disturbances play in creating wildlife habitat, since they are strongly associated with recently-killed forests. However, management practices aimed at reducing the economic impact of natural disturbances can result in habitat loss for this species. Although black-backed woodpeckers occupy habitats created by wildfire, prescribed fire, and mountain pine beetle infestations, the relative value of these habitats remains unknown. We studied habitat-specific adult and juvenile survival probabilities and reproductive rates between April 2008 and August 2012 in the Black Hills, South Dakota. We estimated habitat-specific adult and juvenile survival probability with Bayesian multi-state models and habitat-specific reproductive success with Bayesian nest survival models. We calculated asymptotic population growth rates from estimated demographic rates with matrix projection models. Adult and juvenile survival and nest success were highest in habitat created by summer wildfire, intermediate in MPB infestations, and lowest in habitat created by fall prescribed fire. Mean posterior distributions of population growth rates indicated growing populations in habitat created by summer wildfire and declining populations in fall prescribed fire and mountain pine beetle infestations. Our finding that population growth rates were positive only in habitat created by summer wildfire underscores the need to maintain early post-wildfire habitat across the landscape. The lower growth rates in fall prescribed fire and MPB infestations may be attributed to differences in predator communities and food resources relative to summer wildfire.     

Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles

In recent years, the increasing availability of genomic resources has provided an opportunity to develop phylogenetic markers for phylogenomics. Efficient methods to search for candidate markers from the huge number of genes within genomic data are particularly needed in the era of phylogenomics. Here, rather than using the traditional approach of comparing genomes of two distantly related taxa to develop conserved primers, we take advantage of the multiple genome alignment resources from the the University of California-San Cruz Genome Browser and present a simple and straightforward bioinformatic approach to automatically screen for candidate nuclear protein-coding locus (NPCL) markers. We tested our protocol in tetrapods and successfully obtained 21 new NPCL markers with high success rates of polymerase chain reaction amplification (mostly over 80%) in 16 diverse tetrapod taxa. These 21 newly developed markers together with two reference genes (RAG1 and mitochondrial 12S-16S) are used to infer the higher level relationships of tetrapods, with emphasis on the debated position of turtles. Both maximum likelihood (ML) and Bayesian analyses on the concatenated data combining the 23 markers (21,137 bp) yield the same tree, with ML bootstrap values over 95% and Bayesian posterior probability equaling 1.0 for most nodes. Species tree estimation using the program BEST without data concatenation produces similar results. In all analyses, turtles are robustly recovered as the sister group of Archosauria (birds and crocodilians). The jackknife analysis on the concatenated data showed that the minimum sequence length needed to robustly resolve the position of turtles is 13-14 kb. Based on the large 23-gene data set and the well-resolved tree, we also estimated evolutionary timescales for tetrapods with the popular Bayesian method MultiDivTime. Most of the estimated ages among tetrapods are similar to the average estimates of the previous dating studies summarized by the book The Timetree of Life.     

Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative partitioning schemes, based on Bayesian and maximum likelihood (ML) criteria, is shown here to produce an optimal number of partitions. We tested this method using sequence data of 10 nuclear genes collected from 52 ray-finned fish (Actinopterygii) and four tetrapods. The concatenated sequences included 7995 nucleotide sites maximally split into 30 partitions defined a priori based on gene and codon position. Our results show that a model based on only 10 partitions defined by cluster analysis performed better than partitioning by both gene and codon position. Alternative data partitioning schemes also are shown to affect the topologies resulting from phylogenetic analysis, especially when Bayesian methods are used, suggesting that overpartitioning may be of major concern. The phylogenetic relationships among the major clades of ray-finned fish were assessed using the best data-partitioning schemes under ML and Bayesian methods. Some significant results include the monophyly of "Holostei" (Amia and Lepisosteus), the sister-group relationships between (1) esociforms and salmoniforms and (2) osmeriforms and stomiiforms, the polyphyly of Perciformes, and a close relationship of cichlids and atherinomorphs.     

Birds nesting survival in disturbed and protected Neotropical savannas

Fragmentation and other habitat disturbances are long known to negatively affect birds, in large part by decreasing nest success due to high nest predation rates. The factors, however, that cause this decrease in nest success are still poorly understood and may vary among regions or species. Here, we show that nest survival is also lower in a disturbed landscape versus a protected cerrado (savanna-like) Neotropical landscape. Also, we tested the importance of garbage in the nest, brood parasitism, microhabitat and bird family in nest survival, controlling for temporal effects. We monitored 144 birds’ nests in a disturbed landscape and 150 nests in a natural reserve of cerrado vegetation in central Brazil, between September and December 2006. We used Program MARK to estimate nest survival probabilities and evaluate the effect of covariates in nest success in the disturbed area. Nest daily survival rate (DSR) was higher in the reserve (survival probability = 29.4%) than in the disturbed landscape (survival probability = 16.6%). Nest daily survival rate (DSR) was smaller in nests with garbage (survival probability = 9.3%) than in nests without garbage (survival probability = 19.5%) in the disturbed landscape. Effects of habitat disturbance on nest survival differed among bird families, with finches and tanagers being more affected mostly due to high nest predation rates. Conservation and management of birds in disturbed landscapes should include actions to decrease nest predation. In poor rural or suburban areas in developing countries, such as Brazil, actions like better garbage treatment may help conserve birds in disturbed landscapes.     

Density-dependent nest predation – an experiment with simulated Mallard nests in contrasting landscapes

Breeding success is a key element of animal population dynamics. In many taxa including birds, nest success, or the proportion of laid clutches that actually hatch, is mainly determined by predation. Previous research gives an inconsistent picture of the prevalence of density-dependent nest predation and one reason for this is the general lack of well-designed replicated experiments. Using simulated Mallard Anas platyrhynchos nests and a crossover design for 20 lakes in the nemoral and boreal biotic zones, we tested the predictions that nest survival is negatively density-dependent and that nest predation is higher in agricultural than in forested landscapes. Study day and daily abundance of waterfowl, other waterbirds, as well as avian predators were included as covariates in the analysis. Model fitting in program mark revealed a general negative effect of nest density on nest survival. In addition, nest survival rate was higher at forest lakes than at lakes in agricultural landscapes, irrespective of nest density. The only covariate producing model improvement was study day; older nests had higher survival rates than recently initiated ones. This is the first replicated lake-level experimental study showing that nest predation is density-dependent in waterfowl. The pattern was consistent between landscape types, implying that density-dependent nest predation may affect habitat choice and population dynamics over large parts of the Mallard's range.     

Managing multiple vital rates to maximize greater sage-grouse population growth

Despite decades of field research on greater sage-grouse, range-wide demographic data have yet to be synthesized into a sensitivity analysis to guide management actions. We reviewed range-wide demographic rates for greater sage-grouse from 1938 to 2011 and used data from 50 studies to parameterize a 2-stage, female-based population matrix model. We conducted life-stage simulation analyses to determine the proportion of variation in population growth rate (λ) accounted for by each vital rate, and we calculated analytical sensitivity, elasticity, and variance-stabilized sensitivity to identify the contribution of each vital rate to λ. As expected for an upland game bird, greater sage-grouse showed marked annual and geographic variation in several vital rates. Three rates were demonstrably important for population growth: female survival, chick survival, and nest success. Female survival and chick survival, in that order, had the most influence on λ per unit change in vital rates. However, nest success explained more of the variation in λ than did the survival rates. In lieu of quantitative data on specific mortality factors driving local populations, we recommend that management efforts for greater sage-grouse first focus on increasing female survival by restoring large, intact sagebrush-steppe landscapes, reducing persistent sources of human-caused mortality, and eliminating anthropogenic habitat features that subsidize species that prey on juvenile, yearling, and adult females. Our analysis also supports efforts to increase chick survival and nest success by eliminating anthropogenic habitat features that subsidize chick and nest predators, and by managing shrub, forb, and grass cover, height, and composition to meet local brood-rearing and nesting habitat guidelines. We caution that habitat management to increase chick survival and nest success should not reduce the cover or height of sagebrush below that required for female survival in other seasons (e.g., fall, winter). The success or failure of management actions for sage-grouse should be assessed by measuring changes in vital rates over long time periods to avoid confounding with natural, annual variation. © 2011 The Wildlife Society.     

Using artificial nests to predict nest survival at reintroduction sites

Artificial nests are frequently used to assess factors affecting survival of natural bird nests. We tested the potential for artificial nests to be used in a novel application, the prediction of nest predation rates at potential reintroduction sites where exotic predators are being controlled. We collected artificial nest data from nine sites with different predator control regimes around the North Island of New Zealand, and compared the nest survival rates with those of North Island robin (Petroica longipes) nests at the same sites. Most of the robin populations had been reintroduced in the last 10 years, and were known to vary in nest survival and status (increasing/stable or declining). We derived estimates of robin nest survival for each site based on Stanley estimates of daily survival probabilities and the known incubation and brooding periods of robins. Estimates of artificial nest survival for each site were derived using the known fate model in MARK. We identified the imprints on the clay eggs in the artificial nests, and obtained different estimates of artificial nest survival based on imprints made by different potential predators. We then compared the value of these estimates for predicting natural nest survival, assuming a relationship of the form s = αpβ, where s is natural nest survival and p is artificial nest survival. Artificial nest survival estimates based on imprints made by rats (Rattus spp.) and brushtail possums (Trichosurus vulpecula) were clearly the best predictors (based on AICc), and explained 64% of the variation in robin nest survival among sites. Inclusion of bird imprints in the artificial nest survival estimates substantially reduced their predictive value. We suggest that artificial nests may provide a useful tool for predicting the suitability of potential reintroduction sites for New Zealand forest birds as long as imprints on clay eggs are correctly identified.     

Modeling compositional heterogeneity

Compositional heterogeneity among lineages can compromise phylogenetic analyses, because models in common use assume compositionally homogeneous data. Models that can accommodate compositional heterogeneity with few extra parameters are described here, and used in two examples where the true tree is known with confidence. It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree. Tree searching and placement of composition vectors on the tree are done in a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. Assessment of fit of the model to the data is made in both maximum likelihood (ML) and Bayesian frameworks. In an ML framework, overall model fit is assessed using the Goldman-Cox test, and the fit of the composition implied by a (possibly heterogeneous) model to the composition of the data is assessed using a novel tree-and model-based composition fit test. In a Bayesian framework, overall model fit and composition fit are assessed using posterior predictive simulation. It is shown that when composition is not accommodated, then the model does not fit, and incorrect trees are found; but when composition is accommodated, the model then fits, and the known correct phylogenies are obtained.     

A Bayesian multinomial logistic exposure model for estimating probabilities of competing sources of nest failure

Understanding causes of nest loss is critical for the management of endangered bird populations. Available methods for estimating nest loss probabilities to competing sources do not allow for random effects and covariation among sources, and there are few data simulation methods or goodness‐of‐fit (GOF) tests for such models. We developed a Bayesian multinomial extension of the widely used logistic exposure (LE) nest survival model which can incorporate multiple random effects and fixed‐effect covariates for each nest loss category. We investigated the performance of this model and the accompanying GOF test by analysing simulated nest fate datasets with and without age‐biased discovery probability, and by comparing the estimates with those of traditional fixed‐effects estimators. We then exemplify the use of the multinomial LE model and GOF test by analysing Piping Plover Charadrius melodus nest fate data (n = 443) to explore the effects of wire cages (exclosures) constructed around nests, which are used to protect nests from predation but can lead to increased nest abandonment rates. Mean parameter estimates of the random‐effects multinomial LE model were all within 1 sd of the true values used to simulate the datasets. Age‐biased discovery probability did not result in biased parameter estimates. Traditional fixed‐effects models provided estimates with a high bias of up to 43% with a mean of 71% smaller standard deviations. The GOF test identified models that were a poor fit to the simulated data. For the Piping Plover dataset, the fixed‐effects model was less well‐supported than the random‐effects model and underestimated the risk of exclosure use by 16%. The random‐effects model estimated a range of 1–6% probability of abandonment for nests not protected by exclosures across sites and 5–41% probability of abandonment for nests with exclosures, suggesting that the magnitude of exclosure‐related abandonment is site‐specific. Our results demonstrate that unmodelled heterogeneity can result in biased estimates potentially leading to incorrect management recommendations. The Bayesian multinomial LE model offers a flexible method of incorporating random effects into an analysis of nest failure and is robust to age‐biased nest discovery probability. This model can be generalized to other staggered‐entry, time‐to‐hazard situations.     

Bayesian hierarchical model assessment of nest site and landscape effects on nest survival of aplomado falcons

We investigated potential effects of nest site and landscape scale factors, including anthropogenic disturbance and habitat patchiness, on the nesting success of a reintroduced population of northern aplomado falcons (Falco femoralis septentrionalis) in southern Texas. We monitored 62 nesting attempts during 2002–2004 in the Lower Rio Grande Valley. We developed hierarchical models describing daily nest survival rates (DSR) and compared the models using a Bayesian approach in R and WinBUGS. We considered possible effects of nest age, temporal trends, nest site variables, landscape structure, territory (a random effect), and 3 measures of anthropogenic disturbance: distance to paved road, proximity to power pole, and nocturnal light intensity. Whether evaluated by Deviance Information Criterion (DIC) scores or the models' overall posterior probabilities as estimated with a reversible jump Markov Chain Monte Carlo algorithm, none of our landscape or disturbance measures affected DSR. Rather, variation in DSR was best described by nest height, overhead cover, and nest source (artificial or natural). These nest site level factors may be manipulated by managers through provision of artificial nests. We recommend that artificial nests continue to be provided, as such nests are highly successful when located on moderately tall substrates, and they permit researchers to access nest contents for population monitoring. © 2011 The Wildlife Society.