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Long-term trends in the avifauna of the Sierra Nevada: community dynamics and species occupancy over a century of climate change
Full text linkClimate change is widely considered to be one of the most important and omnipresent threats to global environmental health and biodiversity. Responding to changing climates, species are expected to shift their geographic distributions in order to remain in physiologically and ecologically favorable climates. These shifts may be species-specific, and different responses of species to a rapidly changing climate have unknown consequences for biotic communities. Despite recent evidence of shifts in mammals and plants, evidence for major changes in the distributions of birds in response to climate change is sorely lacking. Additionally, our understanding of the ecological patterns in which range shifts occur is rudimentary. This is particularly true of montane regions, where there is no clear picture yet as to how animals respond to warming along elevational gradients. To investigate this subject, I, along with the Grinnell Resurvey Project at the Museum of Vertebrate Zoology (MVZ), resurveyed birds at 95 sites in the Sierra Nevada mountains of California. These sites were originally visited 80-100 years ago by Joseph Grinnell and colleagues from MVZ. The sites were distributed among three primary elevational transects, each extending from near sea level in the Central Valley to the highest peaks of the Sierra Nevada. Comparisons of bird species assemblages at sites across time allowed unique inference on the long-term changes to species' ranges and community composition in California's montane regions.Our knowledge of current and recent climate-induced impacts have lagged behind predictive work due in part to the difficulties inherent in studying changes over time, requiring both reliable historical data and a robust method to compare these data to contemporary observations. Resurvey studies, where sites with historical species lists are revisited, often after many decades, are critical tools in understanding distributional changes over time. As we show in my first chapter, resurvey studies are increasingly used in ecology to infer extinction, colonization, and range shifts, yet most authors struggle with or completely ignore the problems arising from comparing occurrence data collected by different observers using different methods, sometimes even in different locations. A modeling technique known as occupancy modeling provides a flexible framework by which range shifts can be estimated while accounting for the diverse problems associated with historical data, particularly detectability. In subsequent chapters, occupancy modeling is the key analytical tool I employ permitting robust comparisons of occurrence data across time.Given climate change, any particular species is expected to shift in geographical space in order to track, or remain within, its favorable niche in climate space. Using occurrence data for 53 western US birds from all resurveyed sites, my second chapter investigates whether documented occurrence changes over the 20th century provide evidence in support of niche tracking. Based on movement directions of occurrence in climate space, we found evidence of climatic niche tracking for 91% of species, with some species tracking only temperature and some tracking only precipitation. Additionally, there was a strong relationship between the environmental factors limiting species' ranges on a continental scale, and the factors tracked over time. Two-season occupancy models further demonstrated that extinction and colonization probabilities for a species were most strongly related to the climatic relationship between a site and the species' niche centroid.Evidence that species are tracking their climatic niche does not, per se, describe how species are moving in geographic space. Using a larger sample of 99 bird species, my third chapter catalogues the elevational movements of species over time and seeks to test the naïve hypothesis that all species will shift upward in elevation in order to track a warming climate. While species did, on the whole, shift up more than they shifted down, this naïve hypothesis only described 56% of measured range shifts. Alternative hypotheses providing species specific predictions of upward or downward shifts based on site-specific climate change almost universally outperformed the naïve hypothesis. Many species did not shift in parts or all of their range, despite climatic expectations to do so, and traits defining these species and differentiating them from moving species are explored.The cumulative effect of hundreds of species shifting geographic ranges in an individualistic manner has an unknown effect on local species diversity. My fourth chapter uses a hierarchical multi-species occupancy model to estimate richness change and turnover at sites based on all 210 observed breeding bird species in the Sierra Nevada. The results illustrate that richness has broadly declined across all elevations, but that turnover has been greatest at the lowest and the highest elevations. The results also demonstrate the importance of accounting for detectability using methods such as occupancy modeling, as analyses of community change using naïve detections of species show opposite trends than those inferred when accounting for false absences.Overall, my dissertation provides a detailed picture, over a uniquely long time span and broad geographic area, of how bird species have responded spatially to changing climates over a century. These movements have been shown to be more diverse than previously described and are not likely to be predicted by simple ecological relationships. As we prepare for greater climate shifts during the 21st century, recovering and utilizing our knowledge of the past will be critical to anticipating and understanding the impacts of the future
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The Effects of Landscape, Movement, and Spillover on Avian Occupancy in the Sierra Nevada Foothills of California
Full text linkOne of the most fundamental questions facing ecologists is: why do animals live where they do? Patch occupancy depends on a myriad of biotic and abiotic factors, any of which may encourage or discourage the presence of a species. Understanding the relationship between occupancy and environmental characteristics is integral to managing and conserving species in a dynamic environment. This dissertation studies avian occupancy in widely dispersed emergent wetlands in the Sierra Nevada foothills of California and relates occupancy to the characteristics of wetland patches, behaviors of the birds using those wetlands, and landscape composition. The first chapter of this dissertation focuses on violations of the assumption of closure in occupancy models for two secretive marsh birds, Black Rails (Laterallus jamaicensis) and Virginia Rails (Rallus limicola). For occupancy models, a key assumption is that there is no immigration and emigration between survey periods. Violating this assumption could overestimate occupancy and lead to an improper understanding of the characteristics that influence site occupancy. I found that there were significant closure violations for both Black and Virginia Rails, although the characteristics of those violations differed. Black Rails were more likely to colonize wetlands between surveys, and the wetlands colonized were those that were occupied in the previous year. Virginia Rails were more sensitive to environmental changes and would abandon drying wetlands more readily than Black Rails.
The second chapter of this dissertation uses a multispecies occupancy model to understand the importance of spillover effects on occupancy across the entire avian assemblage using wetlands in the Sierra Nevada Foothills. The presence of animals in a patch of habitat is dependent not only on the characteristics of that patch, but also the landscape surrounding it. I investigated whether there was a spillover effect from matrix habitats such as grassland and forest on wetland bird species or the reverse, a spillover effect from the wetlands on species inhabiting the matrix habitat surrounding each wetland. I observed spillover effects in both directions, with matrix species assemblages depending on wetland water source and wetland species assemblages depending on the landscape composition around the wetland.
The final chapter of this dissertation uses aerial remote sensing to assess Black and Virginia Rail habitat, compares the predictive power of remote sensing to ground-truthed data, and assess the ability of occupancy models to predict rail occupancy at novel sites using only aerial imagery. For this chapter, I differentiated occupied habitat from unoccupied habitat using known locations and occupancy status at wetlands. I classified sites using a maximum likelihood classifier and high resolution imagery from the National Agriculture Imagery Program. I found that raw spectral reflectance accurately predicted wetland occupancy for both Black and Virginia Rails, although the effectiveness of characterizing a wetland varied between years. For Black Rails, spectral reflectance was most similar to the wetland structure, whereas for Virginia rails, spectral reflectance was most similar to wetland wetness. However, in both cases, spectral reflectance was informative when included alongside ground-collected data.
Although the data collected in this dissertation are focused on a very specific habitat type and location, my results clearly demonstrate the importance of biological context on understanding animal occupancy. My results are broadly applicable in other study systems and help inform conservation strategies for multiple species. By understanding landscape composition, the drivers of animal movement, and the biotic and abiotic factors correlated with occupancy, I can better predict changes in animal populations in an increasingly changing environment
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Linked Landscapes: Metapopulation Connectivity of Secretive Wetland Birds
Full text linkDispersal and gene flow connect habitat patches, linking demographic and genetic processes within metapopulations. Demographic connectivity can prevent local extinctions and increase species persistence. It allows species to colonize new areas, making it possible for them to shift their ranges in response to changes in the environment. Genetic connectivity may impede local adaptation, but is often advantageous because it minimizes the negative effects of habitat loss and fragmentation, such as inbreeding. This research explored different methodologies for estimating dispersal and gene flow, and estimated connectivity for two species of secretive wetland birds, the California black rail (Laterallus jamaicensis coturniculus) and the Virginia rail (Rallus limicola), from an inland metapopulation in the Sierra Nevada foothills and a coastal metapopulation in the San Francisco Bay Area, California. The research presented includes: (1) a synthesis of landscape genetics methods used to examine spatial patterns of genetic variation, (2) a validation of dispersal distances estimated from occupancy models using dispersal distances estimated from genetic parentage assignments within the inland metapopulation, (3) an estimate of the frequency and distance of long-distance dispersal events between the inland and coastal metapopulations, and (4) an assessment of the effects of habitat loss and fragmentation on gene flow within the coastal metapopulation. Despite its importance in ecology and evolution, dispersal distances are poorly understood for many species, especially those that are secretive and rare, such as rails. For these species, indirect methods, including the use of occupancy models, genetics, and isotopic markers, may be optimal for estimating dispersal. In the Sierra Nevada foothills, Black and Virginia rails exhibited contrasting relationships between connectivity metrics and patch colonization. For black rails, model-averaged dispersal distances from occupancy models (Buffer Radius Metric = 3.46 km; Incidence Function Metric = 3.70 km) showed good agreement with the mean dispersal distance from genetic parentage assignments (5.58 ± 1.92 km). For Virginia rails, however, it was difficult to identify a spatial scale with the best fit in occupancy models, and the sample size for estimating dispersal distance from parentage assignments was limited. Combined inference from genetic and isotopic population assignments suggested that long-distance dispersal of black rails between the Sierra Nevada foothills and the San Francisco Bay Area occurred infrequently, but, somewhat surprisingly, three dispersal events greater than 100 km were recorded during the study. The first was recorded from a band return for a black rail that traveled 128 km. Two other long-distance dispersal estimates were obtained using isotopic and genetic population assignments. Within the San Francisco Bay Area, estimates of gene flow for black rails among 11 wetlands (FST range: 0.014 to 0.067) indicated rails dispersed frequently between wetlands at shorter spatial scales (tens of kilometers), but that gene flow at a larger spatial scale (greater than 50 km) between the North Bay and South Bay (FST = 0.018) was limited. Although previously thought to be dispersal-limited, black rails appear to be capable of dispersing and maintaining some level of gene flow at spatial scales less than 50 km. Therefore, wetland mitigation and restoration efforts for rails should focus on protecting and creating habitat at smaller spatial scales (tens of kilometers) to maintain demographic and genetic connectivity and metapopulation viability
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A century of change in avifauna of California's most transformed landscapes
Full text linkAnthropogenic climate and land-use change are widely considered to be the two greatest threats to global biodiversity and ecosystem functioning. Although species may respond to changing environments in a variety of ways, the majority of species are expected to shift their distributions to track ecologically favorable habitats. The extent of these shifts may be heterogenous across species or even within a species occupying different regions, but our knowledge of what drives this heterogeneity is still sorely lacking. In particular, the effects of climate and land-use change on shifting species distributions have largely been studied independently. In more realistic scenarios, most species will experience both drivers simultaneously, creating the potential for heterogeneous changes in species composition across regions with different histories of climate and land-use change, as well as species with different sensitivities to that change.To investigate the combined effects of climate and land-use change on species occupancy and community composition, I surveyed avian diversity at 71 sites in the California Central Valley and Los Angeles. These sites were originally surveyed in the early 1900s by Joseph Grinnell and colleagues from the Museum of Vertebrate Zoology, providing a unique opportunity to directly compare bird occupancy and its relation to site-specific climate and land-use covariates across a century of change. Historic surveys paired with modern resurveys documented changing distributions by 148 bird species across two regions with similar initial species and habitat composition but differing patterns of climate and land-use change.Our knowledge of species’ ecological and life history traits as predictors of sensitivity to land-use change is well developed, but the same cannot be said for traits as predictors of climate-induced range shifts. There is strong theoretical support that range shifts under climate change may be mediated by traits that facilitate dispersal and population establishment, but empirical evidence for this relationship has been mixed. In my first chapter, I conducted a meta-analysis of studies that analyzed climate-induced range shifts as a function of species’ traits, with the goal of identifying which traits have provided the strongest results. I show that the majority of traits failed to predict range shifts consistently across studies, while a much smaller number of traits, particularly habitat breadth, had strong empirical support. In subsequent chapters, I use the most informative species’ traits revealed by this meta-analysis to explore differences in species-specific occupancy change across my Central Valley and Los Angeles survey sites.Both climate and land-use change are expected to favor exotic and generalist species over specialists, resulting in declining occupancy and diversity. Using occurrence data for 122 bird species from 41 resurvey sites in the California Central Valley, my second chapter examined how occupancy and diversity changed over the past 100 years in this predominantly agricultural region, as well as the relative influence of climate versus land-use covariates to occupancy within each survey period. In contrast to expectations that occupancy and diversity would decline, both remained stable: species that increased in occupancy (predominantly habitat generalists or human adapters) roughly balanced species that decreased in occupancy (predominantly open-habitat species), resulting in no significant change in average species richness or between-site diversity. Equally surprising was the far greater importance of water availability (precipitation and water cover) to occupancy within each survey period as compared to urbanization or agricultural cover.The relative importance of climate versus land-use change to changes in species occupancy is poorly known and may result in heterogeneous patterns of diversity change across regions with different climate and land-use change histories. In my third chapter, I used occurrence data for 148 bird species across the full set of 42 Central Valley sites and 29 Los Angeles sites. I directly assessed the relative importance of climate and land-use covariates to probabilities of occupancy, persistence, and colonization, as well as compared patterns of occupancy and diversity change between the two regions. Climate and land-use covariates were both important, but to different aspects of occupancy and turnover, with climate driving initial occupancy, climate and land-use both having similar influence on colonization, and urban cover emerging as the biggest driver of local persistence. In contrast to stability in occupancy and diversity in the Central Valley, both declined in Los Angeles. This diversity loss resulted from a greater amount of urban development in Los Angeles and larger species-specific occupancy decreases in particularly forest and open-habitat species.Overall, my dissertation provides a detailed picture of how bird species have responded to over a century of climate and land-use change. These changes were highly heterogeneous across species – driven by traits, namely habitat preference – and across very similar ecological regions – driven by divergent patterns in both climate change and urbanization. As we continue to create range projections and plans to conserve future diversity, it will be important to utilize knowledge generated by long-term historical datasets and to incorporate multiple drivers of heterogeneity in species’ responses to global change
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The Dynamics and Resilience to Drought of Wetlands and Avian Metapopulations in a Coupled Human and Natural System
Full text linkIn working landscapes where natural resource extraction co-occurs with habitat conservation, species are often structured as a metapopulation occupying fragmented patches of habitat. Because patches change due to human management decisions, understanding how metapopulations persist in working landscapes requires assessing both how the species’ intrinsic factors drive turnover and how the behaviors of key actors drive patch changes. Coupled human and natural systems (CHANS) research uses a multidisciplinary approach to identify the key actors, processes, and feedbacks that drive the dynamics of a region. This dissertation integrates five diverse datasets—wildlife occupancy surveys, land-use change mapping, a survey of landowner decision-making, hydrological databases, and disease vector trapping—to assess how wetlands, irrigation, and two avian metapopulations function as a CHANS in the rangelands of the foothills of the California Sierra Nevada. The threatened, dispersal-limited black rail (Laterallus jamaicensis) and widespread, vagile Virginia rail (Rallus limicola) inhabit patchy wetlands throughout the foothills. The black rail has declined over the past decade, with drought and the arrival of West Nile virus potential causes. The first chapter assesses how the human-induced diversity of hydrological processes altered the CHANS’ resilience to an exceptional disturbance, a historically severe drought from 2012–2015. The second chapter tests if the “rescue effect” (dispersing individuals preventing local extinctions) actually occurs as predicted by theory and occupancy models. The third chapter integrates these interdisciplinary datasets into a simulation model that combines agent-based models of land-use change with stochastic patch occupancy models of metapopulations, in order to (1) quantify the relative importance of different drivers of metapopulation dynamics, (2) test predictions of the behavior of metapopulations in dynamic landscapes, and (3) evaluate the potential impacts of mandated irrigation cutbacks during drought and wetland incentive policies on metapopulation persistence.Complex metapopulation dynamics emerged from the CHANS, and irrigation water was critical for black rail persistence. Wetlands were primarily fed by “waste” from the irrigation system. Landowners and water sources showed response diversity to drought, increasing the resilience of the wetland landscape and maintaining the black rail metapopulation through the 2012–2015 drought. The rescue effect was operating for both rail metapopulations during this period, providing one of the first empirical validations of this process, and occurred at notably higher rates during the lowest precipitation year. However, inferences from occupancy models were unreliable and underestimated the rescue effect (1) when using autoregressive measures that incorporated patch area, (2) when the species was not dispersal-limited, and (3) during a period of nonequilibrium metapopulation dynamics. Simulations showed rail metapopulations were strongly top-down regulated by precipitation, with synergistic negative impacts because droughts affected multiple system processes at the same time. The black rail decline was caused by the combination of West Nile virus and drought. Two key theoretical predictions were not borne out due to the CHANS’ complexity. First, dispersal limitations of black rails did not result in greater sensitivity to patch change rates compared to Virginia rails, because patch heterogeneity affected patch change rates and the two species’ colonization and extinction rates in different ways. Second, because incentive programs were coupled to CHANS dynamics they made the black rail metapopulation more sensitive to other parameters, not less. Drought irrigation cutbacks posed a substantial extinction risk that incentive policies were unable to reduce. Integrating “waste” water into regional wetland management may thus offer more cost-effective conservation than attempting to restore a lost “natural” state. These results highlight that conserving metapopulations in working landscapes requires assessing how human transformation of CHANS may create new diversity in system processes that benefits wildlife
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A Century of Avian Community Change in the Desert Southwest
Full text linkSpecies extinctions and population declines have accelerated over recent decades due to habitat destruction, overexploitation, and invasive species, with cascading effects on ecosystem functions and services as well as human well-being. Climate change has emerged as another powerful driver of species decline, one whose effects are beginning to intensify. It should lead to shifts in species distributions and rearranged communities, unless climatic disruption acts as a systemic threat leading to a community collapse. Desert birds comprise a species-rich, easily detectable assemblage, and are closely coupled to their physical environment, which makes them suitable indicators of climatic change. I assessed how desert bird populations have been impacted over the past century by resurveying 106 sites throughout the Mojave and Great Basin deserts that were originally surveyed for avian diversity in the early 20th century by Joseph Grinnell and colleagues from the Museum of Vertebrate Zoology at University of California, Berkeley. Multispecies occupancy models were employed throughout this research to capture the dynamics of the entire avian community. In my first chapter, I review the impacts of imperfect detection on the estimation of community diversity and how the application of multispecies occupancy models to estimate these measures can alleviate this source of error. The hierarchical structure of the model allows data from the entire sample to inform the estimation of occupancy, colonization, survival, and detection probabilities, despite encounter histories being stratified by historic and modern surveys, species, site, and visit. Data from all species’ informs the estimation of community-level values, and the structure of the model itself facilitates the modeling of all species, including rare ones. Correcting for detection is particularly important when using historic data, because differences in methodology and changes in technology that can alter the detectability of species through time can also influence the conclusions drawn from the comparison.Deserts, already defined by climatic extremes, have warmed and dried more than other regions in the contiguous United States due to climate change. In my second chapter, I assessed how climate change and habitat disturbance have impacted bird populations of the Mojave Deserts. The resurveys of sites originally visited in the early 20th century found Mojave Desert birds strongly declined in occupancy and sites lost nearly half of their species. Declines were associated with climate change, particularly decreased precipitation. The magnitude of the decline in the avian community and the absence of species that were local climatological “winners” is exceptional. Our results provide evidence that bird communities in the Mojave Desert have collapsed to a new, lower baseline. Declines could accelerate with future climate change, as this region is predicted to become drier and hotter by the end of the century.Where the Mojave and Great Basin meet is a juncture of two distinct avifauna. My third chapter uses a dynamic multispecies occupancy model to evaluate the cumulative effects of the redistribution of all 162 observed breeding species across space, time, and biomes. Cross-system comparisons can verify that trends are more than just regional in nature, which legitimizes their application to the development of broad-scale predictive models or management recommendations. The Mojave, a warm desert, and the Great Basin, a cold desert, are two very different systems with distinct vegetation and animal assemblages. The contiguity of the deserts creates an ideal place to study how 20th century climate change is differentially impacting communities across biomes. A transition zone can persist through a changing climate if biotic factors lag behind climate, such as the leading and trailing-edge range disequilibria in vegetation response, and inherent abiotic factors, such as topography and edaphic factors that contribute to the Mojave-Great Basin transition. Barriers to northward expansion for birds could result in range collapse if the southern limits of warm desert species are also contracting. I evaluated whether species of the warmer Mojave, which continues to warm, are expanding into the colder Great Basin Desert, which has incurred less warming, or whether the transition zone behaves as a barrier to northward expansion. Individual species experienced occupancy changes in consistent directions in both deserts. A substantial proportion of species were in decline in one or both deserts (39.5%), while relatively few species were increasing (6.2%). Most species (n = 80) shifted one or both of their latitudinal range limits. Range shifts were highly idiosyncratic in nature, causing the avifaunas of the two deserts to be less strongly structured than they were in the past. The redistribution of species is driving the genesis of novel communities which may have ecological consequences that are yet to be realized.This dissertation presents a detailed picture of how desert avifauna has change over the past century. The unique ecology of the deserts means that can serve as bellwethers of climate change. Community collapse of the Mojave avifauna and the redistribution of species across both deserts would have been overlooked without the original faunal surveys of Joseph Grinnell and colleagues from the early 20th century. Although similar changes may be occurring in other ecoregions that lack comparable historical data, the harsh nature of desert environments makes them more likely to become less suitable for life and offers a prescient warning for biodiversity loss as future climates are pushed further toward extremes
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Inferring ecological relationships from occupancy patterns for California Black Rails in the Sierra Nevada foothills
Full text linkOccupancy models provide a useful tool for examining relationships between species' occurrences and environmental or ecological covariates when detection probability is less than one. This research is focused on the secretive and rare California Black Rail (Laterallus jamaicensis coturniculus) and its wetland habitats in a newly discovered part of its range in the Sierra Nevada foothills of California, USA. In order to examine the Black Rail's distribution, residency, density, relationship to a larger conspecific, the Virginia Rail (Laterallus limicola), and relationship to livestock grazing, three classes of occupancy models were utilized: single-species/single-season models, single season/two-species models, and multi-season/single-species models. In order to develop a wetland classification procedure for identifying potential Black Rail habitats, we evaluated the utility of combining topographic features with spectral and geometric features using high-resolution satellite imagery and a digital elevation model (DEM). The secretive California Black Rail 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. The probability of detecting occupancy from a single call playback survey at a marsh was high (mean = 0.84), and the estimated proportion of marshes occupied (across all years) was 0.58. The proportion of sites occupied by Black Rails in the foothills remained relatively stable from 2002-2006 despite turnover from year to year of specific sites. Irrigation ditches were the primary water source at 75% of the marshes that had Black Rails. Approximately two-thirds of marshes with Black Rails were on private land. Black Rails are more widespread in the Sierra foothills than was previously known, and the foothills distribution appears to be discontinuous with populations in the San Francisco Bay-Delta Estuary. Occupancy surveys may be an improved method for monitoring population trends of this secretive marsh bird where habitat patches are highly fragmented. Two-species occupancy models that account for false absences provide a robust method for testing for evidence of competitive exclusion, but previous model parameterizations were inadequate for incorporating covariates. We present a new parameterization that is stable when covariates are included, the conditional two-species occupancy model, that can be used to examine alternative hypotheses for species' distribution patterns. This new model estimates the probability of occupancy for a subordinate species conditional upon the presence of a dominant species. It can also be used to test if the detection of either species differs when one or both species are present, and if detection of the subordinate species depends on the detection of the dominant species when both are present. We apply the model to test if the presence of the larger Virginia Rail 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. Our results contrast with recent findings from patchy forest systems, where small birds were presumed to be excluded from small habitat patches by larger competitors. Impacts of grazing are often magnified in aquatic environments where livestock congregate for shade, cooler temperatures, green forage and water. 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. Residual dry matter (RDM), a commonly used metric of grazing intensity, may help to explain variation in summer wetland vegetation cover; however, spring cover was not well predicted by RDM. Accurate, transferable and efficient mapping procedures are needed for wetland inventory, assessment and monitoring. Wetland mapping is typically carried out using two types of inputs: (1) spectral reflectance data from imagery and (2) topographic/hydrologic data derived from digital elevation models (DEMs). Hybrid approaches that integrate remotely-sensed imagery with topographic data have shown improved wetland mapping accuracy in several studies. Here 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 (naïve 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. Occupancy models provide a robust method for examining species-environment relationships when detection probability is imperfect. The Black Rail study system in the Sierra foothills provides a unique and valuable opportunity for examining the effects of interspecific competition and grazing on a threatened subspecies at a regional scale. Further development of wetland mapping procedures will allow for a more complete description of the distribution of this rare and enigmatic marsh bird
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