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At least 271 records · Page 15Linked to original sources
USGS2018

A new tool for studying waterfowl immune and metabolic responses: Molecular level analysis using kinome profiling

Here, we describe the design of an Anas‐ specific kinome peptide array that can be used to study the immunometabolic responses of mallard and American black duck to pathogens, contaminants, and environmental stress. The peptide arrays contain 2,642 unique phosphorylate‐able peptide sequences representing 1,900 proteins. These proteins cover a wide array of metabolic and immunological processes, and 758 Gene Ontology Biological processes are statistically significantly represented on the duck peptide array of those 164 contain the term “metabolic” and 25 “immune.” In addition, we conducted a comparison of mallard to American black duck at a genetic and proteomic level. Our results show a significant genomic and proteomic overlap between these two duck species, so that we have designed a cross‐reactive peptide array capable of studying both species. This is the first reported development of a wildlife species‐specific kinome peptide array.

Ecology and Evolution↗
USGS2018

Local factors associated with on‐host flea distributions on prairie dog colonies

Outbreaks of plague, a flea‐vectored bacterial disease, occur periodically in prairie dog populations in the western United States. In order to understand the conditions that are conducive to plague outbreaks and potentially predict spatial and temporal variations in risk, it is important to understand the factors associated with flea abundance and distribution that may lead to plague outbreaks. We collected and identified 20,041 fleas from 6,542 individual prairie dogs of four different species over a 4‐year period along a latitudinal gradient from Texas to Montana. We assessed local climate and other factors associated with flea prevalence and abundance, as well as the incidence of plague outbreaks. Oropsylla hirsuta , a prairie dog specialist flea, and Pulex simulans, a generalist flea species, were the most common fleas found on our pairs. High elevation pairs in Wyoming and Utah had distinct flea communities compared with the rest of the study pairs. The incidence of prairie dogs with Yersinia pestis detections in fleas was low ( n = 64 prairie dogs with positive fleas out of 5,024 samples from 4,218 individual prairie dogs). The results of our regression models indicate that many factors are associated with the presence of fleas. In general, flea abundance (number of fleas on hosts) is higher during plague outbreaks, lower when prairie dogs are more abundant, and reaches peak levels when climate and weather variables are at intermediate levels. Changing climate conditions will likely affect aspects of both flea and host communities, including population densities and species composition, which may lead to changes in plague dynamics. Our results support the hypothesis that local conditions, including host, vector, and environmental factors, influence the likelihood of plague outbreaks, and that predicting changes to plague dynamics under climate change scenarios will have to consider both host and vector responses to local factors.

Ecology and Evolution↗
USGS2018

Estimating distemper virus dynamics among wolves and grizzly bears using serology and Bayesian state‐space models

Many parasites infect multiple hosts, but estimating the transmission across host species remains a key challenge in disease ecology. We investigated the within and across host species dynamics of canine distemper virus (CDV) in grizzly bears ( Ursus arctos ) and wolves ( Canis lupus ) of the Greater Yellowstone Ecosystem (GYE). We hypothesized that grizzly bears may be more likely to be exposed to CDV during outbreaks in the wolf population because grizzly bears often displace wolves while scavenging carcasses. We used serological data collected from 1984 to 2014 in conjunction with Bayesian state‐space models to infer the temporal dynamics of CDV. These models accounted for the unknown timing of pathogen exposure, and we assessed how different testing thresholds and the potential for testing errors affected our conclusions. We identified three main CDV outbreaks (1999, 2005, and 2008) in wolves, which were more obvious when we used higher diagnostic thresholds to qualify as seropositive. There was some evidence for increased exposure rates in grizzly bears in 2005, but the magnitude of the wolf effect on bear exposures was poorly estimated and depended upon our prior distributions. Grizzly bears were exposed to CDV prior to wolf reintroduction and during time periods outside of known wolf outbreaks, thus wolves are only one of several potential routes for grizzly bear exposures. Our modeling approach accounts for several of the shortcomings of serological data and is applicable to many wildlife disease systems, but is most informative when testing intervals are short. CDV circulates in a wide range of carnivore species, but it remains unclear whether the disease persists locally within the GYE carnivore community or is periodically reintroduced from distant regions with larger host populations.

Ecology and Evolution↗
USGS2018

Cytonuclear discordance in the Florida Everglades invasive Burmese python (Python bivittatus) population reveals possible hybridization with the Indian python (P. molurus)

The invasive Burmese python ( Python bivittatus ) has been reproducing in the Florida Everglades since the 1980s. These giant constrictor snakes have caused a precipitous decline in small mammal populations in southern Florida following escapes or releases from the commercial pet trade. To better understand the invasion pathway and genetic composition of the population, two mitochondrial (mtDNA) loci across 1,398 base pairs were sequenced on 426 snakes and 22 microsatellites were assessed on 389 snakes. Concatenated mtDNA sequences produced six haplotypes with an average nucleotide and haplotype diversity of π = 0.002 and h = 0.097, respectively. Samples collected in Florida from morphologically identified P. bivittatus snakes were similar to published cytochrome oxidase 1 and cytochrome b sequences from both P. bivittatus and Python molurus and were highly divergent (genetic distances of 5.4% and 4.3%, respectively). The average number of microsatellite alleles and expected heterozygosity were N A = 5.50 and H E = 0.60, respectively. Nuclear Bayesian assignment tests supported two genetically distinct groups and an admixed group, not geographically differentiated. The effective population size ( N E = 315.1) was lower than expected for a population this large, but reflected the low genetic diversity overall. The patterns of genetic diversity between mtDNA and microsatellites were disparate, indicating nuclear introgression of separate mtDNA lineages corresponding to cytonuclear discordance. The introgression likely occurred prior to the invasion, but genetic information on the native range and commercial trade is needed for verification. Our finding that the Florida python population is comprised of distinct lineages suggests greater standing variation for adaptation and the potential for broader areas of suitable habitat in the invaded range.

Florida↗
USGS2019

Interactive effects of severe drought and grazing on the life history cycle of a bioindicator species on the edge of its range

Recurring drought and grazing are ecological drivers of semi-arid grasslands on the Southern High Plains, USA; however, ecological drivers are currently undergoing human-induced alterations, which likely have implications for wildlife. We used the lesser prairie-chicken (Tympanuchus pallidicinctus), an iconic grouse species that exhibits a boom-bust life history strategy, on the Southern High Plains, USA, as a bioindicator of main and interactive effects of severe drought and grazing. This region encompasses the southern and westernmost part of the lesser prairie-chicken range and experienced the worst drought on record in 2011. We surveyed lesser prairie-chicken leks (i.e., communal breeding grounds) across 12 years that represented 7 years before the 2011 drought ("pre-drought") and 4 years during and following the 2011 drought ("post-drought"). Grazing was annually managed with the objective of achieving ≤50% utilization of above-ground vegetation biomass. We used lek (n = 49) count data and covariates of weather and managed grazing to: 1) estimate long-term lesser prairie-chicken abundance and compare abundance pre-drought and post-drought; 2) examine annually the influence of drought (modified Palmer Drought Index), temperature, the number of days with maximum temperature >75th percentile, and precipitation on long-term lesser prairie-chicken survival and recruitment; and 3) assess and compare the influence of grazing on lesser prairie-chickens pre-drought and post-drought. Lesser prairie-chicken abundance was nearly 7 times greater pre-drought than post-drought, and population declines were attributed to decreased survival and recruitment. The number of days with temperature >75th percentile had the greatest effect, particularly on recruitment. The population exhibited a substantial bust during 2011 and 2012 without a boom to recover in 4 post-drought years. Adaptive grazing positively influenced the population pre-drought, but had no effects post-drought. Results suggest that the severe drought in 2011 may have been beyond the range of environmental conditions to which lesser prairie-chickens, and likely other species, have adapted. Land management practices, such as grazing, should remain adaptive to ensure potential negative influences to all species are avoided. Increasing habitat quantity and quality by reducing habitat loss and fragmentation likely will increase resiliency of the ecosystem and individual species.

Southern High Plains↗
USGS2018

Genetic analyses reveal cryptic introgression in secretive marsh bird populations

Hybridization is common in bird populations but can be challenging for management, especially if one of the two parent species is of greater conservation concern than the other. King rails (Rallus elegans) and clapper rails (R. crepitans) are two marsh bird species with similar morphologies, behaviors, and overlapping distributions. The two species are found along a salinity gradient with the king rail in freshwater marshes and the clapper in estuarine marshes. However, this separation is not absolute; they are occasionally sympatric, and there are reports of interbreeding. In Virginia, USA, both king and clapper rails are identified by the state as Species of Greater Conservation Need, although clappers are thought to be more abundant and king rails have a higher priority ranking. We used a mitochondrial DNA marker and 13 diagnostic nuclear single nucleotide polymorphisms (SNPs) to identify species, classify the degree of introgression, and explore the evolutionary history of introgression in two putative clapper rail focal populations along a salinity gradient in coastal Virginia. Genetic analyses revealed cryptic introgression with site-specific rates of admixture. We identified a pattern of introgression where clapper rail alleles predominate in brackish marshes. These results suggest clapper rails may be displacing king rails in Virginia coastal waterways, most likely as a result of ecological selection. As introgression can result in various outcomes from outbreeding depression to local adaptation, continued monitoring of these populations would allow further exploration of hybrid fitness and inform conservation management.

Georgia, New Jersey, North Carolina, Rhode Island,↗
USGS2018

Behavioral differences following ingestion of large meals and consequences for management of a harmful invasive snake: A field experiment

Many snakes are uniquely adapted to ingest large prey at infrequent intervals. Digestion of large prey is metabolically and aerobically costly, and large prey boluses can impair snake locomotion, increasing vulnerability to predation. Cessation of foraging and use of refugia with microclimates facilitating digestion are expected to be strategies employed by free‐ranging snakes to cope with the demands of digestion while minimizing risk of predation. However, empirical observations of such submergent behavior from field experiments are limited. The brown treesnake (Serpentes: Colubridae: Boiga irregularis ) is a nocturnal, arboreal, colubrid snake that was accidentally introduced to the island of Guam, with ecologically and economically costly consequences. Because tools for brown treesnake damage prevention generally rely on snakes being visible or responding to lures or baits while foraging, cessation of foraging activities after feeding would complicate management. We sought to characterize differences in brown treesnake activity, movement, habitat use, and detectability following feeding of large meals (rodents 33% of the snake's unfed body mass) via radio telemetry, trapping, and visual surveys. Compared to unfed snakes, snakes in the feeding treatment group showed drastic decreases in hourly and nightly activity rates, differences in refuge height and microhabitat type, and a marked decrease in detectability by trapping and visual surveys. Depression of activity lasted approximately 5–7 days, a period that corresponds to previous studies of brown treesnake digestion and cycles of detectability. Our results indicate that management strategies for invasive brown treesnakes need to account for cycles of unavailability and underscore the importance of preventing spread of brown treesnakes to new environments where large prey are abundant and periods of cryptic behavior are likely to be frequent. Characterization of postfeeding behavior changes provides a richer understanding of snake ecology and foraging models for species that consume large prey.

Ecology and Evolution↗
USGS2018

Dynamic occupancy modeling of temperate marine fish in area-based closures

Species distribution models (SDMs) are commonly used to model the spatial structure of species in the marine environment, however, most fail to account for detectability of the target species. This can result in underestimates of occupancy, where nondetection is conflated with absence. The site occupancy model (SOM) overcomes this failure by treating occupancy as a latent variable of the model and incorporates a detection submodel to account for variability in detection rates. These have rarely been applied in the context of marine fish and never for the multiseason dynamic occupancy model (DOM). In this study, a DOM is developed for a designated species of concern, cusk ( Brosme brosme ), over a four-season period. Making novel use of a high-resolution 3-dimensional hydrodynamic model, detectability of cusk is considered as a function of current speed and algae cover. Algal cover on the seabed is measured from video surveys to divide the study area into two distinct regions: those with canopy forming species of algae and those without (henceforth bottom types). Modeled estimates of the proportion of sites occupied in each season are 0.88, 0.45, 0.74, and 0.83. These are significantly greater than the proportion of occupied sites measured from underwater video observations which are 0.57, 0.28, 0.43, and 0.57. Individual fish are detected more frequently with increasing current speed in areas lacking canopy and less frequently with increasing current speed in areas with canopy. The results indicate that, where possible, SDM studies for all marine species should take account of detectability to avoid underestimating the proportion of sites occupied at a given study area. Sampling closed areas or areas of conservation often requires the use of nonphysical, low impact sampling methods like camera surveys. These methods inherently result in detection probabilities less than one, an issue compounded by time-varying features of the environment that are rarely accounted for marine studies. This work highlights the use of modeled hydrodynamics as a tool to correct some of this imbalance.

Gulf of Maine↗
USGS2018

Hidden cost of disease in a free‐ranging ungulate: brucellosis reduces mid‐winter pregnancy in elk

Demonstrating disease impacts on the vital rates of free‐ranging mammalian hosts typically requires intensive, long‐term study. Evidence for chronic pathogens affecting reproduction but not survival is rare, but has the potential for wide‐ranging effects. Accurately quantifying disease‐associated reductions in fecundity is important for advancing theory, generating accurate predictive models, and achieving effective management. We investigated the impacts of brucellosis ( Brucella abortus ) on elk ( Cervus canadensis ) productivity using serological data from over 6,000 captures since 1990 in the Greater Yellowstone Ecosystem, USA. Over 1,000 of these records included known age and pregnancy status. Using Bayesian multilevel models, we estimated the age‐specific pregnancy probabilities of exposed and naïve elk. We then used repeat‐capture data to investigate the full effects of the disease on life history. Brucellosis exposure reduced pregnancy rates of elk captured in mid‐ and late‐winter. In an average year, we found 60% of exposed 2‐year‐old elk were pregnant compared to 91% of their naïve counterparts (a 31 percentage point reduction, 89% HPDI = 20%–42%), whereas exposed 3‐ to 9‐year‐olds were 7 percentage points less likely to be pregnant than naïve elk of their same age (89% HPDI = 2%–11%). We found these reduced rates of pregnancy to be independent from disease‐induced abortions, which afflict a portion of exposed elk. We estimate that the combination of reduced pregnancy by mid‐winter and the abortions following mid‐winter reduces the reproductive output of exposed female elk by 24%, which affects population dynamics to a similar extent as severe winters or droughts. Exposing hidden reproductive costs of disease is essential to avoid conflating them with the effects of climate and predation. Such reproductive costs cause complex population dynamics, and the magnitude of the effect we found should drive a strong selection gradient if there is heritable resistance.

Ecology and Evolution↗
USGS2018

Non‐linear effect of sea ice: Spectacled Eider survival declines at both extremes of the ice spectrum

Understanding the relationship between environmental factors and vital rates is an important step in predicting a species’ response to environmental change. Species associated with sea ice are of particular concern because sea ice is projected to decrease rapidly in polar environments with continued levels of greenhouse gas emissions. The relationship between sea ice and the vital rates of the Spectacled Eider, a threatened species that breeds in Alaska and Russia and winters in the Bering Sea, appears to be complex. While severe ice can impede foraging for benthic prey, ice also suppresses wave action and provides a platform on which eiders roost, thereby reducing thermoregulation costs. We analyzed a 23‐year mark‐recapture dataset for Spectacled Eiders nesting on Kigigak Island in western Alaska, and tested survival models containing different ice and weather‐related covariates. We found that much of the variation in eider survival could be explained by the number of days per year with >95% sea ice concentration at the Bering Sea core wintering area. Furthermore, the data supported a quadratic relationship with sea ice rather than a linear one, indicating that intermediate sea ice concentrations were optimal for survival. We then used matrix population models to project population trajectories using General Circulation Model (GCM) outputs of daily sea ice cover. GCMs projected reduced sea ice at the wintering area by year 2100 under a moderated emissions scenario (RCP 4.5) and nearly ice‐free conditions under an unabated emissions scenario (RCP 8.5). Under RCP 4.5, stochastic models projected an increase in population size until 2069 coincident with moderate ice conditions, followed by a decline in population size as ice conditions shifted from intermediate to mostly ice‐free. Under RCP 8.5, eider abundance increased until 2040 and then decreased to near extirpation toward the end of the century as the Bering Sea became ice‐free. Considerable uncertainty around parameter estimates for survival in years with minimal sea ice contributed to variation in stochastic projections of future population size, and this uncertainty could be reduced with additional survival data from low‐ice winters.

Alaska↗
USGS2018

Sympatry or syntopy? Investigating drivers of distribution and co‐occurrence for two imperiled sea turtle species in Gulf of Mexico neritic waters

Animals co‐occurring in a region (sympatry) may use the same habitat (syntopy) within that region. A central aim in ecology is determining what factors drive species distributions (i.e., abiotic conditions, dispersal limitations, and/or biotic interactions). Assessing the degree of biotic interactions can be difficult for species with wide ranges at sea. This study investigated the spatial ecology of two sea turtle species that forage on benthic invertebrates in neritic GoM waters: Kemp's ridleys ( Lepidochelys kempii ) and loggerheads ( Caretta caretta ). We used satellite tracking and modeled behavioral modes, then calculated individual home ranges, compared foraging areas, and determined extent of co‐occurrence. Using six environmental variables and principal component analysis, we assessed similarity of chosen foraging sites. We predicted foraging location (eco‐region) based on species, nesting site, and turtle size. For 127 turtles (64 Kemp's ridleys, 63 loggerheads) tracked from 1989 to 2013, foraging home ranges were nine to ten times larger for Kemp's ridleys than for loggerheads. Species intersected off all U.S. coasts and the Yucatán Peninsula, but co‐occurrence areas were small compared to species' distributions. Kemp's ridley foraging home ranges were concentrated in the northern GoM, whereas those for loggerheads were concentrated in the eastern GoM. The two species were different in all habitat variables compared (latitude, longitude, distance to shore, net primary production, mean sea surface temperature, and bathymetry). Nesting site was the single dominant variable that dictated foraging ecoregion. Although Kemp's ridleys and loggerheads may compete for resources, the separation in foraging areas, significant differences in environmental conditions, and importance of nesting location on ecoregion selection (i.e., dispersal ability) indicate that adult females of these species do not interact greatly during foraging and that dispersal and environmental factors more strongly determine their distributions. These species show sympatry in this region but evidence for syntopy was rare.

Ecology and Evolution↗
USGS2018

Quantitative acoustic differentiation of cryptic species illustrated with King and Clapper rails

Reliable species identification is vital for survey and monitoring programs. Recently, the development of digital technology for recording and analyzing vocalizations has assisted in acoustic surveying for cryptic, rare, or elusive species. However, the quantitative tools that exist for species differentiation are still being refined. Using vocalizations recorded in the course of ecological studies of a King Rail ( Rallus elegans ) and a Clapper Rail ( Rallus crepitans ) population, we assessed the accuracy and effectiveness of three parametric (logistic regression, discriminant function analysis, quadratic discriminant function analysis) and six nonparametric (support vector machine, CART, Random Forest, k ‐nearest neighbor, weighted k ‐nearest neighbor, and neural networks) statistical classification methods for differentiating these species by their kek mating call. We identified 480 kek notes of each species and quantitatively characterized them with five standardized acoustic parameters. Overall, nonparametric classification methods outperformed parametric classification methods for species differentiation (nonparametric tools were between 57% and 81% accurate, parametric tools were between 57% and 60% accurate). Of the nine classification methods, Random Forest was the most accurate and precise, resulting in 81.1% correct classification of kek notes to species. This suggests that the mating calls of these sister species are likely difficult for human observers to tell apart. However, it also implies that appropriate statistical tools may allow reasonable species‐level classification accuracy of recorded calls and provide an alternative to species classification where other capture‐ or genotype‐based survey techniques are not possible.

Ecology and Evolution↗
USGS2019

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs ( Rana pipiens ) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east–west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified population clusters was also found. Spatial principal component analysis (sPCA) and variance partitioning analysis identified distance, river basins, and the Missouri River as the most important landscape factors differentiating R. pipiens populations across the state. Bayesian reconstruction of coalescence times suggested the major east–west split occurred ~13–18 kya during a period of glacial retreat in the northern Great Plains and substructuring largely occurred ~5–11 kya during a period of extreme drought cycles. A range‐wide species distribution model (SDM) for R. pipiens was developed and applied to prehistoric climate conditions during the Last Glacial Maximum (21 kya) and the mid‐Holocene (6 kya) from the CCSM4 climate model to identify potential refugia. The SDM indicated potential refugia existed in South Dakota or further south in Nebraska. The ancestral populations of R. pipiens in North Dakota may have inhabited these refugia, but more sampling outside the state is needed to reconstruct the route of colonization. Using microsatellite genotype data, this study determined that colonization from glacial refugia, drought dynamics in the northern Great Plains, and major rivers acting as barriers to gene flow were the defining forces shaping the regional population structure of R. pipiens in North Dakota.

North Dakota↗
USGS2018

Observer-free experimental evaluation of habitat and distance effects on the detection of anuran and bird vocalizations

Acoustic surveys of vocalizing animals are conducted to determine density, distribution, and diversity. Acoustic surveys are traditionally performed by human listeners, but automated recording devices (ARD) are becoming increasingly popular. Signal strength decays, or attenuates, with increasing distance between source and receiver and some habitat types may differentially increase attenuation beyond the effects of distance alone. These combined effects are rarely accounted for in acoustic monitoring programs. We evaluated the performance of three playback devices and three ARD models using the calls of six anurans, six birds, and four pure tones. Based on these evaluations, we determined the optimal playback and recording devices. Using these optimal devices, we broadcast and recorded vocalizations in five habitat types along 1,000 m transects. We used generalized linear models to test for effects of habitat, distance, species, environmental, and landscape variables. We predicted detection probabilities for each vocalization, in each habitat type, from 0 to 1,000 m. Among playback devices, only a remote predator caller simulated vocalizations consistently. Differences of ~10 dB were observed among ARDs. For all species, we found differences in detectability between open and closed canopy habitats. We observed large differences in predicted detection probability among species in each habitat type, as well as along 1,000 m transects. Increases in temperature, barometric pressure, and wind speed significantly decreased detection probability. However, aside from differences among species, habitat, and distance, topography impeding a line‐of‐sight between sound source and receiver had the greatest negative influence on detections. Our results suggest researchers should model the effects of habitat, distance, and frequency on detection probability when performing acoustic surveys. To optimize survey design, we recommend pilot measurements among varying habitats.

Ecology and Evolution↗
USGS2019

Flooding regimes increase avian predation on wildlife prey in tidal marsh ecosystems

Within isolated and fragmented populations, species interactions such as predation can cause shifts in community structure and demographics in tidal marsh ecosystems. It is critical to incorporate species interactions into our understanding when evaluating the effects of sea‐level rise and storm surges on tidal marshes. In this study, we hypothesize that avian predators will increase their presence and hunting activities during high tides when increased inundation makes their prey more vulnerable. We present evidence that there is a relationship between tidal inundation depth and time of day on the presence, abundance, and behavior of avian predators. We introduce predation pressure as a combined probability of predator presence related to water level. Focal surveys were conducted at four tidal marshes in the San Francisco Bay, California where tidal inundation patterns were monitored across 6 months of the winter. Sixteen avian predator species were observed. During high tide at Tolay Slough marsh, ardeids had a 29‐fold increase in capture attempts and 4 times greater apparent success rate compared with low tide. Significantly fewer raptors and ardeids were found on low tides than on high tides across all sites. There were more raptors in December and January and more ardeids in January than in other months. Ardeids were more prevalent in the morning, while raptors did not exhibit a significant response to time of day. Modeling results showed that raptors had a unimodal response to water level with a peak at 0.5 m over the marsh platform, while ardeids had an increasing response with water level. We found that predation pressure is related to flooding of the marsh surface, and short‐term increases in sea levels from high astronomical tides, sea‐level rise, and storm surges increase vulnerability of tidal marsh wildlife.

California↗
USGS2019

Impact of prey occupancy and other ecological and anthropogenic factors on Tiger distribution in Thailand’s Western Forest Complex

Despite conservation efforts, large mammals such as tigers (Panthera tigris) and their main prey, gaur (Bos gaurus), banteng (Bos javanicus), and sambar (Rusa unicolor), are highly threatened and declining across their entire range. The only large viable source population of tigers in mainland Southeast Asia occurs in Thailand's Western Forest Complex (WEFCOM), an approximately 19,000 km 2 landscape of 17 contiguous protected areas. We used an occupancy modeling framework, which accounts for imperfect detection, to identify the factors that affect tiger distribution at the approximate scale of a female tiger's home range, 64 km 2 , and site use at a scale of 1-km 2 . At the larger scale, we estimated the proportion of sites at WEFCOM that were occupied by tigers; at the finer scale, we identified the key variables that influence site-use and developed a predictive distribution map. At both scales, we examined key anthropogenic and ecological factors that help explain tiger distribution and habitat use, including probabilities of gaur, banteng, and sambar occurrence from a companion study. Occupancy estimated at the 64-km 2 scale was primarily influenced by the combined presence of all three large prey species, and 37% or 5,858 km 2 of the landscape was predicted to be occupied by tigers. In contrast, site use estimated at the scale of 1 km 2 was most strongly influenced by the presence of sambar. By modeling occupancy while accounting for imperfect probability of detection, we established reliable benchmark data on the distribution of tigers in WEFCOM. This study also identified factors that limit tiger distributions; which managers can then target to expand tiger distribution and guide recovery elsewhere in Southeast Asia.

Ecology and Evolution↗
USGS2019

Disease‐structured N‐mixture models: A practical guide to model disease dynamics using count data

Obtaining inferences on disease dynamics (e.g., host population size, pathogen prevalence, transmission rate, host survival probability) typically requires marking and tracking individuals over time. While multistate mark–recapture models can produce high‐quality inference, these techniques are difficult to employ at large spatial and long temporal scales or in small remnant host populations decimated by virulent pathogens, where low recapture rates may preclude the use of mark–recapture techniques. Recently developed N ‐mixture models offer a statistical framework for estimating wildlife disease dynamics from count data. N ‐mixture models are a type of state‐space model in which observation error is attributed to failing to detect some individuals when they are present (i.e., false negatives). The analysis approach uses repeated surveys of sites over a period of population closure to estimate detection probability. We review the challenges of modeling disease dynamics and describe how N ‐mixture models can be used to estimate common metrics, including pathogen prevalence, transmission, and recovery rates while accounting for imperfect host and pathogen detection. We also offer a perspective on future research directions at the intersection of quantitative and disease ecology, including the estimation of false positives in pathogen presence, spatially explicit disease‐structured N ‐mixture models, and the integration of other data types with count data to inform disease dynamics. Managers rely on accurate and precise estimates of disease dynamics to develop strategies to mitigate pathogen impacts on host populations. At a time when pathogens pose one of the greatest threats to biodiversity, statistical methods that lead to robust inferences on host populations are critically needed for rapid, rather than incremental, assessments of the impacts of emerging infectious diseases.

Ecology and Evolution↗
USGS2019

Fire legacies in eastern ponderosa pine forests

Disturbance legacies structure communities and ecological memory, but due to increasing changes in disturbance regimes, it is becoming more difficult to characterize disturbance legacies or determine how long they persist. We sought to quantify the characteristics and persistence of material legacies (e.g., biotic residuals of disturbance) that arise from variation in fire severity in an eastern ponderosa pine forest in North America. We compared forest stand structure and understory woody plant and bird community composition and species richness across unburned, low‐, moderate‐, and high‐severity burn patches in a 27‐year‐old mixed‐severity wildfire that had received minimal post‐fire management. We identified distinct tree densities (high: 14.3 ± 7.4 trees per ha, moderate: 22.3 ± 12.6, low: 135.3 ± 57.1, unburned: 907.9 ± 246.2) and coarse woody debris cover (high: 8.5 ± 1.6% cover per 30 m transect, moderate: 4.3 ± 0.7, low: 2.3 ± 0.6, unburned: 1.0 ± 0.4) among burn severities. Understory woody plant communities differed between high‐severity patches, moderate‐ and low‐severity patches, and unburned patches (all p < 0.05). Bird communities differed between high‐ and moderate‐severity patches, low‐severity patches, and unburned patches (all p < 0.05). Bird species richness varied across burn severities: low‐severity patches had the highest (5.29 ± 1.44) and high‐severity patches had the lowest (2.87 ± 0.72). Understory woody plant richness was highest in unburned (5.93 ± 1.10) and high‐severity (5.07 ± 1.17) patches, and it was lower in moderate‐ (3.43 ± 1.17) and low‐severity (3.43 ± 1.06) patches. We show material fire legacies persisted decades after the mixed‐severity wildfire in eastern ponderosa forest, fostering distinct structures, communities, and species in burned versus unburned patches and across fire severities. At a patch scale, eastern and western ponderosa system responses to mixed‐severity fires were consistent.

Nebraska↗