Application of multiple-population viability analysis to evaluate species recovery alternatives.

Population viability analysis (PVA) is a powerful conservation tool, but it remains impractical for many species, particularly species with multiple, broadly distributed populations for which collecting suitable data can be challenging. A recently developed method of multiple-population viability analysis (MPVA), however, addresses many limitations of traditional PVA. We built on previous development of MPVA for Lahontan cutthroat trout (LCT) (Oncorhynchus clarkii henshawi), a species listed under the U.S. Endangered Species Act, that is distributed broadly across habitat fragments in the Great Basin (U.S.A.). We simulated potential management scenarios and assessed their effects on population sizes and extinction risks in 211 streams, where LCT exist or may be reintroduced. Conservation populations (those managed for recovery) tended to have lower extinction risks than nonconservation populations (mean = 19.8% vs. 52.7%), but not always. Active management or reprioritization may be warranted in some cases. Eliminating non-native trout had a strong positive effect on overall carrying capacities for LCT populations but often did not translate into lower extinction risks unless simulations also reduced associated stochasticity (to the mean for populations without non-native trout). Sixty fish or 5-10 fish/km was the minimum reintroduction number and density, respectively, that provided near-maximum reintroduction success. This modeling framework provided crucial insights and empirical justification for conservation planning and specific adaptive management actions for this threatened species. More broadly, MPVA is applicable to a wide range of species exhibiting geographic rarity and limited availability of abundance data and greatly extends the potential use of empirical PVA for conservation assessment and planning.

Aplicación de un Análisis de Viabilidad Multi-Poblacional para Evaluar Alternativas de Recuperación de Especies Resumen El análisis de viabilidad poblacional (AVP) es una herramienta poderosa de conservación, que desafortunadamente sigue siendo impráctica para muchas especies, en particular para aquellas con poblaciones múltiples distribuidas ampliamente, para las cuales puede ser un reto la recolección de datos apropiados. Sin embargo, un método recientemente desarrollado de análisis de viabilidad multi-poblacional (AVMP) aborda muchas de las limitaciones de los AVP tradicionales. Partimos del desarrollo previo de un AVMP para la trucha degollada lahontana (LCT, en inglés) (Oncorhynchus clarkii henshawi), una especie enlistada bajo el Acta de Especies en Peligro de los Estados Unidos, la cual está distribuida ampliamente a lo largo de los fragmentos de hábitat que se encuentran en la Gran Cuenca (E.U.A.). Simulamos los escenarios potenciales de manejo y evaluamos sus efectos sobre el tamaño de las poblaciones y los riesgos de extinción en 211 arroyos en donde existe la LCT o en donde podría ser reintroducida. Las poblaciones de conservación (aquellas manejadas para su recuperación) tuvieron una tendencia hacia un riesgo de extinción más bajo que las poblaciones sin conservación (media = 19.8% vs. 52.7%), pero no en todos los casos. El manejo activo o la repriorización podrían ser justificadas en algunos casos. La eliminación de las truchas no nativas tuvo un fuerte efecto positivo generalizado sobre las capacidades de carga de las poblaciones de LCT, aunque frecuentemente esto no se transformó en un riesgo de extinción más bajo a menos que las simulaciones también redujeran la estocasticidad asociada (para la media de las poblaciones sin truchas no nativas). Para proporcionar un éxito de reintroducción cercano al máximo, el número mínimo de reintroducción debió ser de 60 peces o una densidad de 5-10 peces/km. Este marco de trabajo para el modelo proporcionó una percepción muy importante y una justificación empírica para la planeación de la conservación y para las acciones de manejo adaptativo para esta especie amenazada. En términos más generales, el AVMP puede aplicarse a una gama amplia de especies que exhiban una rareza geográfica y una disponibilidad limitada de datos de abundancia, además de que expande enormemente el uso potencial de AVP empíricos para la evaluación y planeación de la conservación.

Hierarchical multi-population viability analysis.

Population viability analysis (PVA) uses concepts from theoretical ecology to provide a powerful tool for quantitative estimates of population dynamics and extinction risks. However, conventional statistical PVA requires long-term data from every population of interest, whereas many species of concern exist in multiple isolated populations that are only monitored occasionally. We present a hierarchical multi-population viability analysis model that increases inference power from sparse data by sharing information among populations to assess extinction risks while accounting for incomplete detection and sampling biases with explicit observation and sampling sub-models. We present a case study in which we customized this model for historical population monitoring data (1985-2015) from federally threatened Lahontan cutthroat trout populations in the Great Basin, USA. Data were counts of fish captured during backpack electrofishing surveys from locations associated with 155 isolated populations. Some surveys (25%) included multi-pass removal sampling, which provided valuable information about capture efficiency. GIS and remote sensing were used to estimate August stream temperatures, peak flows, and riparian vegetation condition in each population each year. Field data were used to derive an annual index of nonnative trout densities. Results indicated that population growth rates were higher in colder streams and that nonnative trout reduced carrying capacities of native trout. Extinction risks increased with more environmental stochasticity and were also related to population extent, water temperatures, and nonnative densities. We developed a graphical user interface to interact with the fitted model results and to simulate future habitat scenarios and management actions to assess their influence on extinction risks in each population. Hierarchical multi-population viability analysis bridges the gap between site-level field observations and population-level processes, making effective use of existing datasets to support management decisions with robust estimates of population dynamics, extinction risks, and uncertainties.

Mercury and drought along the lower Carson River, Nevada: IV. Snowy egret post-fledging dispersal, timing of migration and survival, 2002-2004.

This telemetry study is an extension of our 1997-2006 research on historical mercury contamination on snowy egrets (Egretta thula) up to ~ 20 days of age. Findings from initial studies at the mercury-contaminated Carson River colony at Lahontan Reservoir (LR) and a similar-sized reference (REF) colony on the Humboldt River included mercury-related physiological, biochemical, histopathological and reproductive effects up to ~20 days of age; with poor water years (2000-04), i.e., reduced prey availability, exacerbating effects. Herein, we compare timing of dispersal and migration at LR vs. REF, but the primary question now addressed is "whether survival of young mercury-exposed snowy egrets from LR would be further compromised beyond ~20 days of age? " Based upon telemetry signals until 90-110 days of age (including dead bird counts and survival rate estimates), we conclude that mercury did not further compromise survival. Dead bird counts and survival rate estimates included time in the colony when fed by adults, plus the critical period when young dispersed from the colony to forage independently. The extended drought during this 3-year study was most critical in 2002 when production of ~20d old egrets at LR was only 0.24 young/nest. In 2002, survival rates were low at both colonies and we documented the highest counts of dead egrets for both colonies. We suggest the losses in 2002 beyond 20 days of age were more a function of prey availability influenced by drought than exposure to mercury, especially at LR, because higher mercury concentrations, higher survival rates and fewer dead birds were documented at LR in 2003 when water conditions improved. Furthermore, total mercury (THg) in blood in 2003 was more than double 2002 (geometric mean, 3.39 vs 1.47µg/g wet weight (ww). This higher THg exposure at LR in 2003 was associated with a redistribution of parent and post-dispersal feeding activities upstream (where there was higher mercury from historic mining) related to slightly improved water levels. When comparing the 3-year telemetry findings based upon ~20d old young at LR (blood THg, geo. means 1.47, 3.39 and 1.89µg/g ww), we found no evidence that age at dispersal, Julian date at dispersal, timing of migration, or pre-migration survival (~20 to ~100 days post-hatch) were adversely affected by elevated mercury.

Connectivity and conditional models of access and abundance of species in stream networks.

Barriers to passage of aquatic organisms at stream road crossings are a major cause of habitat fragmentation in stream networks. Accordingly, large investments have been made to restore passage at these crossings, but often without estimation of population-level benefits. Here, we describe a broad-scale approach to quantifying the effectiveness of passage restoration in terms interpretable at population levels, namely numbers of fish and length of stream gained through restoration, by sampling abundance in a study design that accounts for variable biogeographic species pools, variable stream and barrier configurations, and variable probabilities of capture and detectability for multiple species. We modified an existing zero-inflated negative-binomial model to estimate the probability of site access, abundance conditional on access, and capture probability of individual fish. Therein, we modeled probability of access as a function of gradient, stream road-crossing type, and downstream access by fish simultaneously with a predictive model for abundance at sites accessible to fish. Results indicated that replacement of barriers with new crossing designs intended to allow for greater movement was associated with dramatically higher probability of access for all fishes, including migratory Pacific salmon, trout, sculpin, and lamprey. Conversely, existing non-replaced crossings negatively impacted fish distributions. Assuming no downstream constraints on access, we estimated the potential length of stream restored by the program ranged between 7.33 (lamprey) and 15.28 km (small coastal cutthroat and rainbow trout). These contributions represented a fraction of the total length available upstream (187 km) of replaced crossings. When limited ranges of species were considered, the estimated contributions of culvert replacement were reduced (1.65-km range, for longnose dace to 12.31 km for small coastal cutthroat and rainbow trout). Numbers of fish contributed ranged from less than 500 (longnose dace) to greater than 100 000 (sculpin). Although our framework can address the question of effectiveness in a broad array of stream and crossing configurations, much stronger inferences would be possible if future restoration efforts were designed to address the limitations we encountered in this study, particularly the lack of available information on crossings and species presence prior to restoration, and nonrandom selection of crossings to be replaced.

Using multilevel spatial models to understand salamander site occupancy patterns after wildfire.

Studies of the distribution of elusive forest wildlife have suffered from the confounding of true presence with the uncertainty of detection. Occupancy modeling, which incorporates probabilities of species detection conditional on presence, is an emerging approach for reducing observation bias. However, the current likelihood modeling framework is restrictive for handling unexplained sources of variation in the response that may occur when there are dependence structures such as smaller sampling units that are nested within larger sampling units. We used multilevel Bayesian occupancy modeling to handle dependence structures and to partition sources of variation in occupancy of sites by terrestrial salamanders (family Plethodontidae) within and surrounding an earlier wildfire in western Oregon, USA. Comparison of model fit favored a spatial N-mixture model that accounted for variation in salamander abundance over models that were based on binary detection/non-detection data. Though catch per unit effort was higher in burned areas than unburned, there was strong support that this pattern was due to a higher probability of capture for individuals in burned plots. Within the burn, the odds of capturing an individual given it was present were 2.06 times the odds outside the burn, reflecting reduced complexity of ground cover in the burn. Ther was weak support that true occupancy was lower within the burned area. While the odds of occupancy in the burn were 0.49 times the odds outside the burn among the five species, the magnitude of variation attributed to the burn was small in comparison to variation attributed to other landscape variables and to unexplained, spatially autocorrelated random variation. While ordinary occupancy models may separate the biological pattern of interest from variation in detection probability when all sources of variation are known, the addition of random effects structures for unexplained sources of variation in occupancy and detection probability may often more appropriately represent levels of uncertainty.

Using occupancy models to understand the distribution of an amphibian pathogen, Batrachochytrium dendrobatidis.

Batrachochytrium dendrobatidis is a fungal pathogen that is receiving attention around the world for its role in amphibian declines. Study of its occurrence patterns is hampered by false negatives: the failure to detect the pathogen when it is present. Occupancy models are a useful but currently underutilized tool for analyzing detection data when the probability of detecting a species is <1. We use occupancy models to evaluate hypotheses concerning the occurrence and prevalence of B. dendrobatidis and discuss how this application differs from a conventional occupancy approach. We found that the probability of detecting the pathogen, conditional on presence of the pathogen in the anuran population, was related to amphibian development stage, day of the year, elevation, and human activities. Batrachochytrium dendrobatidis was found throughout our study area but was only estimated to occur in 53.4% of 78 populations of native amphibians and 66.4% of 40 populations of nonnative Rana catesbeiana tested. We found little evidence to support any spatial hypotheses concerning the probability that the pathogen occurs in a population, but did find evidence of some taxonomic variation. We discuss the interpretation of occupancy model parameters, when, unlike a conventional occupancy application, the number of potential samples or observations is finite.

Widespread occurrence of the chytrid fungus Batrachochytrium dendrobatidis on Oregon spotted frogs (Rana pretiosa).

The pathogen Batrachochytrium dendrobatidis (Bd) has been associated with amphibian declines in multiple continents, including western North America. We investigated Bd prevalence in Oregon spotted frog (Rana pretiosa), a species that has declined across its range in the Pacific Northwest. Polymerase chain reaction analysis of skin swabs indicated that Bd was prevalent within populations (420 of 617 juvenile and adults) and widespread among populations (36 of 36 sites) where we sampled R. pretiosa in Oregon and Washington. We rarely detected Bd in R. pretiosa larvae (2 of 72). Prevalence of Bd in postmetamorphic R. pretiosa was inversely related to frog size. We found support for an interactive effect of elevation and sampling date on Bd: prevalence of Bd generally increased with date, but this effect was more pronounced at lower elevations. We also found evidence that the body condition of juvenile R. pretiosa with Bd decreased after their first winter. Our data indicate that some Oregon spotted frog populations are currently persisting with relatively high Bd prevalence, but the risk posed by Bd is unknown.

Carryover aquatic effects on survival of metamorphic frogs during pond emigration.

In organisms with complex life cycles, physiological stressors during early life stages may have fitness-level impacts that are delayed into later stages or habitats. We tested the hypothesis that body size and date of metamorphosis, which are highly responsive to aquatic stressors, influence post-metamorphic survival and movement patterns in the terrestrial phase of an ephemeral pond-breeding frog by examining these traits in two populations of northern red-legged frogs (Rana aurora aurora). To increase variation of body size at metamorphosis, we manipulated food availability for 314 of 1045 uniquely marked tadpoles and estimated the probability that frogs survived and emigrated using concentric rings of drift fencing surrounding ponds and Bayesian capture-recapture modeling. The odds of surviving and emigrating from the ponds to the innermost drift fences, approximately 12 m, increased by factors of 2.20 (95% credibility intervals 1.39-4.23) and 2.54 (0.94-4.91) with each millimeter increase in snout-vent length and decreased by factors of 0.91 (0.85-0.96) and 0.89 (0.80-1.00) with each day's delay in metamorphosis for the two ponds. The odds of surviving and moving to the next ring of fencing, 12 m to approximately 40 m from the ponds, increased by a factor of 1.20 (0.45-4.06) with each millimeter increase in size. Our results demonstrated that body size and timing of metamorphosis relate strongly to the performance of newly metamorphosed frogs during their initial transition into terrestrial habitat. Carryover effects of aquatic stressors that reduce size and delay metamorphosis may have population-level impacts that are not expressed until terrestrial stages. Since changes in both aquatic and terrestrial systems are implicated in many amphibian declines, quantifying both immediate and delayed effects of stressors on demographic rates is critical to sound management.

Effects of El Niño on distribution and reproductive performance of Black Brant.

Climate in low-latitude wintering areas may influence temperate and high-latitude breeding populations of birds, but demonstrations of such relationships have been rare because of difficulties in linking wintering with breeding populations. We used long-term aerial surveys in Mexican wintering areas and breeding areas in Alaska, USA, to assess numbers of Black Brant (Branta bernicla nigricans; hereafter brant) on their principal wintering and breeding area in El Niño and non-El Niño years. We used Pollock's robust design to directly estimate probability of breeding and apparent annual survival of individually marked brant at the Tutakoke River (TR) colony, Alaska, in each year between 1988 and 2001. Fewer brant wintered in Mexico during every El Niño event since 1965. Fewer brant were observed on the principal breeding area following each El Niño since surveys began in 1985. Probability of breeding was negatively related to January sea surface temperature along the subtropical coast of North America during the preceding winter. Between 23% (five-year-olds or older) and 30% (three-year-olds) fewer brant nested in 1998 following the strong El Niño event in the winter of 1997-1998 than in non-El Niño years. This finding is consistent with life history theory, which predicts that longer-lived species preserve adult survival at the expense of reproduction. Oceanographic conditions off Baja California, apparently by their effect on Zostera marina (eelgrass), strongly influence winter distribution of brant geese and their reproduction (but not survival), which in turn affects ecosystem dynamics in Alaska.