I compared the utility of two continuous time-series data measures for applied conservation biology by investigating how well each could predict future local persistence of a diverse set of bird species. I used 37 years of data from the North American Breeding Bird Survey to calculate abundance from yearly point-counts and permanence (i.e., consistent occupancy over time) from yearly presence-absence data in the early portion of the study period, then used the later portion of data to empirically evaluate how well each measure predicted persistence two decades into the future. I found that permanence could only match the ability of abundance to accurately predict local species persistence if multiple within-year repeated observations contributed to its calculation. Neither measure was effective at predicting persistence for regionally rarer species. I suggest the yearly and within-year repeated collection of abundance estimating data for use in applied conservation biology to best ensure biodiversity persistence.

I compared the utility of two continuous time-series data measures for applied conservation biology by investigating how well each could predict future local persistence of a diverse set of bird species. I used 37 years of data from the North American Breeding Bird Survey to calculate abundance from yearly point-counts and permanence (i.e., consistent occupancy over time) from yearly presence-absence data in the early portion of the study period, then used the later portion of data to empirically evaluate how well each measure predicted persistence two decades into the future. I found that permanence could only match the ability of abundance to accurately predict local species persistence if multiple within-year repeated observations contributed to its calculation. Neither measure was effective at predicting persistence for regionally rarer species. I suggest the yearly and within-year repeated collection of abundance estimating data for use in applied conservation biology to best ensure biodiversity persistence.

Aim MaxEnt, a very popular species distribution modelling technique, has been used extensively to relate species’ geographic distributions to environmental variables and to predict changes in species’ distributions in response to environmental change. Here, we test its predictive ability through time (rather than through space, as is commonly done) by modeling colonizations and extinctions. Location Continental U.S. and southern Canada. Time period 1979-2009 Major taxa studied Twenty-one species of passerine birds. Methods We used MaxEnt to relate species’ geographic distributions to the variation in environmental conditions across North America. We then modelled site-specific colonizations and extinctions between 1979 and 2009 as functions of MaxEnt-estimated previous habitat suitability and inter- annual change in habitat suitability and neighborhood occupancy. We evaluated whether the effects were in the expected direction, we partitioned model’s explained deviance, and we compared colonization and extinction model’s accuracy to MaxEnt’s AUC. Results IV Colonization and extinction probabilities both varied as functions of previous habitat suitability, change in habitat suitability, and neighborhood occupancy, in the expected direction. Change in habitat suitability explained very little deviance compared to other predictors. Neighborhood occupancy accounted for more explained deviance in colonization models than in extinction models. MaxEnt AUC correlates with extinction models’ predictive ability, but not with that of colonization models. Main conclusions MaxEnt appears to sometime capture a real effect of the environment on species’ distributions since a statistical effect of habitat suitability is detected through both time and space. However, change in habitat suitability (which is much smaller through time than through space) is a poor predictor of change in occupancy. Over short time scales, proximity of sites occupied by conspecifics predicts changes in occupancy just as well as MaxEnt. The ability of MaxEnt models to predict spatial variation in occupancy (as measured by AUC) gives little indication of transferability through time. Thus, the predictive value of species distribution models may be overestimated when evaluated through space only. Future prediction of species’ responses to climate change should make a distinction between colonization and extinction, recognizing that the two processes are not equally well predicted by SDMs.

Obtaining accurate estimates of animal abundance is made difficult by the fact that most animal species are detected imperfectly. Early attempts at building likelihood models that account for unknown detection probability impose a simplifying assumption unrealistic for many populations, however: no births, deaths, migration or emigration can occur in the population throughout the study (i.e., population closure). In this dissertation, I develop likelihood models that account for unknown detection and do not require assuming population closure. In fact, the proposed models yield a statistical test for population closure. The basic idea utilizes a procedure in three steps: (1) condition the probability of the observed data on the (unobserved) period- specific abundances; (2) multiply this conditional probability by the (prior) likelihood for the period abundances; and (3) remove (via summation) the period- specific abundances from the joint likelihood, leaving the marginal likelihood of the observed data. The utility of this procedure is two-fold: step (1) allows detection probability to be more accurately estimated, and step (2) allows population dynamics such as entering migration rate and survival probability to be modeled. The main difficulty of this procedure arises in the summation in step (3), although it is greatly simplified by assuming abundances in one period depend only the most previous period (i.e., abundances have the Markov property). I apply this procedure to form abundance and site occupancy rate estimators for both the setting where observed point counts are available and the setting where only the presence or absence of an animal species is ob- served. Although the two settings yield very different likelihood models and estimators, the basic procedure forming these estimators is constant in both. / Graduation date: 2012

Multiple studies have documented declines of forest breeding birds in the eastern United States, but the temporal and spatial scales of most studies limit inference regarding large scale bird-habitat trends. A potential solution to this challenge is integrating existing long-term datasets such as the U.S. Forest Service Forest Inventory and Analysis (FIA) program and U.S. Geological Survey Breeding Bird Survey (BBS) that span large geographic regions. The purposes of this study were to determine if FIA metrics can be related to BBS population indices at multiple spatial and temporal scales and to develop predictive models from these relationships that identify forest conditions favorable to forest songbirds. I accumulated annual route-level BBS data for 4 species guilds (canopy nesting, ground and shrub nesting, cavity nesting, early successional), each containing a minimum of five bird species, from 1966-2004. I developed 41 forest variables describing forest structure at the county level using FIA data from for the 2000 inventory cycle within 5 physiographic regions in 14 states (AL, GA, IL, IN, KY, MD, NC, NY, OH, PA, SC, TN, VA, and WV). I examine spatial relationships between the BBS and FIA data at 3 hierarchical scales: 1) individual BBS routes, 2) FIA units, and 3) and physiographic sections. At the BBS route scale, I buffered each BBS route with a 100m, 1km, and 10km buffer, intersected these buffers with the county boundaries, and developed a weighted average for each forest variable within each buffer, with the weight being a function of the percent of area each county had within a given buffer. I calculated 28 variables describing landscape structure from 1992 NLCD imagery using Fragstats within each buffer size. I developed predictive models relating spatial variations in bird occupancy and abundance to changes in forest and landscape structure using logistic regression and classification and regression trees (CART). Models were developed for each of the 3 buffer sizes, and I pooled the variables selected for the individual models and used them to develop multiscale models with the BBS route still serving as the sample unit. At the FIA unit and physiographic section scales I calculated average abundance/route for each bird species within each FIA unit and physiographic section and extrapolated the plot-level FIA variables to the FIA unit and physiographic section levels. Landscape variables were recalculated within each unit and section using NCLD imagery resampled to a 400 m pixel size. I used regression trees (FIA unit scale) and general linear models (GLM, physiographic section scale) to relate spatial variations in bird abundance to the forest and landscape variables. I examined temporal relationships between the BBS and FIA data between 1966 and 2000. I developed 13 forest variables from statistical summary reports for 4 FIA inventory cycles (1965, 1975, 1989, and 2000) within NY, PA, MD, and WV. I used linear interpolation to estimate annual values of each FIA variable between successive inventory cycles and GLMs to relate annual variations in bird abundance to the forest variables. At the BBS route scale, the CART models accounted for > 50% of the variation in bird presence-absence and abundance. The logistic regression models had sensitivity and specificity rates > 0.50. By incorporating the variables selected for the models developed within each buffer (100m, 1km, and 10km) around the BBS routes into a multiscale model, I was able to further improve the performance of many of the models and gain additional insight regarding the contribution of multiscale influences on bird-habitat relationships. The majority of the best CART models tended to be the multiscale models, and many of the multiscale logistic models had greater sensitivity and specificity than their single-scale counter parts. The relatively fine resolution and extensive coverage of the BBS, FIA, and NLCD datasets coupled with the overlapping multiscale approach of these analyses allowed me to incorporate levels of variation in both habitat and bird occurrence and abundance into my models that likely represented a more comprehensive range of ecological variability in the bird-habitat relationships relative to studies conducted at smaller scales and/or using data at coarser resolutions. At the FIA unit and physiographic section scales, the regression trees accounted for an average of 54.1% of the variability in bird abundance among FIA units, and the GLMs accounted for an average of 66.3% of the variability among physiographic sections. However, increasing the observational and analytical scale to the FIA unit and physiographic section decreased the measurement resolution of the bird abundance and landscape variables. This limits the applicability and interpretive strength of the models developed at these scales, but they may serve as indices to those habitat components exerting the greatest influences on bird abundance at these broader scales. The GLMs relating average annual bird abundance to annual estimates of forest variables developed using statistical report data from the 1965, 1975, 1989, and 2000 FIA inventories explained an average of 62.0% of the variability in annual bird abundance estimates. However, these relationships were a function of both the general habitat characteristics and the trends in bird abundance specific to the 4-state region (MD, NY, PA, and WV) used for these analyses and may not be applicable to other states or regions. The small suite of variables available from the FIA statistical reports and multicollinearity among all forest variables further limited the applicability of these models. As with those developed at the FIA unit and physiographic sections scales, these models may serve as general indices to the habitat components exerting the greatest influences on bird abundance trends through time at regional scales. These results demonstrate that forest variables developed from the FIA, in conjunction with landscape variables, can explain variations in occupancy and abundance estimated from BBS data for forest bird species with a variety of habitat requirements across spatial and temporal scales. / Ph. D.

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