Inferring ecological relationships from occupancy patterns for California Black Rails in the Sierra Nevada foothills

The secretive California Black Rail (Laterallus jamaicensis coturniculus ) has a disjunct and poorly understood distribution. After a new population was discovered in Yuba County in 1994, we conducted call playback surveys from 1994--2006 in the Sierra foothills and Sacramento Valley region to determine the distribution and residency of Black Rails, estimate densities, and obtain estimates of site occupancy and detection probability. We found Black Rails at 164 small, widely scattered marshes distributed along the lower western slopes of the Sierra Nevada foothills, from just northeast of Chico (Butte County) to Rocklin (Placer County). Marshes were surrounded by a matrix of unsuitable habitat, creating a patchy or metapopulation structure. We observed Black Rails nesting and present evidence that they are year-round residents. Assuming perfect detectability we estimated a lower-bound mean Black Rail density of 1.78 rails ha-1, and assuming a detection probability of 0.5 we estimated a mean density of 3.55 rails ha-1.;We test if the presence of the larger Virginia Rail (Laterallus limicola) affects probabilities of detection or occupancy of the smaller California Black Rail in small freshwater marshes that range in size from 0.013-13.99 ha. We hypothesized that Black Rail occupancy should be lower in small marshes when Virginia Rails are present than when they are absent, because resources are presumably more limited and interference competition should increase. We found that Black Rail detection probability was unaffected by the detection of Virginia Rails, while, surprisingly, Black and Virginia Rail occupancy were positively associated even in small marshes. The average probability of Black Rail occupancy was higher when Virginia Rails were present (0.74 +/- 0.053) than when they were absent (0.36 +/- 0.069), and for both species occupancy increased with marsh size.;We assessed the impact of winter (November-May) cattle grazing on occupancy of California Black Rails inhabiting a network of freshwater marshes in the northern Sierra Nevada foothills of California. As marsh birds are difficult to detect, we collected repeated presence/absence data via call playback surveys and used the "random changes in occupancy" parameterization of a multi-season occupancy model to examine relationships between occupancy and covariates, while accounting for detection probability. Wetland vegetation cover was significantly lower at winter-grazed sites than at ungrazed sites during the grazing season in 2007 but not in 2008. Winter grazing had little effect on Black Rail occupancy at irrigated marshes. However, at non-irrigated marshes fed by natural springs and streams, winter-grazed sites had lower occupancy than ungrazed sites, especially at larger marsh sizes (>0.5 ha). Black Rail occupancy was positively associated with marsh area, irrigation as a water source and summer cover, and negatively associated with isolation.;We evaluate the performance of nine topographic features (aspect, downslope flow distance to streams, elevation, horizontal distance to sinks, horizontal distance to streams, plan curvature, profile curvature, slope and topographic wetness index) on freshwater wetland classification accuracy in the Sierra foothills of California. To evaluate object-based classification accuracy we test both within-image and between-image predictions using six different classification schemes (naive Bayes, the C4.5 decision tree classifier, k-nearest neighbors, boosted logistic regression, random forest, and a support vector machine classifier) in the classification software package Weka 3.6.2. Adding topographic features had mostly positive effects on classification accuracy for within-image tests, but mostly negative effects on accuracy for between-image tests. The topographic wetness index was the most beneficial topographic feature in both the within-image and between-image tests for distinguishing wetland objects from other "green" objects (irrigated pasture and woodland) and shadows. Our results suggest that there is a benefit to using a more complex index of topography than simple measures such as elevation for the goal of mapping small palustrine emergent wetlands, but this benefit, for the most part, has poor transferability when applied between image sections. (Abstract shortened by UMI.)...