Comparative Analysis of Mourning Dove Population Change in North America

ABSTRACT Mourning doves (Zenaida macroura) are surveyed in North America with a Call-Count Survey (CCS) and the North American Breeding Bird Survey (BBS). Analyses in recent years have identified inconsistencies in results between surveys, and a need exists to analyze the surveys using modern methods and examine possible causes of differences in survey results. Call-Count Survey observers collect separate information on number of doves heard and number of doves seen during counting, whereas BBS observers record one index containing all doves observed. We used hierarchical log-linear models to estimate trend and annual indices of abundance for 1966–2007 from BBS data, CCS-heard data, and CCS-seen data. Trend estimates from analyses provided inconsistent results for several states and for eastern and central dove-management units. We examined differential effects of change in land use and noise-related disturbance on the CCS indices. Changes in noise-related disturbance along CCS routes had a larger influence on the heard index than on the seen index, but association analyses among states of changes in temperature and of amounts of developed land suggest that CCS indices are differentially influenced by changes in these environmental features. Our hierarchical model should be used to estimate population change from dove surveys, because it provides an efficient framework for estimating population trends from dove indices while controlling for environmental features that differentially influence the indices.     

Detecting population decline of birds using long-term monitoring data

Abrupt population change in birds may be caused by various factors. When such events occur, it is important to understand the population-level impact on the species. We applied a change point analysis with Markov chain Monte Carlo using long-term population count data to address this question. We first investigated the method with a simple Poisson model using synthetic data sets for different population decline scenarios and number of observations. Estimated change points were particularly accurate when a large decline in counts occurred. Accuracy and precision of posterior change magnitude tended to increase when actual change magnitude became larger. We applied the method to two cases using data from the North American Breeding Bird Survey: epidemic mortality of Florida scrub-jays (Aphelocoma coerulescens) in central Florida and population decline of American crows (Corvus brachyrhynchos) in Maryland and Virginia after West Nile virus emergence. The Florida scrub-jay case study indicated that the estimated change point was accurate compared with that reported by local monitoring. A Poisson-log model that included observer and year variability resulted in better fit to the data than a simple Poisson model. The American crow case study showed that the method detected change points towards the end of observational data, but not all change point parameters converged, which may suggest that a population decline did not occur or was small for some survey routes we analyzed. Our study demonstrates the utility of change point analysis to examine abrupt population change. Data from systematic long-term monitoring can be a basis of such an analysis.     

Representation of Landcover Along Breeding Bird Survey Routes in the Northern Plains

ABSTRACT The North American Breeding Bird Survey (BBS) is used extensively to make inferences about populations of many North American bird species and is increasingly being used for avian conservation planning. How well BBS routes represent the landscape is poorly known, even though accuracy of representation could significantly affect inferences made from BBS data. We used digital landcover data to examine how well landcover within 400-m buffers around BBS routes represented the surrounding landscape (the route neighborhood) for 52 routes in the Prairie Pothole Region of North Dakota and South Dakota. Differences in composition between landcover along BBS routes and the route neighborhood were not statistically significant for upland cover classes. The area of temporary and seasonal wetland basins was accurately represented by BBS routes in our study area, but the area of semipermanent and permanent wetland basins was significantly underrepresented along BBS routes. Number of wetland basins and upland patches was higher along routes. Area of urban, forest, and hay landcover classes was higher along routes, although differences were not statistically significant. Amount of bias in landcover representation was negatively correlated with the proportion of each landcover type in the study area, but bias was not correlated with area of the route neighborhoods. Differences between landcover along BBS routes and the route neighborhood were primarily attributable to increased anthropogenic activity along roads and siting of roads away from relatively large, deep water bodies. Our results suggest that inferences made from BBS data in our study region are likely biased for species that are associated with deeper-water habitats or are strongly influenced by landscape fragmentation. Inferences made from BBS data for species associated with uplands or shallow wetlands are less likely to be biased because of differences in landcover composition.     

Changes in the number and distribution of Greater Sandhill Cranes in the Eastern Population

Once nearly extirpated, the Eastern Population (EP) of Greater Sandhill Cranes (Grus canadensis tabida) has increased in number and expanded its range in breeding and wintering areas. Data from Christmas Bird Counts (CBCs) and Breeding Bird Surveys (BBSs) were used to delineate changes in the wintering and breeding area distributions during the period from 1966 to 2013. Crane densities were plotted to the centroid of CBC circles or BBS routes, and the Geographic Mean Centers (GMCs) for wintering and breeding populations were calculated. The number of Greater Sandhill Cranes detected during the breeding season has steadily increased since 1966, with just six birds observed in 1966 and 1046 observed in 2013. The GMC of the Sandhill Crane breeding population has remained in Wisconsin during the 47‐yr time frame. The total number of Sandhill Cranes counted in the eastern United States during CBCs grew from 423 in 1965–1966 to 46,194 in 2012–2013, with a peak number of 55,826 in 2011–2012. The GMC of wintering Greater Sandhill Cranes was located in Florida during the periods from 1966 to 1977 and 1978 to 1989, but shifted north‐northwest by nearly 4° of latitude (into Georgia) by 1990–2001. By 2002–2013, the GMC had shifted an additional degree north as well as almost a degree west in longitude. Greater Sandhill Cranes in the EP may continue to winter further north and remain in more northerly areas later in the fall before migrating further south. Factors such as annual weather, long‐term climate change, and changes in land use may influence future population trends and changes in both the breeding and wintering ranges of the EP of Sandhill Cranes.     

Bayesian analysis of a time series of counts with covariates: an application to the control of an infectious disease

This paper presents a Bayesian analysis of a time series of counts to assess its dependence on an explanatory variable. The time series represented is the incidence of the infectious disease ESBL-producing Klebsiella pneumoniae in an Australian hospital and the explanatory variable is the number of grams of antibiotic (third generation) cephalosporin used during that time. We demonstrate that there is a statistically significant relationship between disease occurrence and use of the antibiotic, lagged by three months. The model used is a parameter-driven model in the form of a generalized linear mixed model. Comparison of models is made in terms of mean square error.     

Assessing Landbird Monitoring Programs and Demographic Causes of Population Trends

Abstract: Population trend data from the North American Breeding Bird Survey (BBS) have been used to identify conservation priorities and justify major conservation initiatives. Yet the BBS has been criticized for potential habitat bias and reliance on abundance indices to estimate trends. We compared 1992–2003 BBS trend estimates to trend estimates derived from bird-banding data collected as part of the Monitoring Avian Productivity and Survivorship (MAPS) program for 36 wood warbler species. Similarity in trends between the 2 monitoring programs at the survey-wide and program-wide scales suggested that each program can provide accurate trend information. The MAPS program, however, was designed primarily to complement (rather than duplicate) count-based efforts, such as the BBS, by providing estimates or indices of demographic rates. Demographic data from MAPS can be used to lend insight into proximate (demographic) causes of population trends and inform management. We illustrate this with analyses of 1992–2003 MAPS data for yellow warbler (Dendroica petechia). We used reverse-time capture-recapture models to evaluate importance of new recruits (including immigrating adults and young from the previous year) relative to surviving adults in explaining variation in trend among BBS physiographic strata. We included the number of young per adult captured (an index of productivity) as a covariate in models to assess effects of productivity on trends. Survival was the key demographic driver of recent population trends. Comparison of MAPS productivity indices and adult apparent survival rate estimates to BBS trend estimates largely confirmed this inference. We suggest that increased MAPS coverage, better coordination between MAPS and the BBS, and continued development of analytical methods that link the 2 programs will enhance the value of these monitoring efforts to land managers and conservation planners working at a variety of spatial scales.     

Species‐specific and temporal scale‐dependent responses of birds to drought

Global climate change is increasing the frequency and intensity of weather extremes, including severe droughts in many regions. Drought can impact organisms by inhibiting reproduction, reducing survival and abundance, and forcing range shifts. For birds, considering temporal scale by averaging drought‐related variables over different time lengths (i.e., temporal grains) captures different hydrologic attributes which may uniquely influence food supplies, vegetation greenness/structure, and other factors affecting populations. However, studies examining drought impacts on birds often assess a single temporal grain without considering that different species have different life histories that likely determine the temporal grain of their drought response. Furthermore, while drought is known to influence bird abundance and drive between‐year range shifts, less understood is whether it causes within‐range changes in species distributions. Our objectives were to (a) determine which temporal grain of drought (if any) is most related to bird presence/absence and whether this response is species specific; and (b) assess whether drought alters bird distributions by quantifying probability of local colonization and extinction as a function of drought intensity. We used North American Breeding Bird Survey data collected over 16 years, generalized linear mixed models, and dynamic occupancy models to meet these objectives. Different bird species responded to drought at different temporal grains, with most showing the strongest signal at annual or near‐annual grains. For all drought‐responsive species, increased drought intensity at any temporal grain always correlated with decreased occupancy. Additionally, colonization/extinction analyses indicated that one species, the dickcissel (Spiza americana), is more likely to colonize novel areas within the southern/core portion of its range during drought. Considering drought at different temporal grains, along with hydrologic attributes captured by each grain, may better reveal mechanisms behind drought impacts on birds and other organisms, and therefore improve understanding of how global climate change impacts species and the landscapes they inhabit.     

Integrating broad‐scale data to assess demographic and climatic contributions to population change in a declining songbird

Climate variation and trends affect species distribution and abundance across large spatial extents. However, most studies that predict species response to climate are implemented at small spatial scales or are based on occurrence‐environment relationships that lack mechanistic detail. Here, we develop an integrated population model (IPM) for multi‐site count and capture‐recapture data for a declining migratory songbird, Wilson's warbler (Cardellina pusilla), in three genetically distinct breeding populations in western North America. We include climate covariates of vital rates, including spring temperatures on the breeding grounds, drought on the wintering range in northwest Mexico, and wind conditions during spring migration. Spring temperatures were positively related to productivity in Sierra Nevada and Pacific Northwest genetic groups, and annual changes in productivity were important predictors of changes in growth rate in these populations. Drought condition on the wintering grounds was a strong predictor of adult survival for coastal California and Sierra Nevada populations; however, adult survival played a relatively minor role in explaining annual variation in population change. A latent parameter representing a mixture of first‐year survival and immigration was the largest contributor to variation in population change; however, this parameter was estimated imprecisely, and its importance likely reflects, in part, differences in spatio‐temporal distribution of samples between count and capture‐recapture data sets. Our modeling approach represents a novel and flexible framework for linking broad‐scale multi‐site monitoring data sets. Our results highlight both the potential of the approach for extension to additional species and systems, as well as needs for additional data and/or model development.     

Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences

The rate of molecular evolution can vary among lineages. Sources of this variation have differential effects on synonymous and nonsynonymous substitution rates. Changes in effective population size or patterns of natural selection will mainly alter nonsynonymous substitution rates. Changes in generation length or mutation rates are likely to have an impact on both synonymous and nonsynonymous substitution rates. By comparing changes in synonymous and nonsynonymous rates, the relative contributions of the driving forces of evolution can be better characterized. Here, we introduce a procedure for estimating the chronological rates of synonymous and nonsynonymous substitutions on the branches of an evolutionary tree. Because the widely used ratio of nonsynonymous and synonymous rates is not designed to detect simultaneous increases or simultaneous decreases in synonymous and nonsynonymous rates, the estimation of these rates rather than their ratio can improve characterization of the evolutionary process. With our Bayesian approach, we analyze cytochrome oxidase subunit I evolution in primates and infer that nonsynonymous rates have a greater tendency to change over time than do synonymous rates. Our analysis of these data also suggests that rates have been positively correlated.