Use of classical bird census transects as spatial replicates for hierarchical modeling of an avian community

New monitoring programs are often designed with some form of temporal replication to deal with imperfect detection by means of occupancy models. However, classical bird census data from earlier times often lack temporal replication, precluding detection‐corrected inferences about occupancy. Historical data have a key role in many ecological studies intended to document range shifts, and so need to be made comparable with present‐day data by accounting for detection probability. We analyze a classical bird census conducted in the region of Murcia (SE Spain) in 1991 and 1992 and propose a solution to estimating detection probability for such historical data when used in a community occupancy model: the spatial replication of subplots nested within larger plots allows estimation of detection probability. In our study, the basic sample units were 1‐km transects, which were considered spatial replicates in two aggregation schemes. We fit two Bayesian multispecies occupancy models, one for each aggregation scheme, and evaluated the linear and quadratic effect of forest cover and temperature, and a linear effect of precipitation on species occupancy probabilities. Using spatial rather than temporal replicates allowed us to obtain individual species occupancy probabilities and species richness accounting for imperfect detection. Species‐specific occupancy and community size decreased with increasing annual mean temperature. Both aggregation schemes yielded estimates of occupancy and detectability that were highly correlated for each species, so in the design of future surveys ecological reasons and cost‐effective sampling designs should be considered to select the most suitable aggregation scheme. In conclusion, the use of spatial replication may often allow historical survey data to be applied formally hierarchical occupancy models and be compared with modern‐day data of the species community to analyze global change process.     

Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR‐based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross‐reactions with the predator and related species genomes. Here, we use PCR‐free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h^?1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h^?1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1–2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts.     

Encounter Rates From Road-Based Surveys of Rio Grande Wild Turkeys in Texas

ABSTRACT Traditional index-based techniques have indicated declines in Rio Grande wild turkey (Meleagris gallopavo intermedia; hereafter, wild turkey) populations across much of Texas, USA. However, population indices can be unreliable. Research has indicated that road-based surveys may be an efficacious technique for monitoring wild turkey populations on an ecoregion level. Therefore, our goal was to evaluate applicability of road-based distance sampling in the Cross Timbers, Edwards Plateau, Rolling Plains, and South Texas ecoregions of Texas. We conducted road-based surveys in each ecoregion during December 2007—March 2008 to estimate wild turkey flock encounter rates and to determine survey effort (i.e., km of roads) required to obtain adequate sample sizes for distance sampling in each ecoregion. With simulations using inflatable turkey decoys, we also evaluated effects of distance to a flock, flock size, and vegetative cover on turkey flock detectability. Encounter rates of wild turkey flocks from road-based surveys varied from 0.1 (95% CI = 0.0–0.6) to 2.2 (95% CI = 0.8–6.0) flocks/100 km surveyed. Encounter rates from surveys restricted to riparian communities (i.e., areas ≤1 km from a river or stream) varied from 0.2 (95% CI = 0.1–0.6) to 2.9 (95% CI = 1.5–6.7) flocks/100 km surveyed. Flock detection probabilities from field simulations ranged from 22.5% (95% CI = 16.3–29.8%) to 25.0% (95% CI = 13.6–39.6%). Flock detection probabilities were lower than expected in all 4 ecoregions, which resulted in low encounter rates. Estimated survey effort required to obtain adequate sample sizes for distance sampling ranged from 2,765 km (95% CI = 2,597–2,956 km) in the Edwards Plateau to 37,153 km (95% CI = 12,861–107,329 km) in South Texas. When we restricted road-based surveys to riparian communities, estimated survey effort ranged from 2,222 km (95% CI = 2,092–2,370 km) in the Edwards Plateau to 22,222 km (95% CI = 19,782–25,349 km) in South Texas.     

Aerial Surveys for Estimating Wild Turkey Abundance in the Texas Rolling Plains

Abstract: Aerial surveys have been used to estimate abundance of several wild bird species including wild turkeys (Meleagris gallopavo). We used inflatable turkey decoys at 3 study sites in the Texas Rolling Plains to simulate Rio Grande wild turkey (M. g. intermedia) flocks. We evaluated detectability of flocks and errors in counting flock size during fixed-wing (Cessna 172) aerial surveys using logistic and linear regression models. Flock detectability was primarily influenced by flock size and vegetative cover, and errors in counting flock size were primarily influenced by size of flocks. We conducted computer simulations to evaluate the accuracy and precision of fixed-wing aerial surveys and examined power to detect trends in population change. Our simulations suggested abundance estimates from fixed-wing aerial surveys may be underestimated by 10-15% (2.0-4.8% CV). Power analyses suggested that fixed-wing aerial surveys can provide sufficient power (>0.80) to detect a population change of 10-25% over a 4-5-year period. We concluded fixed-wing aerial surveys are feasible on ecoregion scales.     

Distribution-abundance relationship for passerines breeding in Tunisian oases: test of the sampling hypothesis

The positive relationship between local abundance and distribution of species is a widely recognized pattern in community ecology. However, it has been suggested that this relationship can simply be an artefact of sampling because locally rare species are less detectable then locally abundant ones, and hence their distribution can easily be underestimated. Here, we use count data to investigate the relationship between distribution and abundance of passerines breeding in a sample of oases from southern Tunisia, and we provide a test of the sampling artefact hypothesis. In particular, we checked for a difference in detection probability between localized and widespread species, and we tested if increasing the sampling effort affects the significance of the relationship. A significant positive relationship between the average local abundance of passerine species and the proportion of occupied oases was found. The use of a capture-recapture approach allowed us to estimate and to compare the detection probabilities of localized and widespread species subsets. We found that localized species were locally less detectable than widespread species, which is consistent with the main assumption of the sampling artefact hypothesis. However, increasing the detection probability of species by conducting more counts did not affect the significance of the relationship, which did not give support to the sampling artefact hypothesis. Our work implies that sampling contributed to the distribution-abundance relationship we found, but that it is unlikely that such a relationship could entirely be explained by an artefact of sampling. It also underlines the insight that can be gained by using probabilistic approaches of estimating species number and detection probability when attempting to disentangle sampling from ecological effects in community ecology studies.     

Selection of line-transect methods for estimating the density of group-living animals: lessons from the primates

We review the four major contemporary methods for estimating density of group-living animals from line-transect sampling: perpendicular modelling of group centers, perpendicular modelling of center of measurable individuals, strip transects and animal-observer distance. The efficacy of each method is evaluated to produce a simple selection guide. We review the literature and use field data from the Udzungwa Mountains, Tanzania. The review is relevant to all group-living animals; however, examples are drawn from the primates. Perpendicular methods have better mathematical justification than non-perpendicular methods. For perpendicular methods using detection function models, it is preferable to measure group location using center of measurable individuals, as group centers are hard to estimate. The assumptions of detection function models are often broken in poor visibility habitats or with unhabituated animals. Alternatively strip transects may be used where there are reliable data on group spread and/or visibility. Strip transects are also the most practical, along with the animal-observer method; however, the latter lacks mathematical justification. We conclude that there are arguments for continued use of all four methods. In certain situations the use of raw encounter rates may also be considered. The appropriate method is determined by minimizing bias and considering time, resources and field conditions.     

Performance evaluation of contrast-detail in full field digital mammography systems using ideal (Hotelling) observer vs. conventional automated analysis of CDMAM images for quality control of contrast-detail characteristics

PurposeThe purpose of this work was to evaluate the contrast-detail performance of full field digital mammography (FFDM) systems using ideal (Hotelling) observer Signal-to-Noise Ratio (SNR) methodology and ascertain whether it can be considered an alternative to the conventional, automated analysis of CDMAM phantom images.MethodsFive FFDM units currently used in the national breast screening programme were evaluated, which differed with respect to age, detector, Automatic Exposure Control (AEC) and target/filter combination. Contrast-detail performance was analysed using CDMAM and ideal observer SNR methodology. The ideal observer SNR was calculated for input signal originating from gold discs of varying thicknesses and diameters, and then used to estimate the threshold gold thickness for each diameter as per CDMAM analysis. The variability of both methods and the dependence of CDMAM analysis on phantom manufacturing discrepancies also investigated.ResultsResults from both CDMAM and ideal observer methodologies were informative differentiators of FFDM systems' contrast-detail performance, displaying comparable patterns with respect to the FFDM systems' type and age. CDMAM results suggested higher threshold gold thickness values compared with the ideal observer methodology, especially for small-diameter details, which can be attributed to the behaviour of the CDMAM phantom used in this study. In addition, ideal observer methodology results showed lower variability than CDMAM results.ConclusionThe Ideal observer SNR methodology can provide a useful metric of the FFDM systems' contrast detail characteristics and could be considered a surrogate for conventional, automated analysis of CDMAM images.