Cory T. Overton

Wetland Accretion Rate Model of Ecosystem Resilience (WARMER) and Its Application to Habitat Sustainability for Endangered Species in the San Francisco Estuary

Salt marsh faunas are constrained by specific habitat requirements for marsh elevation relative to sea level and tidal range. As sea level rises, changes in relative elevation of the marsh plain will have differing impacts on the availability of habitat for marsh obligate species. The Wetland Accretion Rate Model for Ecosystem Resilience (WARMER) is a 1-D model of elevation that incorporates both biological and physical processes of vertical marsh accretion. Here, we use WARMER to evaluate changes in marsh surface elevation and the impact of these elevation changes on marsh habitat for specific species of concern. Model results were compared to elevation-based habitat criteria developed for marsh vegetation, the endangered California clapper rail (Rallus longirostris obsoletus), and the endangered salt marsh harvest mouse (Reithrodontomys raviventris) to determine the response of marsh habitat for each species to predicted >1-m sea-level rise by 2100. Feedback between vertical accretion mechanisms and elevation reduced the effect of initial elevation in the modeled scenarios. Elevation decreased nonlinearly with larger changes in elevation during the latter half of the century when the rate of sea-level rise increased. Model scenarios indicated that changes in elevation will degrade habitat quality within salt marshes in the San Francisco Estuary, and degradation will accelerate in the latter half of the century as the rate of sea-level rise accelerates. A sensitivity analysis of the model results showed that inorganic sediment accumulation and the rate of sea-level rise had the greatest influence over salt marsh sustainability.

Endangered species management and ecosystem restoration: finding the common ground

Management actions to protect endangered species and conserve ecosystem function may not always be in precise alignment. Efforts to recover the California Ridgways Rail (Rallus obsoletus obsoletus; hereafter, California rail), a federally and state- listed species, and restoration of tidal marsh ecosystems in the San Francisco Bay estuary provide a prime example of habitat restoration that has conflicted with species conservation. On the brink of extinction from habitat loss and degradation, and non-native predators in the 1990s, California rail populations responded positively to introduction of a non-native plant, Atlantic cordgrass (Spartina alterniflora). California rail populations were in substantial decline when the non-native Spartina was initially introduced as part of efforts to recover tidal marshes. Subsequent hybridization with the native Pacific cordgrass (Spartina foliosa) boosted California rail populations by providing greater cover and increased habitat area. The hybrid cordgrass (S. alterniflora × S. foliosa) readily invaded tidal mudflats and channels, and both crowded out native tidal marsh plants and increased sediment accretion in the marsh plain. This resulted in modification of tidal marsh geomorphology, hydrology, productivity, and species composition. Our results show that denser California rail populations occur in invasive Spartina than in native Spartina in San Francisco Bay. Herbicide treatment between 2005 and 2012 removed invasive Spartina from open intertidal mud and preserved foraging habitat for shorebirds. However, removal of invasive Spartina caused substantial decreases in California rail populations. Unknown facets of California rail ecology, undesirable interim stages of tidal marsh restoration, and competing management objectives among stakeholders resulted in management planning for endangered species or ecosystem restoration that favored one goal over the other. We have examined this perceived conflict and propose strategies for moderating harmful effects of restoration while meeting the needs of both endangered species and the imperiled native marsh ecosystem.

Does mercury contamination reduce body condition of endangered California clapper rails

We examined mercury exposure in 133 endangered California clapper rails (Rallus longirostris obsoletus) within tidal marsh habitats of San Francisco Bay, California from 2006 to 2010. Mean total mercury concentrations were 0.56 μg/g ww in blood (range: 0.15-1.43), 9.87 μg/g fw in head feathers (3.37-22.0), 9.04 μg/g fw in breast feathers (3.68-20.2), and 0.57 μg/g fww in abandoned eggs (0.15-2.70). We recaptured 21 clapper rails and most had low within-individual variation in mercury. Differences in mercury concentrations were largely attributed to tidal marsh site, with some evidence for year and quadratic date effects. Mercury concentrations in feathers were correlated with blood, and slopes differed between sexes (R(2) = 0.58-0.76). Body condition was negatively related to mercury concentrations. Model averaged estimates indicated a potential decrease in body mass of 20-22 g (5-7%) over the observed range of mercury concentrations. Our results indicate the potential for detrimental effects of mercury contamination on endangered California clapper rails in tidal marsh habitats.

Integrating spatially explicit indices of abundance and habitat quality: an applied example for greater sage-grouse management.

Summary Predictive species distributional models are a cornerstone of wildlife conservation planning. Constructing such models requires robust underpinning science that integrates formerly disparate data types to achieve effective species management. Greater sage‐grouse Centrocercus urophasianus, hereafter ‘sage‐grouse’ populations are declining throughout sagebrush‐steppe ecosystems in North America, particularly within the Great Basin, which heightens the need for novel management tools that maximize the use of available information. Herein, we improve upon existing species distribution models by combining information about sage‐grouse habitat quality, distribution and abundance from multiple data sources. To measure habitat, we created spatially explicit maps depicting habitat selection indices (HSI) informed by >35 500 independent telemetry locations from >1600 sage‐grouse collected over 15 years across much of the Great Basin. These indices were derived from models that accounted for selection at different spatial scales and seasons. A region‐wide HSI was calculated using the HSI surfaces modelled for 12 independent subregions and then demarcated into distinct habitat quality classes. We also employed a novel index to describe landscape patterns of sage‐grouse abundance and space use (AUI). The AUI is a probabilistic composite of the following: (i) breeding density patterns based on the spatial configuration of breeding leks and associated trends in male attendance; and (ii) year‐round patterns of space use indexed by the decreasing probability of use with increasing distance to leks. The continuous AUI surface was then reclassified into two classes representing high and low/no use and abundance. Synthesis and applications. Using the example of sage‐grouse, we demonstrate how the joint application of indices of habitat selection, abundance and space use derived from multiple data sources yields a composite map that can guide effective allocation of management intensity across multiple spatial scales. As applied to sage‐grouse, the composite map identifies spatially explicit management categories within sagebrush steppe that are most critical to sustaining sage‐grouse populations as well as those areas where changes in land use would likely have minimal impact. Importantly, collaborative efforts among stakeholders guide which intersections of habitat selection indices and abundance and space use classes are used to define management categories. Because sage‐grouse are an umbrella species, our joint‐index modelling approach can help target effective conservation for other sagebrush obligate species and can be readily applied to species in other ecosystems with similar life histories, such as central‐placed breeding.

Hunting influences the diel patterns in habitat selection by northern pintails Anas acuta

Northern pintail Anas acuta (hereafter pintail) populations wintering within Suisun Marsh, a large estuarine managed wetland near San Francisco Bay, California, USA, have declined markedly over the last four decades. The reasons for this decline are unclear. Information on how hunting and other factors influence the selection of vegetation types and sanctuaries would be beneficial to manage pintail populations in Suisun Marsh. During 1991-1993, we radio-marked and relocated female pintails (individuals: N = 203, relocations: N = 7,688) within Suisun Marsh to investigate habitat selection during the non-breeding months (winter). We calculated selection ratios for different vegetation types and for sanctuaries, and examined differences in those ratios between hunting season (i.e. hunting and non-hunting), age (hatch-year and after-hatch-year), and time of day (daylight or night hours). We found that diel patterns in selection were influenced by hunting disturbance. For example, prior to the hunting season and during daylight hours, pintails selected areas dominated by brass buttons Cotula coronopifolia, a potentially important food source, usually outside of sanctuary boundaries. However, during the hunting season, pintails did not select brass buttons during daylight hours, but instead highly selected permanent pools, mostly within sanctuaries. Also, during the hunting season, pintails showed strong selection for brass buttons at night. Sanctuaries provided more area of permanent water pools than within hunting areas and appeared to function as important refugia during daylight hours of the hunting season. Wildlife managers should encourage large protected permanent pools adjacent to hunted wetlands to increase pintail numbers within wetland environments and responsibly benefit hunting opportunities while improving pintail conservation.

Evaluation of current population indices for band-tailed pigeons

Abstract There is no formal population survey specifically designed to index population abundance of band-tailed pigeons (Patagioenas fasciata) throughout their range. Data from the Breeding Bird Survey (BBS), Washington and Oregon Mineral-Site (WAORMS) surveys, and Washington Call Count (WACC) survey offer evidence of long-term population decline. We investigated the potential to augment BBS, WACC, and WAORMS surveys to provide more precise population indices for the Pacific Coast band-tailed pigeon (P. f. monilis) and augment the BBS to index the Interior or “Four Corners” population (P. f. fasciata). We calculated statistical power, the probability of detecting population change given that a change exists, and analyzed survey data to investigate the effect of route length, survey repetition, and sample size. Sample sizes of 50 sites or routes yielded corresponding powers of 99% for WAORMS, 54% for WACC, and 30% for Pacific BBS, to detect a 10% annual change over a 5-year period (a = 0.10). Route length and repetition of surveys had little impact on power. Mineral-site surveys provide the greatest potential to monitor breeding populations and detect short-term trends in the Pacific Coast population. New survey techniques are needed for the Interior band-tailed pigeon.

Post-precipitation bias in band-tailed pigeon surveys conducted at mineral sites

Abstract Many animal surveys to estimate populations or index trends include protocol prohibiting counts during rain but fail to address effects of rainfall preceding the count. Prior research on Pacific Coast band-tailed pigeons (Patagioenas fasciata monilis) documented declines in use of mineral sites during rainfall. We hypothesized that prior precipitation was associated with a short-term increase in use of mineral sites following rain. We conducted weekly counts of band-tailed pigeons at 19 Pacific Northwest mineral sites in 2001 and 20 sites in 2002. Results from regression analysis indicated higher counts ≤2 days after rain (11.31 ± 5.00% [x̄ ± SE]) compared to ≥3 days. Individual index counts conducted ≤2 days after rain were biased high, resulting in reduced ability to accurately estimate population trends. Models of band-tailed pigeon visitation rates throughout the summer showed increased mineral-site counts during both June and August migration periods, relative to the July breeding period. Our research supported previous studies recommending that mineral-site counts used to index the band-tailed pigeon population be conducted during July. We further recommend conducting counts ≥3 days after rain to avoid weather-related bias in index estimation. The design of other population sampling strategies that rely on annual counts should consider the influence of aberrant weather not only coincident with but also preceding surveys if weather patterns are thought to influence behavior or detection probability of target species.

A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (Rallus obsoletus obsoletus)

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.

Linking Landscape Characteristics to Mineral Site Use by Band-Tailed Pigeons in Western Oregon: Coarse-Filter Conservation with Fine-Filter Tuning

Abstract Mineral sites are scarce resources of high ion concentration used heavily by the Pacific Coast subpopulation of band-tailed pigeons. Over 20% of all known mineral sites used by band-tailed pigeons in western Oregon, including all hot springs, have been abandoned. Prior investigations have not analyzed stand or landscape level habitat composition in relation to band-tailed pigeon use of mineral sites. We used logistic regression models to evaluate the influence of habitat types, identified from Gap Analysis Program (GAP) products at two spatial scales, on the odds of mineral site use in Oregon (n = 69 currently used and 20 historically used). Our results indicated that the odds of current use were negatively associated with non-forested terrestrial and private land area around mineral sites. Similarly, the odds of current mineral site use were positively associated with forested and special status (GAP stewardship codes 1 and 2) land area. The most important variable associated with the odds of mineral site use was the amount of non-forested land cover at either spatial scale. Our results demonstrate the utility of meso-scale geographic information designed for regional, coarse-filter approaches to conservation in fine-filter investigation of wildlife-habitat relationships. Adjacent landcover and ownership status explain the pattern of use for known mineral sites in western Oregon. In order for conservation and management activities for band-tailed pigeons to be successful, mineral sites need to be addressed as important and vulnerable resources. Management of band-tailed pigeons should incorporate the potential for forest management activities and land ownership patterns to influence the risk of mineral site abandonment.

Dietary mercury exposure to endangered California Clapper Rails in San Francisco Bay

California Clapper Rails (Rallus longirostris obsoletus) are an endangered waterbird that forage in tidal-marsh habitats that pose risks from mercury exposure. We analyzed total mercury (Hg) in six macro-invertebrate and one fish species representing Clapper Rail diets from four tidal-marshes in San Francisco Bay, California. Mercury concentrations among individual taxa ranged from lowest at Colma Creek (mean range: 0.09-0.2 μg/g dw) to highest at Cogswell (0.2-0.7), Laumeister (0.2-0.9) and Arrowhead Marshes (0.3-1.9). These spatial patterns for Hg matched patterns reported previously in Clapper Rail blood from the same four marshes. Over 25% of eastern mudsnails (Ilyanassa obsolete) and staghorn sculpin (Leptocottus armatus) exceeded dietary Hg concentrations (ww) often associated with avian reproductive impairment. Our results indicate that Hg concentrations vary considerably among tidal-marshes and diet taxa, and Hg concentrations of prey may provide an appropriate proxy for relative exposure risk for Clapper Rails.