Global forest loss disproportionately erodes biodiversity in intact landscapes.

Global biodiversity loss is a critical environmental crisis, yet the lack of spatial data on biodiversity threats has hindered conservation strategies. Theory predicts that abrupt biodiversity declines are most likely to occur when habitat availability is reduced to very low levels in the landscape (10-30%). Alternatively, recent evidence indicates that biodiversity is best conserved by minimizing human intrusion into intact and relatively unfragmented landscapes. Here we use recently available forest loss data to test deforestation effects on International Union for Conservation of Nature Red List categories of extinction risk for 19,432 vertebrate species worldwide. As expected, deforestation substantially increased the odds of a species being listed as threatened, undergoing recent upgrading to a higher threat category and exhibiting declining populations. More importantly, we show that these risks were disproportionately high in relatively intact landscapes; even minimal deforestation has had severe consequences for vertebrate biodiversity. We found little support for the alternative hypothesis that forest loss is most detrimental in already fragmented landscapes. Spatial analysis revealed high-risk hot spots in Borneo, the central Amazon and the Congo Basin. In these regions, our model predicts that 121-219 species will become threatened under current rates of forest loss over the next 30 years. Given that only 17.9% of these high-risk areas are formally protected and only 8.9% have strict protection, new large-scale conservation efforts to protect intact forests are necessary to slow deforestation rates and to avert a new wave of global extinctions.

A new parameterization for integrated population models to document amphibian reintroductions.

Managers are increasingly implementing reintroduction programs as part of a global effort to alleviate amphibian declines. Given uncertainty in factors affecting populations and a need to make recurring decisions to achieve objectives, adaptive management is a useful component of these efforts. A major impediment to the estimation of demographic rates often used to parameterize and refine decision-support models is that life-stage-specific monitoring data are frequently sparse for amphibians. We developed a new parameterization for integrated population models to match the ecology of amphibians and capitalize on relatively inexpensive monitoring data to document amphibian reintroductions. We evaluate the capability of this model by fitting it to Oregon spotted frog (Rana pretiosa) monitoring data collected from 2007 to 2014 following their reintroduction within the Klamath Basin, Oregon, USA. The number of egg masses encountered and the estimated adult and metamorph abundances generally increased following reintroduction. We found that survival probability from egg to metamorph ranged from 0.01 in 2008 to 0.09 in 2009 and was not related to minimum spring temperatures, metamorph survival probability ranged from 0.13 in 2010-2011 to 0.86 in 2012-2013 and was positively related to mean monthly temperatures (logit-scale slope = 2.37), adult survival probability was lower for founders (0.40) than individuals recruited after reintroduction (0.56), and the mean number of egg masses per adult female was 0.74. Our study is the first to test hypotheses concerning Oregon spotted frog egg-to-metamorph and metamorph-to-adult transition probabilities in the wild and document their response at multiple life stages following reintroduction. Furthermore, we provide an example to illustrate how the structure of our integrated population model serves as a useful foundation for amphibian decision-support models within adaptive management programs. The integration of multiple, but related, data sets has an advantage of being able to estimate complex ecological relationships across multiple life stages, offering a modeling framework that accommodates uncertainty, enforces parsimony, and ensures all model parameters can be confronted with monitoring data.

Effects of salinization on the occurrence of a long-lived vertebrate in a desert river.

The lower Pecos River located in the southwest USA, is a naturally saline river system that has been significantly altered in relatively recent years. Climate change, coupled with anthropogenic disturbances such as dam construction have led to portions of the river becoming more susceptible to increased salinization and declines in water quality. These alterations have been documented to be detrimental to multiple freshwater communities; however, there is a lack of knowledge on how these alterations influence long-lived species in the river, such as freshwater turtles, where the effects can appear over dramatically different temporal scales. The Rio Grande Cooter (Pseudemys gorzugi) is a species of concern known to occur in the Pecos River. To understand the current distribution and habitat requirements for P. gorzugi in the Pecos River, we used a single-season, single-species occupancy modeling framework to estimate occurrence while accounting for the sampling process. Day of year, water surface area, and water visibility had the greatest influence on the ability to detect the species given a sampling unit is occupied. Conductivity (a measure of salinity) had the greatest influence on the occupancy probability for the species, where sites with higher conductivity coincided with lower occupancy probabilities. This study indicates that increased salinization on the lower Pecos River is a cause for concern regarding freshwater turtle populations within the Chihuahuan Desert.

Space-for-time is not necessarily a substitution when monitoring the distribution of pelagic fishes in the San Francisco Bay-Delta.

Occupancy models are often used to analyze long-term monitoring data to better understand how and why species redistribute across dynamic landscapes while accounting for incomplete capture. However, this approach requires replicate detection/non-detection data at a sample unit and many long-term monitoring programs lack temporal replicate surveys. In such cases, it has been suggested that surveying subunits within a larger sample unit may be an efficient substitution (i.e., space-for-time substitution). Still, the efficacy of fitting occupancy models using a space-for-time substitution has not been fully explored and is likely context dependent. Herein, we fit occupancy models to Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys) catch data collected by two different monitoring programs that use the same sampling gear in the San Francisco Bay-Delta, USA. We demonstrate how our inferences concerning the distribution of these species changes when using a space-for-time substitution. Specifically, we found the probability that a sample unit was occupied was much greater when using a space-for-time substitution, presumably due to the change in the spatial scale of our inferences. Furthermore, we observed that as the spatial scale of our inferences increased, our ability to detect environmental effects on system dynamics was obscured, which we suspect is related to the tradeoffs associated with spatial grain and extent. Overall, our findings highlight the importance of considering how the unique characteristics of monitoring programs influences inferences, which has broad implications for how to appropriately leverage existing long-term monitoring data to understand the distribution of species.

Impact of Mycoplasma ovipneumoniae on juvenile bighorn sheep (Ovis canadensis) survival in the northern Basin and Range ecosystem.

Determining the demographic impacts of wildlife disease is complex because extrinsic and intrinsic drivers of survival, reproduction, body condition, and other factors that may interact with disease vary widely. Mycoplasma ovipneumoniae infection has been linked to persistent mortality in juvenile bighorn sheep (Ovis canadensis), although mortality appears to vary widely across subspecies, populations, and outbreaks. Hypotheses for that variation range from interactions with nutrition, population density, genetic variation in the pathogen, genetic variation in the host, and other factors. We investigated factors related to survival of juvenile bighorn sheep in reestablished populations in the northern Basin and Range ecosystem, managed as the formerly-recognized California subspecies (hereafter, "California lineage"). We investigated whether survival probability of 4-month juveniles would vary by (1) presence of M. ovipneumoniae-infected or exposed individuals in populations, (2) population genetic diversity, and (3) an index of forage suitability. We monitored 121 juveniles across a 3-year period in 13 populations in southeastern Oregon and northern Nevada. We observed each juvenile and GPS-collared mother semi-monthly and established 4-month capture histories for the juvenile to estimate survival. All collared adult females were PCR-tested at least once for M. ovipneumoniae infection. The presence of M. ovipneumoniae-infected juveniles was determined by observing juvenile behavior and PCR-testing dead juveniles. We used a known-fate model with different time effects to determine if the probability of survival to 4 months varied temporally or was influenced by disease or other factors. We detected dead juveniles infected with M. ovipneumoniae in only two populations. Derived juvenile survival probability at four months in populations where infected juveniles were not detected was more than 20 times higher. Detection of infected adults or adults with antibody levels suggesting prior exposure was less predictive of juvenile survival. Survival varied temporally but was not strongly influenced by population genetic diversity or nutrition, although genetic diversity within most study area populations was very low. We conclude that the presence of M. ovipneumoniae can cause extremely low juvenile survival probability in translocated bighorn populations of the California lineage, but found little influence that genetic diversity or nutrition affect juvenile survival. Yet, after the PCR+ adult female in one population died, subsequent observations found 11 of 14 ( 79%) collared adult females had surviving juveniles at 4-months, suggesting that targeted removals of infected adults should be evaluated as a management strategy.

Elk population dynamics when carrying capacities vary within and among herds.

Population and land management relies on understanding population regulation and growth, which may be impacted by variation in population growth parameters within and among populations. We explored the interactions between variation in carrying capacity (K), intrinsic population growth rate (r), and strength of density dependence (ß) within and among elk (Cervus elaphus) herds in a small part of the geographic range of the species. We also estimated stochastic fluctuations in abundance around K for each herd. We fit linear Ricker growth models using Bayesian statistics to seven time series of elk population survey data. Our results indicate that K and ß varied among herds, and that r and ß varied temporally within herds. We also found that herds with smaller K had less stochastic fluctuation in abundances around K, but higher temporal variation in ß within herds. Population regulation and the rate of return to the equilibrium abundance is often understood in terms of ß, but ecological populations are dynamic systems, and temporal variation in population growth parameters may also influence regulation. Population models which accommodate variation both within and among herds in population growth parameters are necessary, even in mild climates, to fully understand population dynamics and manage populations.

Comparison of hoop-net trapping and visual surveys to monitor abundance of the Rio Grande cooter (Pseudemys gorzugi).

Abundance estimates play an important part in the regulatory and conservation decision-making process. It is important to correct monitoring data for imperfect detection when using these data to track spatial and temporal variation in abundance, especially in the case of rare and elusive species. This paper presents the first attempt to estimate abundance of the Rio Grande cooter (Pseudemys gorzugi) while explicitly considering the detection process. Specifically, in 2016 we monitored this rare species at two sites along the Black River, New Mexico via traditional baited hoop-net traps and less invasive visual surveys to evaluate the efficacy of these two sampling designs. We fitted the Huggins closed-capture estimator to estimate capture probabilities using the trap data and distance sampling models to estimate detection probabilities using the visual survey data. We found that only the visual survey with the highest number of observed turtles resulted in similar abundance estimates to those estimated using the trap data. However, the estimates of abundance from the remaining visual survey data were highly variable and often underestimated abundance relative to the estimates from the trap data. We suspect this pattern is related to changes in the basking behavior of the species and, thus, the availability of turtles to be detected even though all visual surveys were conducted when environmental conditions were similar. Regardless, we found that riverine habitat conditions limited our ability to properly conduct visual surveys at one site. Collectively, this suggests visual surveys may not be an effective sample design for this species in this river system. When analyzing the trap data, we found capture probabilities to be highly variable across sites and between age classes and that recapture probabilities were much lower than initial capture probabilities, highlighting the importance of accounting for detectability when monitoring this species. Although baited hoop-net traps seem to be an effective sampling design, it is important to note that this method required a relatively high trap effort to reliably estimate abundance. This information will be useful when developing a larger-scale, long-term monitoring program for this species of concern.

Vegetation changes associated with a population irruption by Roosevelt elk.

Interactions between large herbivores and their food supply are central to the study of population dynamics. We assessed temporal and spatial patterns in meadow plant biomass over a 23-year period for meadow complexes that were spatially linked to three distinct populations of Roosevelt elk (Cervus elaphus roosevelti) in northwestern California. Our objectives were to determine whether the plant community exhibited a tolerant or resistant response when elk population growth became irruptive. Plant biomass for the three meadow complexes inhabited by the elk populations was measured using Normalized Difference Vegetation Index (NDVI), which was derived from Landsat 5 Thematic Mapper imagery. Elk populations exhibited different patterns of growth through the time series, whereby one population underwent a complete four-stage irruptive growth pattern while the other two did not. Temporal changes in NDVI for the meadow complex used by the irruptive population suggested a decline in forage biomass during the end of the dry season and a temporal decline in spatial variation of NDVI at the peak of plant biomass in May. Conversely, no such patterns were detected in the meadow complexes inhabited by the nonirruptive populations. Our findings suggest that the meadow complex used by the irruptive elk population may have undergone changes in plant community composition favoring plants that were resistant to elk grazing.