Browsing by Author "James F. Gilliam, Committee Member"

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Avian conservation in north-central Puerto Rico: Assessing the conservation value of shaded coffee plantations and the influence of nest location and habitat on nest predation rates
(2006-01-23) Gleffe, Jessica Dawn; Jaime A. Collazo, Committee Chair; James F. Gilliam, Committee Member; Kenneth H. Pollock, Committee Member
As size and number of undisturbed forests dwindle due to human encroachment, the importance of disturbed areas, such as secondary forests and shaded coffee plantations, for conservation of avifauna has risen. These 'functional substitutions' are not only recognized and valued at present, but in some cases, they may have played important conservation roles in the past. It is hypothesized that shaded coffee plantations in Puerto Rico played such a role by minimizing extinction rates of resident forest avifauna during periods of widespread deforestation during the 19th and 20th centuries. Implicit in this refugia hypothesis is that shaded coffee plantations harbored successful breeding populations. Data to evaluate this possibility, however, were not available. Likewise, data on breeding productivity and other measures of reproduction were not available for secondary forests, which as of 1992 totaled 41% of the island's forest cover. These measures are intimately related to fitness and, therefore, provide a useful basis to guide habitat conservation initiatives and management. In this study, I report on the reproductive activity and productivity of resident avifauna in shaded coffee plantations and compare them with similar data from secondary forests in Puerto Rico from 1997 to 1999. During that period, 253 nests were found in coffee plantations (12 ha) and 97 in secondary forests (45 ha). The composition of resident species found nesting in shaded coffee plantations and secondary forests was similar. Some of the most common nesting species were endemics. Predation and nest abandonment each accounted for 38% of nest failures. Nest success did not differ between secondary forest and shaded coffee plantations for vireos, tanagers, and hummingbirds. Similarly, breeding productivity did not differ between habitat types for four species for which sufficient data were available. Although the fate of fledglings (e.g., dispersal, survival) was not followed, documenting successful reproduction in shaded coffee plantations confirmed a fundamental assumption of the refugia hypothesis. This finding, coupled with the fact that shaded coffee plantations were more widespread in the past and were managed as rustic plantations and traditional polycultures (resembling primary forests), lends considerable support to the notion that shaded coffee plantations have served as a refuge for resident avian species during periods of widespread deforestation. The production capacity of shaded coffee plantations was dependent on nesting substrates provided by the shade vegetation (canopy) layer, not the coffee tree layer. Nesting activity in secondary forests also occurred primarily in the canopy layer. To investigate the basis of this pattern, I tested whether the observed nesting patterns were influenced by differential predation pressure between the understory and canopy layers. I also tested whether predation pressure differed between canopy layers of plantations and secondary forests to further assess the conservation value of shaded plantations. Tests were conducted using a series of carefully designed artificial nest experiments during the breeding season of 2005. I found that predation rates ranged from 0.44 to 0.77 (average = 0.65 ± 0.06 SE) for understory and from 0.45 to 0.80 (average = 0.65 ± 0.05 SE) for canopy nest heights. Predation rates ranged from 0.67 to 1.0 (average = 0.84 ± 0.06 SE) in shaded coffee plantations, and from 0.63 to 0.97 (average = 0.81 ± 0.06 SE) in adjacent secondary forest. Rates for both experiments were not significantly different (P > 0.05). Based on photographic evidence, avian and mammalian nest predators can prey upon nests regardless of height. Experiments and data from natural nests suggest that birds nesting in shaded plantations are not at a disadvantage compared to those nesting in secondary forests. Moreover, the pervasive nature of nest predation reported in this work, and its influence on habitat quality, affirmed the need to identify and manage habitat features associated with nest success.
Avian Point Count Surveys: Estimating Components of the Detection Process
(2004-05-17) Alldredge, Mathew Wade; Cavell Brownie, Committee Member; Theodore R. Simons, Committee Co-Chair; Kenneth H. Pollock, Committee Co-Chair; James D. Nichols, Committee Member; James F. Gilliam, Committee Member
Point count surveys of birds are commonly used to provide indices of abundance or, in some cases, estimates of true abundance. The most common use of point counts is to provide an index of population abundance or relative abundance. To make spatial or temporal comparisons valid using this type of count requires the very restrictive assumption of equal detection probability for the comparisons being made. We developed a multiple-independent observer approach to estimating abundance for point count surveys as a modification of the primary-secondary observer approach. This approach uses standard capture-recapture models, including models of inherent individual heterogeneity in detection probabilities and models using individual covariates to account for observable heterogeneity in detection probabilities. Two-observer models provided negatively biased estimates because they do not account for individual heterogeneity in detection probabilities. Models accounting for individual heterogeneity are always selected as the most parsimonious models for this data type. We also developed a time of detection approach for estimating avian abundance when birds are detected aurally, which is a modification of the time of removal approach. This approach requires collecting detection histories of individual birds in consecutive time intervals and modeling the detection process using a capture-recapture framework. This approach incorporates both the probability a bird is available for detection and the probability of detection given availability. Analyses presented demonstrate the importance of models accounting for individual heterogeneity in detection probabilities. We recommend time of detection point count surveys be designed with four or more equal intervals. We also present a multiple species modeling strategy since many point count surveys collect data on multiple species and present the approach for distance sampling, multiple observer, and time of detection approaches. The purpose of using a multiple species modeling approach is to obtain more parsimonious models by exploiting similarities in the detection process among species. We present a method for defining species groups which leads to an a priori set of species groups and associated candidate models. Multiple species models worked well and in many cases gave more parsimonious models than a species specific modeling approach, especially for the multiple-observer and time of detection approaches. Parameter estimates for multiple species models are more precise than single species models. We recommend this approach for all situations where data on multiple species is collected. Finally, we present a method for estimating the availability probability of birds during a point count based on singing rate or detailed singing time data. This approach requires data collected in conjunction with point count surveys that describe the singing rates or singing time distribution of the bird population of interest. The singing rate approach requires the assumption that an individual bird sings following a random process but rates may vary between birds. We modeled this using a finite-mixture Poisson model. The singing time approach is a nonparametric approach and does not require this restrictive assumption. Analysis of Ovenbird singing rate data demonstrates the importance of accounting for availability bias when estimating abundance, especially as count lengths get short. We recommend this approach when 'snapshot' type counts are necessary. Analyses presented throughout this thesis demonstrate the importance of accurately modeling the detection process to estimate abundance. The importance of accounting for individual heterogeneity in detection probabilities was evident in every chapter. Using a point count method that accounts for individual heterogeneity is crucial to estimating abundance effectively and making valid spatial, temporal and species comparisons.
Development of an Effective Fish Index of Biotic Integrity for the Sandhills Region of North Carolina
(2008-12-05) Hain, Ernst Frederick; Stacy A.C. Nelson, Committee Chair; Halil I. Cakir, Committee Member; James F. Gilliam, Committee Member; Bryn H. Tracy, Committee Member
We describe a process for developing an index of biotic integrity (IBI) for resident fish assemblages in an ecoregion that exhibits low natural productivity and biodiversity. From 1990 to 2006, 55 fish community samples were collected by the North Carolina Division of Water Quality (NCDWQ) in the Cape Fear, Lumber, and Yadkin river basins within the Sandhills US EPA level IV ecoregion. Initial analyses of these data, using the 12 IBI metrics employed by the NCDWQ in other regions of the state, failed to distinguish significant differences between reference and non-reference streams. To develop a more robust method of measuring responses to anthropogenic disturbance, we delineated contributing watersheds for each of the 36 sample sites using GIS, hydrologic modeling, and 20-foot resolution Digital Elevation Models (DEM) derived from Light Detection and Ranging (LiDAR) data. The 2001 National Land Cover Database (NLCD) and in situ habitat data were used to determine various land use/land cover and hydrologic variables within each watershed. These variables were then used to select the sample sites with absolute minimal anthropogenic impacts. We used the Kruskal-Wallis test to identify eleven fish community metrics, two chemical metrics, and nine individual species that were significantly different in reference and non-reference sites. Of these fifteen metrics, only three exhibited higher values in reference streams. Our results demonstrate that the abundance and diversity of the Sandhills fish fauna are greater in area more highly impacted by anthropogenic activities. By automating the process by which reference sites are chosen, we were able to produce a multi-metric IBI that reflects the varying levels of anthropogenic impacts on wadeable streams in the Sandhills ecoregion.
Factors Influencing the Mortality and Distribution of Subadult Red Drum in North Carolina
(2008-08-13) Bacheler, Nathan Mitchell; Louis B. Daniel, III, Committee Member; James F. Gilliam, Committee Member; Kenneth H. Pollock, Committee Member; Joseph E. Hightower, Committee Co-Chair; Jeffrey A. Buckel, Committee Co-Chair
Subadult red drum Sciaenops ocellatus are ecologically and economically important in North Carolina, but little is known about factors influencing their mortality and distribution in estuaries. I first assessed the effect of fishing on red drum abundance using 24 years of tagging data. The tag-return model incorporated all first returns from fish caught-and-released and accounted for age-dependent selectivities that varied by fate of the fish. Estimated fishing mortality rates (F) were high and variable before regulation changes in 1991, but decreased in magnitude and variability after 1991. A dome-shaped selectivity pattern was estimated to account for migration of older fish into coastal waters. To quantify the natural mortality rate and seasonal Fs for red drum, I conducted the first field test of a combined telemetry – tag return approach. Estimated Fs were similar in seasonal pattern and magnitude between tagging and telemetry, but joint estimates were influenced primarily by tagging. Natural mortality rate was low and influenced primarily by telemetry. The combined approach provides a new tool to estimate mortality rates for myriad fish species. Next, habitat use of subadult red drum was quantified with a combination of fishery-independent sampling, telemetry, and generalized additive models. At a large scale, red drum were associated with shallow, nearshore waters, sometimes with seagrass. To determine the influence of prey, I examined red drum stomachs and used generalized additive models to relate physicochemical and prey attributes to telemetered red drum at a small scale. Telemetered red drum were negatively related to salinity and positively related to dissolved oxygen and total prey. Last, I used tagging and telemetry to quantify the large- and small-scale movements of subadult red drum. Movement rates and directions were influenced by age of fish and region and season of tagging, and suggest that the spatial scale of management and regulations currently employed in North Carolina are appropriate. Tagging and fishery-independent surveys have provided valuable information to improve red drum management.
Sampling Attributes of Puerto Rico Stream Fishes: Bias, Selectivity, and Environmental Influences
(2008-10-16) Brown, Christin Hambrick; Kenneth H. Pollock, Committee Member; Thomas J. Kwak, Committee Chair; James F. Gilliam, Committee Member
Puerto Rico, an island in the Caribbean Sea, is known for its marine sport and commercial fisheries, but the freshwater habitats of the island also support a substantial number of fishes, which provide recreational and subsistence fishery values. There are about 80 fish species that inhabit Puerto Rico freshwaters. Of those, there are fewer than 10 native fish species that reside within the rivers, and they are of primary management concern. Management of these stream fish resources would be enhanced by an understanding of gear catchability, a standardized sampling method, and accurate population estimates. My primary objectives for this study were to (1) quantitatively describe gear efficiency and selectivity relationships to estimate stream fish populations in Puerto Rico; (2) evaluate population models among species using electrofishing catch results analyzed with mark-recapture and removal methods to identify the most suitable parameter-estimating model; (3) use these findings to develop a standardized stream fish sampling protocol to be applied island-wide; and (4) develop empirical, hierarchical models that describe relationships between fish catchability and instream habitat and water quality parameters for each native fish species. In my first research component, I compared two fish sampling gear types (electrofishing and seining) and four models for estimating fish population parameters (Petersen mark-recapture and removal estimators of 2â€“4 sampling passes) to provide the quantitative basis for development of a standardized sampling protocol for Puerto Rico stream fish. I found electrofishing more efficient and logistically feasible for collecting fish in these environments. I determined that three- and four-pass removal models were more accurate than the Petersen mark-recapture model or a two-pass removal model, and that accuracy was similar between three- and four-pass removal models. I investigated variations of models that account for assumption violations and found model Mb, that adjusts for fish behavioral effects, to provide the overall best and most parsimonious fit for estimating population parameters. Based on these findings, I propose a standard fish sampling protocol for Puerto Rico wadeable streams that includes sampling stream reaches from 100 m to 200 m long, using the appropriate electrofishing gear (backpack or barge electrofishers) and conducting three sampling passes of equal effort. A Zippin-type, maximum-likelihood estimator will then be used to calculate estimates of fish population densities. I sampled fish in 81 wadeable stream reaches island-wide, totaling 105 sampling occasions, using the standardized sampling protocol with backpack or barge electrofishers. I estimated fish catchability using the standard maximum-likelihood removal estimator. At each sampling location, I measured seven instream habitat and 13 water quality parameters. I employed a correlation matrix to reduce 20 environmental parameters to seven, then developed hierarchical regression models and used AIC model selection to quantify the most parsimonious relationships between catchability and environmental variables. Mean catchability among six fish species ranged from 0.30 to 0.55. I found no trend relating environmental parameters to variation in catchability among benthic and water-column species. The most influential environmental parameters on fish catchability were mean column velocity, mean stream width, and percent cover. Catchability was negatively correlated to mean column water velocity and mean stream width and positively to percent cover. Turbidity was not closely associated with electrofishing catchability within the range of my sampling. The regression models that I developed can be used to better understand environmental variables that influence electrofishing catchability and may be applied to more efficiently estimate fish populations. Because these models correct for bias associated with varying sampling conditions, they can be utilized with single-pass electrofishing data to estimate stream fish populations. These models will enable fisheries researchers and managers in Puerto Rico to conduct fish population estimates with a single field sample, saving time and expense, with minimal bias. More complete, quantitative estimates of the fish community may then form the basis for improved stream fish and ecosystem management.