Barcoding and mitochondrial phylogenetics of Porites corals

Coral reefs are the most diverse ecosystem on the planet based on the abundance and diversity of phyla and higher taxa. However, it is still difficult to assess the diversity of lower taxa, especially at the species level. One tool for improving the identification of lower taxa are genetic markers that can distinguish cryptic species and assess species boundaries. Here, we present one such approach for an important and challenging group of reef-building corals. Porites corals are the main reef-builders of many coral reefs in the Indo-Pacific, owing to the massive growth forms of some species. The current number of valid Porites species is controversial, inflated with many synonymies, and often based on gross colony morphology although several morphospecies believed to be widespread and common can only be distinguished based on detailed microstructure analyses by taxonomic experts. Here, we test the suitability of multiple regions of mtDNA as genetic barcodes to identify suitable markers for species differentiation and unambiguous identification. Resulting sequencing data was further used for the first phylogenetic analysis of Guam's Porites species. We tested eight different mitochondrial markers and analyzed four in detail for 135 Porites specimens: mtDNA markers were amplified for 67 Porites specimens from Guam, representing 12 nominal Porites species, and combined with 69 mitochondrial genomes, mostly from Hawaii. The combination of all 4 markers distinguished 10 common and 7 uncommon Central-West Pacific Porites species. Most clades separate species along taxonomic boundaries, which is uncommon for Porites corals and testifies to the suitability of our multi-marker approach, and a combination of the two most promising barcodes distinguished 8/10 common species. These barcodes are thus suitable to distinguish virtually cryptic species in one of the most important and challenging coral genera. They offer a cheap, fast and reliable way to identify Porites species for species-level research, monitoring and conservation.

Naegleria fowleri Detected in Grand Teton National Park Hot Springs

The free-living thermophilic amoeba Naegleria fowleri (N. fowleri) causes the highly fatal disease primary amoebic meningoencephalitis. The environmental conditions that are favorable to the growth and proliferation of N. fowleri are not well-defined, especially in northern regions of the United States. In this study, we used culture-based methods and multiple molecular approaches to detect and analyzeN. fowleri and other Naegleria spp. in water, sediment, and biofilm samples from five hot spring sites in Grand Teton National Park, Wyoming, U.S.A. These results provide the first detections of N. fowleri in Grand Teton National Park and provide new insights into the distribution of pathogenic N. fowleri and other nonpathogenic Naegleria spp. in natural thermal water systems in northern latitudes.

Behaviorally segmented audiences for managing sunscreen chemical pollution risk in protected coastal natural resource areas

This audience segmentation of visitors at coastal parks in Hawaii and North Carolina addresses an emergent natural resource management concern and risk to aquatic ecosystems: sunscreen chemical pollution. Four audiences were identified that correspond to different behavioral profiles: sunscreen protection tourists, multimodal sun protection tourists, in-state frequent park visitors, and frequent beachgoers who skip sunscreen. The second-largest audience, sunscreen protection tourists, represents 29% of visitors at Cape Lookout National Seashore and 25% at Kaloko-Honokōhau National Historical Park. This group ranks of most concern for chemical pollution because they use sunscreen, but not typically mineral formulations or other methods such as protective clothing, and they have lower levels of sunscreen chemical issue awareness. The identification of similar audience segments across regions with differing cultural characteristics and sunscreen regulation status suggests the robustness of the model and its indicator variables, with implications for both environmental protection and public health. Further, coastal visitors' interest in enacting pro-environmental sun protection behaviors during their next park or beach visit indicates the potential for natural resource managers to holistically address risks in both domains through targeted interventions with audiences of most concern.

Latent trajectory models for spatio-temporal dynamics in Alaskan ecosystems

The Alaskan landscape has undergone substantial changes in recent decades, most notably the expansion of shrubs and trees across the Arctic. We developed a Bayesian hierarchical model to quantify the impact of climate change on the structural transformation of ecosystems using remotely sensed imagery. We used latent trajectory processes to model dynamic state probabilities that evolve annually, from which we derived transition probabilities between ecotypes. Our latent trajectory model accommodates temporal irregularity in survey intervals and uses spatio-temporally heterogeneous climate drivers to infer rates of land cover transitions. We characterized multi-scale spatial correlation induced by plot and subplot arrangements in our study system. We also developed a Pólya-Gamma sampling strategy to improve computation. Our model facilitates inference on the response of ecosystems to shifts in the climate and can be used to predict future land cover transitions under various climate scenarios.

Wolves alter the trajectory of forests by shaping the central place foraging behaviour of an ecosystem engineer

Predators can directly and indirectly alter the foraging behaviour of prey through direct predation and the risk of predation, and in doing so, initiate indirect effects that influence myriad species and ecological processes. We describe how wolves indirectly alter the trajectory of forests by constraining the distance that beavers, a central place forager and prolific ecosystem engineer, forage from water. Specifically, we demonstrate that wolves wait in ambush and kill beavers on longer feeding trails than would be expected based on the spatio-temporal availability of beavers. This pattern is driven by temporal dynamics of beaver foraging: beavers make more foraging trips and spend more time on land per trip on longer feeding trails that extend farther from water. As a result, beavers are more vulnerable on longer feeding trails than shorter ones. Wolf predation appears to be a selective evolutionary pressure propelled by consumptive and non-consumptive mechanisms that constrain the distance from water beavers forage, which in turn limits the area of forest around wetlands, lakes and rivers beavers alter through foraging. Thus, wolves appear intricately linked to boreal forest dynamics by shaping beaver foraging behaviour, a form of natural disturbance that alters the successional and ecological states of forests.

Empirical estimation of habitat suitability for rare plant restoration in an era of ongoing climatic shifts

Accurate estimates of current and future habitat suitability are needed for species that may require assistance in tracking a shifting climate. Standard species distribution models (SDMs) based on occurrence data are the most common approach for evaluating climatic suitability, but these may suffer from inaccuracies stemming from disequilibrium dynamics and/or an inability to identify suitable climate regions that have no analogues within the current range. An alternative approach is to test performance with experimental introductions, and model suitability from the empirical results. We used this method with the Haleakalā silversword (Argyroxiphium sandwicense subsp. macrocephalum), using a network of out-plant plots across the top of Haleakalā volcano, Hawai'i. Over a ~ 5-year period, survival varied strongly across this network and was effectively explained by a simple model including mean rainfall and air temperature. We then applied this model to estimate current climatic suitability for restoration or translocation activities, to define trends in suitability over the past three decades, and to project future suitability through 2051. This empirical approach indicated that much of the current range has low suitability for long-term successful restoration, but also identified areas of high climatic suitability in a region where plants do not currently occur. These patterns contrast strongly with projections obtained with a standard SDM, which predicted continued suitability throughout the current range. Under continued climatic shifts, these results caution against the common SDM presumption of equilibrium between species' distributions and their environment, even for long-established native species.

Logging, linear features, and human infrastructure shape the spatial dynamics of wolf predation on an ungulate neonate

Humans are increasingly recognized as important players in predator-prey dynamics by modifying landscapes. This trend has been well-documented for large mammal communities in North American boreal forests: logging creates early seral forests that benefit ungulates such as white-tailed deer (Odocoileus virginianus), while the combination of infrastructure development and resource extraction practices generate linear features that allow predators such as wolves (Canis lupus) to travel and forage more efficiently throughout the landscape. Disturbances from recreational activities and residential development are other major sources of human activity in boreal ecosystems that may further alter wolf-ungulate dynamics. Here, we evaluate the influence that several major types of anthropogenic landscape modifications (timber harvest, linear features, and residential infrastructure) have on where and how wolves hunt ungulate neonates in a southern boreal forest ecosystem in Minnesota, USA. We demonstrate that each major anthropogenic disturbance significantly influences wolf predation of white-tailed deer fawns (n = 427 kill sites). In contrast with the "human shield hypothesis" that posits prey use human-modified areas as refuge, wolves killed fawns closer to residential buildings than expected based on spatial availability. Fawns were also killed within recently-logged areas more than expected. Concealment cover was higher at kill sites than random sites, suggesting wolves use senses other than vision, probably olfaction, to detect hidden fawns. Wolves showed strong selection for hunting along linear features, and kill sites were also closer to linear features than expected. We hypothesize that linear features facilitated wolf predation on fawns by allowing wolves to travel efficiently among high-quality prey patches (recently logged areas, near buildings), and also increase encounter rates with olfactory cues that allow them to detect hidden fawns. These findings provide novel insight into the strategies predators use to hunt ungulate neonates and the many ways human activity alters wolf-ungulate neonate predator-prey dynamics, which have remained elusive due to the challenges of locating sites where predators kill small prey. Our research has important management and conservation implications for wolf-ungulate systems subjected to anthropogenic pressures, particularly as the range of overlap between wolves and deer expands and appears to be altering food web dynamics in boreal ecosystems.

Chromosome-level reference genome for North American bison (Bison bison) and variant database aids in identifying albino mutation

We developed a highly contiguous chromosome-level reference genome for North American bison to provide a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. Generated from a F1 hybrid between a North American bison dam and a domestic cattle bull, completeness and contiguity exceed that of other published bison genome assemblies. To demonstrate the utility for genome-wide variant frequency estimation, we compiled a genomic variant database consisting of 3 true albino bison and 44 wild-type pelage color bison. Through the examination of genomic variants fixed in the albino cohort and absent in the controls, we identified a nonsynonymous single nucleotide polymorphism (SNP) mutation on chromosome 29 in exon 3 of the tyrosinase gene (c.1114C>T). A TaqMan SNP Genotyping Assay was developed to genotype this SNP in a total of 283 animals across 29 herds. This assay confirmed the absence of homozygous variants in all animals except 7 true albino bison included in this study. In addition, the only heterozygous animals identified were 2 wild-type pelage color dams of albino offspring. Therefore, we propose that this new high-quality bison genome assembly and incipient variant database provides a highly robust and informative resource for genomics investigations for this iconic North American species.

Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America

Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and diversity of two populations of the bacterial oak pathogen Lonsdalea quercina from western North America (Colorado and California) and compared these populations to other Lonsdalea species found worldwide. Phylogenetic analysis separated Colorado and California populations into two Lonsdalea clades, with genetic divergence near species boundaries, suggesting long isolation and populations that differ in genetic structure and distribution and possibly their polyphyletic origin. Genotypes collected from different host species and habitats were randomly distributed within the California cluster. Most Colorado isolates from introduced planted trees, however, were distinct from three isolates collected from a natural stand of Colorado native Quercus gambelii, indicating cryptic population structure. The California identical core genotypes distribution varied, while Colorado identical core genotypes were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to its long presence in Colorado or due to migrants moving with nursery stock. Overall, results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystems changes. Further studies are warranted to understand evolutionary relationships among L. quercina from different areas, including the red oak native habitat in northeastern USA.

Mitogenomes revealed the history of bison colonization of Northern Plains after the Last Glacial Maximum

American bison demonstrated differential patterns of extinction, survival, and expansion since the terminal Pleistocene. We determined population dynamics of the Northern Great Plains bison using 40 mitochondrial genomes from radiocarbon dated remains with the age ranging from 12,226 to 167 calibrated years before present. Population dynamics correlated with environmental and anthropogenic factors and was characterized by three primary periods: terminal Pleistocene population growth starting 14,000 years ago, mid Holocene demographic stability between 6700 and 2700 years ago, and late Holocene population decline in the last 2700 years. Most diversification of mtDNA haplotypes occurred in the early Holocene when bison colonized new territories opened by retreating ice sheets. Holocene mtDNA lineages were not found in modern bison and lacked association with archaeological sites and morphological forms.

The ethology of wolves foraging on freshwater fish in a boreal ecosystem

Through global positioning system (GPS) collar locations, remote cameras, field observations and the first wild wolf to be GPS-collared with a camera collar, we describe when, where and how wolves fish in a freshwater ecosystem. From 2017 to 2021, we recorded more than 10 wolves (Canis lupus) hunting fish during the spring spawning season in northern Minnesota, USA. Wolves ambushed fish in creeks at night when spawning fish were abundant, available and vulnerable in shallow waters. We observed wolves specifically targeting sections of rivers below beaver (Castor canadensis) dams, suggesting that beavers may indirectly facilitate wolf fishing behaviour. Wolves also cached fish on shorelines. We documented these findings across five different social groups at four distinct waterways, suggesting that wolf fishing behaviour may be widespread in similar ecosystems but has probably remained difficult to study given its annual brevity. Spawning fish may serve as a valuable pulsed resource for packs because the spring spawning season coincides with low primary prey (deer Odocoileus virginianus) availability and abundance, and when packs have higher energetic demands owing to newly born pups. We demonstrate the flexibility and adaptability of wolf hunting and foraging behaviour, and provide insight into how wolves can survive in a myriad of ecosystems.

How to estimate body condition in large lizards? Argentine black and white tegu (Salvator merianae, Duméril and Bibron, 1839) as a case study

Body condition is a measure of the health and fitness of an organism represented by available energy stores, typically fat. Direct measurements of fat are difficult to obtain non-invasively, thus body condition is usually estimated by calculating body condition indices (BCIs) using mass and length. The utility of BCIs is contingent on the relationship of BCIs and fat, thereby validation studies should be performed to select the best performing BCI before application in ecological investigations. We evaluated 11 BCIs in 883 Argentine black and white tegus (Salvator merianae) removed from their non-native range in South Florida, United States. Because the length-mass relationship in tegus is allometric, a segmented linear regression model was fit to the relationship between mass and length to define size classes. We evaluated percent, residual, and scaled fat and determined percent fat was the best measure of fat, because it was the least-associated with snout-vent length (SVL). We evaluated performance of BCIs with the full dataset and within size classes and identified Fulton's K as the best performing BCI for our sampled population, explaining up to 19% of the variation in fat content. Overall, we found that BCIs: 1) maintained relatively weak relationships with measures of fat and 2) splitting data into size classes reduced the strength of the relationship (i.e., bias) between percent fat and SVL but did not improve the performance of BCIs. We postulate that the weak performance of BCIs in our dataset was likely due to the weak association of fat with SVL, the body plan and life-history traits of tegus, and potentially inadequate accounting of available energy resources. We caution against assuming that BCIs are strong indicators of body condition across species and suggest that validation studies be implemented, or that alternative or complimentary measures of health or fitness should be considered.

Animal movement and associated infectious disease risk in a metapopulation

Animal movements among habitat patches or populations are important for maintaining long-term genetic and demographic viability, but connectivity may also facilitate disease spread and persistence. Understanding factors that influence animal movements is critical to understanding potential transmission risk and persistence of communicable disease in spatially structured systems. We evaluated effects of sex, age and Mycoplasma ovipneumoniae infection status at capture on intermountain movements and seasonal movement rates observed in desert bighorn sheep (Ovis canadensis nelsoni) using global positioning system collar data from 135 individuals (27 males, 108 females) in 14 populations between 2013 and 2018, following a pneumonia outbreak linked to the pathogen M. ovipneumoniae in the Mojave Desert, California, USA. Based on logistic regression analysis, intermountain movements were influenced by sex, age and most notably, infection status at capture: males, older animals and uninfected individuals were most likely to make such movements. Based on multiple linear regression analysis, females that tested positive for M. ovipneumoniae at capture also had lower mean daily movement rates that were further influenced by season. Our study provides empirical evidence of a pathogenic infection decreasing an individual's future mobility, presumably limiting that pathogen's ability to spread, and ultimately influencing transmission risk within a spatially structured system.

Breeding displacement in gray wolves (Canis lupus): Three males usurp breeding position and pup rearing from a neighboring pack in Yellowstone National Park

Gray Wolves (Canis lupus) are territorial, group living carnivores that live in packs typically consisting of a dominant breeding pair and their offspring. Breeding tenures are relatively short and competitive, with vacancies usually occurring following a breeder's death, and are often filled by unrelated immigrants or by relatives of the previous breeder. The frequency and conditions of active breeder displacements are poorly understood. Position changes in the dominance hierarchy are common yet rarely documented in detail. We describe a male breeding position turnover in a wolf pack by males from a neighboring pack in mid-summer 2016 in Yellowstone National Park. Over the course of two months, three males from the Mollie's pack displaced the breeding male of the neighboring Wapiti Lake pack, joined the pack's two adult females, and subsequently raised the previous male's four approximately three-month old pups. In the five years following the displacement (2017 to 2021), at least one of the intruding males has successfully bred with the dominant female and most years with a subordinate female (who was one of the pups at the time of displacement). The pack reared pups to adulthood each year. Male breeding displacements are likely influenced by male-male competition and female mate choice. These changes are the result of individuals competing to improve breeding position and may lead to increased pack stability and greater reproductive success. We report in detail on the behavior of a closely observed breeding displacement and we discuss the adaptive benefits of the change.

Long-term use of a shark breeding ground: Three decades of mating site fidelity in the nurse shark, Ginglymostoma cirratum

Understanding shark mating dynamics and mating site use may be vital to species management. The Dry Tortugas courtship and mating ground (DTCMG) has been known as a mating site for nurse sharks, Ginglymostoma cirratum, since 1895. In a 30-yr (1992–2021) study we have documented long-term site fidelity to this area with data from 137 adult sharks (89 female, 48 male) tagged with PIT, fin, and acoustic tags. Of 118 sharks tagged from 1993 to 2014, at least 80 (68%) returned to the DTCMG in subsequent years during the June-July mating season. Known individuals returned in up to 16 different mating seasons and over periods of up 28 years, indicating that life span extends well into the forties for this species. Of all returning sharks, 59% (N = 47) have been monitored for over 10 years and 13% (N = 10) have been monitored for over 20 years. Males arrived annually in May and June and departed in July, whereas females arrived biennially or triennially in June, with a secondary peak in site use in September and August, likely associated with thermoregulation during gestation. During the mating season, males made more frequent visits of shorter duration (median = 34 visits for 1 h per visit) to the DTCMG, whereas females made fewer visits but remained on site for longer periods (median = 12.5 visits for 4.4 h per visit). Females typically mated biennially but showed a triennial cycle in 32% of cases, with many females switching cycles at least once. This pattern would reduce the potential reproductive lifetime output of a female by 11% compared to what would be projected from a strict biennial cycle. The long-term mating site fidelity of this shark population reveals the importance of identifying and protecting mating sites for this and other elasmobranch species.

Physiological and life history changes associated with seasonal adaptation in the cactophilic Drosophila mojavensis

Many insects inhabiting temperate climates are faced with changing environmental conditions throughout the year. Depending on the species, these environmental fluctuations can be experienced within a single generation or across multiple generations. Strategies for dealing with these seasonal changes vary across populations. Drosophila mojavensis is a cactophilic Drosophila species endemic to the Sonoran Desert. The Sonoran Desert regularly reaches temperatures of 50°C in the summer months. As individuals of this population are rare to collect in the summer months, we simulated the cycling temperatures experienced by D. mojavensis in the Sonoran Desert from April to July (four generations) in a temperature- and light-controlled chamber, to understand the physiological and life history changes that allow this population to withstand these conditions. In contrast to our hypothesis of a summer aestivation, we found that D. mojavensis continue to reproduce during the summer months, albeit with lower viability, but the adult survivorship of the population is highly reduced during this period. As expected, stress resistance increased during the summer months in both the adult and the larval stages. This study examines several strategies for withstanding the Sonoran Desert summer conditions which may be informative in the study of other desert endemic species.

A high-resolution map of coastal vegetation for two Arctic Alaskan parklands: An object-oriented approach with point training data

Bering Land Bridge National Preserve and Cape Krusenstern National Monument in northwest Alaska have approximately 1600 km of predominantly soft-sediment coastlines along the Chukchi Sea, a shallow bay of the Arctic Ocean. Over the past decade, marine vessel traffic through the Bering Strait has grown exponentially to take advantage of new ice-free summer shipping routes, increasing the risk of oil spills in these fragile ecosystems. We present a high-resolution coastal vegetation map to serve as a baseline for potential spill response, restoration, and change detection. We segmented 663 km² of high-resolution multispectral satellite images by the mean-shift method and collected 40 spectral, topographic and spatial variables per segment. The segments were classified using photo-interpreted points as training data, and verified with field based plots. Digitizing points, rather than polygons, and intersecting them with the segmentation allows for rapid collection of training data. We classified the map segments using Random Forest because of its high accuracy, computational speed, and ability to incorporate non-normal, high-dimensional data. We found creating separate classification models by each satellite scene gave highly similar results to models combining the entire study area, and that reducing the number of variables had little impact on accuracy. A unified, study area-wide Random Forest model for both parklands produced the highest accuracy of various models attempted. We mapped 18 distinct classes, with an out-of-bag error of 11.6%, resulting in an improvement to the past per-pixel classification of this coast, and in higher spatial and vegetation classification resolution. The resulting map demonstrates the utility of our point-based method and provides baseline data for incident preparedness and change detection. Elevation is highly correlated with the ordination of the vegetation types, and was the most important variable in all tested classification models. The vegetation classification brings together the largest amount of vegetation data for the Chukchi Sea coast yet documented.

Assembling a safe and effective toolbox for integrated flea control and plague mitigation: Fipronil experiments with prairie dogs

Background

Plague, a widely distributed zoonotic disease of mammalian hosts and flea vectors, poses a significant risk to ecosystems throughout much of Earth. Conservation biologists use insecticides for flea control and plague mitigation. Here, we evaluate the use of an insecticide grain bait, laced with 0.005% fipronil (FIP) by weight, with black-tailed prairie dogs (BTPDs, Cynomys ludovicianus). We consider safety measures, flea control, BTPD body condition, BTPD survival, efficacy of plague mitigation, and the speed of FIP grain application vs. infusing BTPD burrows with insecticide dusts. We also explore conservation implications for endangered black-footed ferrets (Mustela nigripes), which are specialized predators of Cynomys.

Principal findings

During 5- and 10-day laboratory trials in Colorado, USA, 2016–2017, FIP grain had no detectable acute toxic effect on 20 BTPDs that readily consumed the grain. During field experiments in South Dakota, USA, 2016–2020, FIP grain suppressed fleas on BTPDs for at least 12 months and up to 24 months in many cases; short-term flea control on a few sites was poor for unknown reasons. In an area of South Dakota where plague circulation appeared low or absent, FIP grain had no detectable effect, positive or negative, on BTPD survival. Experimental results suggest FIP grain may have improved BTPD body condition (mass:foot) and reproduction (juveniles:adults). During a 2019 plague epizootic in Colorado, BTPDs on 238 ha habitat were protected by FIP grain, whereas BTPDs were nearly eliminated on non-treated habitat. Applications of FIP grain were 2–4 times faster than dusting BTPD burrows.

Significance

Deltamethrin dust is the most commonly used insecticide for plague mitigation on Cynomys colonies. Fleas on BTPD colonies exhibit the ability to evolve resistance to deltamethrin after repeated annual treatments. Thus, more tools are needed. Accumulating data show orally-delivered FIP is safe and usually effective for flea control with BTPDs, though potential acute toxic effects cannot be ruled out. With continued study and refinement, FIP might be used in rotation with, or even replace deltamethrin, and serve an important role in Cynomys and black-footed ferret conservation. More broadly, our stepwise approach to research on FIP may function as a template or guide for evaluations of insecticides in the context of wildlife conservation.

Impacts on tundra vegetation from heavy metal-enriched fugitive dust on National Park Service lands along the Red Dog Mine haul road, Alaska

The DeLong Mountain Transportation System (DMTS) haul road links the Red Dog Mine—one of the world’s largest zinc mines—with a shipping port on the Chukchi Sea in northwest Alaska, USA. The road traverses 32 km of National Park Service (NPS) lands managed by Cape Krusenstern National Monument (CAKR). Fugitive dusts from ore concentrate transport and mining operations have dispersed zinc (Zn), lead (Pb), cadmium (Cd), and metal sulfides onto NPS lands since the mine began operating in 1989. This study assessed the effects of metal-enriched road dusts on the diversity and community structure of lichens, bryophytes, and vascular plants in dwarf-shrub tundra within CAKR. In a Bayesian posterior predictions model, lichen species richness (LSR) was highly correlated to distance from the haul road and was distributed on the landscape consistently with the spatial patterns of Zn, Pb and Cd patterns published earlier in this journal. The mean modeled LSR of the 3000–4000 m distance class was 41.3, and LSR decreased progressively down to 9.4 species in the 0–50 m class. An ordination of 93 lichen species by 91 plots revealed strong community patterns based on distance from the haul road. The major community gradient was highly correlated (r = 0.99) with LSR and negatively correlated with Cd, Pb and Zn (-0.79 < r < -0.74). Ordinations of bryophyte classes showed less response than lichens to distance from the road and heavy metals values, and vascular plant ordination showed less still. Measures of bryophyte health such as the midrib blackening and frond width of Hylocomium splendens were positively correlated with distance from the haul road and negatively correlated with this same suite of elements. A total area of approximately 55 km² showed moderate to strong impacts on lichens from fugitive dusts. This is equivalent to an area of almost 1 km on both sides of the haul road running 32 km through CAKR.

Reevaluation of the Role of Blocked Oropsylla hirsuta Prairie Dog Fleas (Siphonaptera: Ceratophyllidae) in Yersinia pestis (Enterobacterales: Enterobacteriaceae) Transmission

Prairie dogs in the western United States experience periodic epizootics of plague, caused by the flea-borne bacterial pathogen Yersinia pestis. An early study indicated that Oropsylla hirsuta (Baker), often the most abundant prairie dog flea vector of plague, seldom transmits Y. pestis by the classic blocked flea mechanism. More recently, an alternative early-phase mode of transmission has been proposed as the driving force behind prairie dog epizootics. In this study, using the same flea infection protocol used previously to evaluate early-phase transmission, we assessed the vector competence of O. hirsuta for both modes of transmission. Proventricular blockage was evident during the first two weeks after infection and transmission during this time was at least as efficient as early-phase transmission 2 d after infection. Thus, both modes of transmission likely contribute to plague epizootics in prairie dogs.

Estimating population size when individuals are asynchronous: A model illustrated with northern elephant seal breeding colonies

Our aim was to develop a method for estimating the number of animals using a single site in an asynchronous species, meaning that not all animals are present at once so that no one count captures the entire population. This is a common problem in seasonal breeders, and in northern elephant seals, we have a model for quantifying asynchrony at the Año Nuevo colony. Here we test the model at several additional colonies having many years of observations and demonstrate how it can account for animals not present on any one day. This leads to correction factors that yield total population from any single count throughout a season. At seven colonies in California for which we had many years of counts of northern elephant seals, we found that female arrival date varied < 2 days between years within sites and by < 5 days between sites. As a result, the correction factor for any one day was consistent, and at each colony, multiplying a female count between 26 and 30 Jan by 1.15 yielded an estimate of total population size that minimized error. This provides a method for estimating the female population size at colonies not yet studied. Our method can produce population estimates with minimal expenditure of time and resources and will be applicable to many seasonal species with asynchronous breeding phenology, particularly colonial birds and other pinnipeds. In elephant seals, it will facilitate monitoring the population over its entire range.

Variable tropical moisture and food availability underlie mixed winter space-use strategies in a migratory songbird

Identifying environmental correlates driving space-use strategies can be critical for predicting population dynamics; however, such information can be difficult to attain for small mobile species such as migratory songbirds. We combined radio-telemetry and high-resolution GPS tracking to examine space-use strategies under different moisture gradients for wood thrush (Hylocichla mustelina). We explored the role moisture plays in driving food abundance and, in turn, space-use strategies at a wintering site in Belize across 3 years. Individuals occupying drier habitats experienced lower food abundance and poorer body condition. Using data from our radio-tracked study population and GPS tracking from across five breeding populations, we detected low rates of overwinter site persistence across the wood thrush wintering range. Contrary to expectations, individuals in wetter habitats were more likely to engage in permanent mid-winter relocations, up to 148 km. We suggest facultative movements are instead a condition-dependent strategy that enables wintering wood thrush to locate alternative habitat as food availability declines throughout the dry season. Increased aridity is predicted across the wintering range of wood thrush, and future research should delve deeper into understanding how moisture impacts within and between season space-use dynamics and its ultimate impact on the population dynamics of this declining species.

Diffusion modeling reveals effects of multiple release sites and human activity on a recolonizing apex predator

BACKGROUND

Reintroducing predators is a promising conservation tool to help remedy human-caused ecosystem changes. However, the growth and spread of a reintroduced population is a spatiotemporal process that is driven by a suite of factors, such as habitat change, human activity, and prey availability. Sea otters (Enhydra lutris) are apex predators of nearshore marine ecosystems that had declined nearly to extinction across much of their range by the early 20th century. In Southeast Alaska, which is comprised of a diverse matrix of nearshore habitat and managed areas, reintroduction of 413 individuals in the late 1960s initiated the growth and spread of a population that now exceeds 25,000.

METHODS

Periodic aerial surveys in the region provide a time series of spatially-explicit data to investigate factors influencing this successful and ongoing recovery. We integrated an ecological diffusion model that accounted for spatially-variable motility and density-dependent population growth, as well as multiple population epicenters, into a Bayesian hierarchical framework to help understand the factors influencing the success of this recovery.

RESULTS

Our results indicated that sea otters exhibited higher residence time as well as greater equilibrium abundance in Glacier Bay, a protected area, and in areas where there is limited or no commercial fishing. Asymptotic spread rates suggested sea otters colonized Southeast Alaska at rates of 1-8 km/yr with lower rates occurring in areas correlated with higher residence time, which primarily included areas near shore and closed to commercial fishing. Further, we found that the intrinsic growth rate of sea otters may be higher than previous estimates suggested.

CONCLUSIONS

This study shows how predator recolonization can occur from multiple population epicenters. Additionally, our results suggest spatial heterogeneity in the physical environment as well as human activity and management can influence recolonization processes, both in terms of movement (or motility) and density dependence.

NABat: A top-down, bottom-up solution to collaborative continental-scale monitoring

Collaborative monitoring over broad scales and levels of ecological organization can inform conservation efforts necessary to address the contemporary biodiversity crisis. An important challenge to collaborative monitoring is motivating local engagement with enough buy-in from stakeholders while providing adequate top-down direction for scientific rigor, quality control, and coordination. Collaborative monitoring must reconcile this inherent tension between top-down control and bottom-up engagement. Highly mobile and cryptic taxa, such as bats, present a particularly acute challenge. Given their scale of movement, complex life histories, and rapidly expanding threats, understanding population trends of bats requires coordinated broad-scale collaborative monitoring. The North American Bat Monitoring Program (NABat) reconciles top-down, bottom-up tension with a hierarchical master sample survey design, integrated data analysis, dynamic data curation, regional monitoring hubs, and knowledge delivery through web-based infrastructure. NABat supports collaborative monitoring across spatial and organizational scales and the full annual lifecycle of bats.

Light pollution affects West Nile virus exposure risk across Florida

Emerging infectious diseases (EIDs) present global health threats, and their emergences are often linked to anthropogenic change. Artificial light at night (ALAN) is one form of anthropogenic change that spans beyond urban boundaries and may be relevant to EIDs through its influence on the behaviour and physiology of hosts and/or vectors. Although West Nile virus (WNV) emergence has been described as peri-urban, we hypothesized that exposure risk could also be influenced by ALAN in particular, which is testable by comparing the effects of ALAN on prevalence while controlling for other aspects of urbanization. By modelling WNV exposure among sentinel chickens in Florida, we found strong support for a nonlinear relationship between ALAN and WNV exposure risk in chickens with peak WNV risk occurring at low ALAN levels. Although our goal was not to discern how ALAN affected WNV relative to other factors, effects of ALAN on WNV exposure were stronger than other known drivers of risk (i.e. impervious surface, human population density). Ambient temperature in the month prior to sampling, but no other considered variables, strongly influenced WNV risk. These results indicate that ALAN may contribute to spatio-temporal changes in WNV risk, justifying future investigations of ALAN on other vector-borne parasites.

Heterospecific pollination by an invasive congener threatens the native American bittersweet, Celastrus scandens

Invasive plants have the potential to interfere with native species’ reproductive success through a number of mechanisms, including heterospecific pollination and hybridization. This study investigated reproductive interactions between a native North American woody vine (American bittersweet, Celastrus scandens) and an introduced congener (oriental bittersweet, C. orbiculatus). The decline of C. scandens in the eastern portion of its range is coincident with the introduction and spread of C. orbiculatus, and the two species are known to hybridize. The relationship between proximity and floral production of conspecific and heterospecific males on fertilization and hybridization rates was measured at a field site in northwestern Indiana, USA where both species occur and reproduce. We found that the invasive vine had an extreme advantage in both male and female floral production, producing nearly 200 times more flowers per staminate plant and 65 times more flowers per pistillate plant than the native. Using nuclear microsatellite DNA markers we found that hybridization rates were asymmetric; 39% of the C. scandens seeds tested were hybrids, compared to only 1.6% of C. orbiculatus seeds. The asymmetric hybridization rates were likely not solely due to greater abundance of C. orbiculatus pollen because experimental hand crosses revealed that C. scandens had a higher rate (41%) of heterospecific fertilization than C. orbiculatus (2.4%). We previously reported that few hybrids were observed in the wild, and hybrids had greatly reduced fecundity. Thus, in our system, the threat posed by heterospecific pollen is not replacement by hybrids or introgression, but rather asymmetric reproductive interference. Reproductive interference extended to distances as great as 100 meters, thus, efforts to conserve the native species must reduce its exposure to C. orbiculatus over a relatively large spatial scale.

Pseudogymnoascus destructans growth in wood, soil and guano substrates

Understanding how a pathogen can grow on different substrates and how this growth impacts its dispersal are critical to understanding the risks and control of emerging infectious diseases. Pseudogymnoascus destructans (Pd) causes white-nose syndrome (WNS) in many bat species and can persist in, and transmit from, the environment. We experimentally evaluated Pd growth on common substrates to better understand mechanisms of pathogen persistence, transmission and viability. We inoculated autoclaved guano, fresh guano, soil, and wood with live Pd fungus and evaluated (1) whether Pd grows or persists on each (2) if spores of the fungus remain viable 4 months after inoculation on each substrate, and (3) whether detection and quantitation of Pd on swabs is sensitive to the choice to two commonly used DNA extraction kits. After inoculating each substrate with 460,000 Pd spores, we collected ~ 0.20 g of guano and soil, and swabs from wood every 16 days for 64 days to quantify pathogen load through time using real-time qPCR. We detected Pd on all substrates over the course of the experiment. We observed a tenfold increase in pathogen loads on autoclaved guano and persistence but not growth in fresh guano. Pathogen loads increased marginally on wood but declined ~ 60-fold in soil. After four months, apparently viable spores were harvested from all substrates but germination did not occur from fresh guano. We additionally found that detection and quantitation of Pd from swabs of wood surfaces is sensitive to the DNA extraction method. The commonly used PrepMan Ultra Reagent protocol yielded substantially less DNA than did the QIAGEN DNeasy Blood and Tissue Kit. Notably the PrepMan Ultra Reagent failed to detect Pd in many wood swabs that were detected by QIAGEN and were subsequently found to contain substantial live conidia. Our results indicate that Pd can persist or even grow on common environmental substrates with results dependent on whether microbial competitors have been eliminated. Although we observed clear rapid declines in Pd on soil, viable spores were harvested four months after inoculation. These results suggest that environmental substrates and guano can in general serve as infectious environmental reservoirs due to long-term persistence, and even growth, of live Pd. This should inform management interventions to sanitize or modify structures to reduce transmission risk as well early detection rapid response (EDRR) planning.

Maritime Paleoindian technology, subsistence, and ecology at an ~11,700 year old Paleocoastal site on California's Northern Channel Islands, USA

During the last 10 years, we have learned a great deal about the potential for a coastal peopling of the Americas and the importance of marine resources in early economies. Despite research at a growing number of terminal Pleistocene archaeological sites on the Pacific Coast of the Americas, however, important questions remain about the lifeways of early Paleocoastal peoples. Research at CA-SRI-26, a roughly 11,700 year old site on California's Santa Rosa Island, provides new data on Paleoindian technologies, subsistence strategies, and seasonality in an insular maritime setting. Buried beneath approximately two meters of alluvium, much of the site has been lost to erosion, but its remnants have produced chipped stone artifacts (crescents and Channel Island Amol and Channel Island Barbed points) diagnostic of early island Paleocoastal components. The bones of waterfowl and seabirds, fish, and marine mammals, along with small amounts of shellfish document a diverse subsistence strategy. These data support a relatively brief occupation during the wetter "winter" season (late fall to early spring), in an upland location several km from the open coast. When placed in the context of other Paleocoastal sites on the Channel Islands, CA-SRI-26 demonstrates diverse maritime subsistence strategies and a mix of seasonal and more sustained year-round island occupations. Our results add to knowledge about a distinctive island Paleocoastal culture that appears to be related to Western Stemmed Tradition sites widely scattered across western North America.

Quantifying the impacts of future sea level rise on nesting sea turtles in the southeastern United States

Sandy beaches, a necessary habitat for nesting sea turtles, are increasingly under threat as they become squeezed between human infrastructure and shorelines that are changing as a result of rising sea levels. Forecasting where shifting sandy beaches will be obstructed and how that directly impacts coastal nesting species is necessary for successful conservation and management. Predicting changes to coastal nesting areas is difficult because of a lack of consensus on the physical attributes used by females in nesting site choice. In this study, we leveraged long-term data sets of nesting localities for two sea turtle species, loggerhead sea turtle, Caretta caretta, and green sea turtle, Chelonia mydas, within four barrier island National Seashores in the southeastern United States to predict future nesting beach area based on where these species currently nest in relation to mean high water. We predicted the future location of nesting areas based on a sea level rise scenario for 2100 and quantified how impervious surfaces will inhibit future beach movement, which will impact both the total available nesting area and the percentage of nesting area predicted to flood following a hurricane-related storm surge. Contrary to our expectations, those barrier islands with the greatest levels of human infrastructure were not projected to experience the greatest percentage of sea turtle nesting area loss due to sea level rise or storm surge events. Notably, loss of nesting beach areas will not have equal impacts across the four Seashores; the Seashore projected to have the least amount of total nesting area lost and percentage nesting area lost currently has the highest nesting densities of our two study species, suggesting that even low levels of beach loss could have substantial impacts on future nesting densities and disproportionate impacts on the population growth of these species. Our novel method of estimating current and future nesting beach area can be broadly applied to studies requiring a bounded area that encompasses the part of a beach used by nesting coastal species and will be useful in comparing future global nesting densities and population trajectories under projected future sea level rise and storm surge activity.

Salt marsh monitoring along the mid-Atlantic coast by Google Earth Engine enabled time series

Salt marshes provide a bulwark against sea-level rise (SLR), an interface between aquatic and terrestrial habitats, important nursery grounds for many species, a buffer against extreme storm impacts, and vast blue carbon repositories. However, salt marshes are at risk of loss from a variety of stressors such as SLR, nutrient enrichment, sediment deficits, herbivory, and anthropogenic disturbances. Determining the dynamics of salt marsh change with remote sensing requires high temporal resolution due to the spectral variability caused by disturbance, tides, and seasonality. Time series analysis of salt marshes can broaden our understanding of these changing environments. This study analyzed aboveground green biomass (AGB) in seven mid-Atlantic Hydrological Unit Code 8 (HUC-8) watersheds. The study revealed that the Eastern Lower Delmarva watershed had the highest average loss and the largest net reduction in salt marsh AGB from 1999–2018. The study developed a method that used Google Earth Engine (GEE) enabled time series of the Landsat archive for regional analysis of salt marsh change and identified at-risk watersheds and salt marshes providing insight into the resilience and management of these ecosystems. The time series were filtered by cloud cover and the Tidal Marsh Inundation Index (TMII). The combination of GEE enabled Landsat time series, and TMII filtering demonstrated a promising method for historic assessment and continued monitoring of salt marsh dynamics.

Using seasonal landscape models to predict space use and migratory patterns of an arctic ungulate

BACKGROUND

Caribou in the Western Arctic Herd undertake one of the longest, remaining intact migrations of terrestrial mammals in the world. They are also the most important subsistence resource for many northern rural residents, who rely on the caribou's migratory movements to bring them near for harvest. Migratory geography has never been static, but subsistence harvesters have reported recent shifts in migration away from areas where they traditionally occurred. The reasons behind these changes are not well-understood, but may be related to rapid climate change and anthropogenic disturbances.

METHODS

To predict changes in distribution and shifting migratory areas over the past decade, we used GPS telemetry data from adult females to develop predictive ecological niche models of caribou across northwestern Alaska. We employed the machine-learning algorithm, TreeNet, to analyze interactive, multivariate relationships between telemetry locations and 37 spatial environmental layers and to predict the distributions of caribou during spring, calving season, insect-harassment season, late summer, fall, and winter from 2009 to 2017. Model results were analyzed to identify regions of repeated predicted use, quantify mean longitude, predict land cover selection, and track migratory changes over time.

RESULTS

Distribution models accurately predicted caribou at a spatially-explicit, 500-m scale. Model analyses identified migratory areas that shifted annually across the region, but which predicted 4 main areas of repeated use. Niche models were defined largely by non-linear relationships with coastally-influenced, climatic variables, especially snow-free date, potential evapo-transpiration, growing season length, proximity to sea ice, winter precipitation and fall temperature. Proximity to roads and communities were also important and we predicted caribou to generally occur more than 20-100 km from these features.

CONCLUSIONS

Western Arctic Herd caribou were predicted to occur in warmer, snow-free and treeless areas that may provide conditions conducive for efficient travel and foraging. Rapidly changing seasonal climates and coastal influences that determine forage availability, and human impediments that slow or divert movements are related to geographically and phenologically dynamic migration patterns that may periodically shift caribou away from traditional harvest areas. An enhanced understanding of the geographic behavior of caribou over time could inform traditional harvests and help conserve important Western Arctic caribou migratory areas.

Time-varying predatory behavior is primary predictor of fine-scale movement of wildland-urban cougars

BACKGROUND

While many species have suffered from the detrimental impacts of increasing human population growth, some species, such as cougars (Puma concolor), have been observed using human-modified landscapes. However, human-modified habitat can be a source of both increased risk and increased food availability, particularly for large carnivores. Assessing preferential use of the landscape is important for managing wildlife and can be particularly useful in transitional habitats, such as at the wildland-urban interface. Preferential use is often evaluated using resource selection functions (RSFs), which are focused on quantifying habitat preference using either a temporally static framework or researcher-defined temporal delineations. Many applications of RSFs do not incorporate time-varying landscape availability or temporally-varying behavior, which may mask conflict and avoidance behavior.

METHODS

Contemporary approaches to incorporate landscape availability into the assessment of habitat selection include spatio-temporal point process models, step selection functions, and continuous-time Markov chain (CTMC) models; in contrast with the other methods, the CTMC model allows for explicit inference on animal movement in continuous-time. We used a hierarchical version of the CTMC framework to model speed and directionality of fine-scale movement by a population of cougars inhabiting the Front Range of Colorado, U.S.A., an area exhibiting rapid population growth and increased recreational use, as a function of individual variation and time-varying responses to landscape covariates.

RESULTS

We found evidence for individual- and daily temporal-variability in cougar response to landscape characteristics. Distance to nearest kill site emerged as the most important driver of movement at a population-level. We also detected seasonal differences in average response to elevation, heat loading, and distance to roads. Motility was also a function of amount of development, with cougars moving faster in developed areas than in undeveloped areas.

CONCLUSIONS

The time-varying framework allowed us to detect temporal variability that would be masked in a generalized linear model, and improved the within-sample predictive ability of the model. The high degree of individual variation suggests that, if agencies want to minimize human-wildlife conflict management options should be varied and flexible. However, due to the effect of recursive behavior on cougar movement, likely related to the location and timing of potential kill-sites, kill-site identification tools may be useful for identifying areas of potential conflict.

Trend estimation for complex survey designs of water chemistry indicators from Sierra Nevada Lakes

Surveys for long-term monitoring programs managing natural resources often incorporate sampling design complexity. However, design weights are often ignored in trend models of data from complex sampling designs. Generalized random tessellation stratified samples of a simulated population of lakes are selected with various levels of survey design complexity, and three trend approaches are compared. We compare an unweighted trend model, linear regression models of the trend in design-based estimates of annual status, and a probability-weighted iterative generalized least squares (PWIGLS) approach with a linearization variance. The bias and confidence interval coverage of the trend estimate and the size and power of the trend test are used to evaluate weighted and unweighted approaches. We find that the unweighted approach often outperforms the other trend approaches by providing high power for trend detection and nominal confidence interval coverage of the true trend regression parameter. We also find that variance composition and revisit design structure affect the performance of the PWIGLS estimator. When a subpopulation exhibiting an extreme trend is sampled disproportionately to its occurrence in the population, the unweighted approach may produce biased estimates of trend with poor confidence interval coverage. We recommend considering variance composition and potential subpopulation trends when selecting sampling designs and trend analysis approaches.

Projected avifaunal responses to climate change across the U.S. National Park System

Birds in U.S. national parks find strong protection from many longstanding and pervasive threats, but remain highly exposed to effects of ongoing climate change. To understand how climate change is likely to alter bird communities in parks, we used species distribution models relating North American Breeding Bird Survey (summer) and Audubon Christmas Bird Count (winter) observations to climate data from the early 2000s and projected to 2041–2070 (hereafter, mid-century) under high and low greenhouse gas concentration trajectories, RCP8.5 and RCP2.6. We analyzed climate suitability projections over time for 513 species across 274 national parks, classifying them as improving, worsening, stable, potential colonization, and potential extirpation. U.S. national parks are projected to become increasingly important for birds in the coming decades as potential colonizations exceed extirpations in 62–100% of parks, with an average ratio of potential colonizations to extirpations of 4.1 in winter and 1.4 in summer under RCP8.5. Average species turnover is 23% in both summer and winter under RCP8.5. Species turnover (Bray-Curtis) and potential colonization and extirpation rates are positively correlated with latitude in the contiguous 48 states. Parks in the Midwest and Northeast are expected to see particularly high rates of change. All patterns are more extreme under RCP8.5 than under RCP2.6. Based on the ratio of potential colonization and extirpation, parks were classified into overall trend groups associated with specific climate-informed conservation strategies. Substantial change to bird and ecological communities is anticipated in coming decades, and current thinking suggests managing towards a forward-looking concept of ecological integrity that accepts change and novel ecological conditions, rather than focusing management goals exclusively on maintaining or restoring a static set of historical conditions.

Urbanization and anticoagulant poisons promote immune dysfunction in bobcats

Understanding how human activities influence immune response to environmental stressors can support biodiversity conservation across increasingly urbanizing landscapes. We studied a bobcat (Lynx rufus) population in urban southern California that experienced a rapid population decline from 2002-2005 due to notoedric mange. Because anticoagulant rodenticide (AR) exposure was an underlying complication in mange deaths, we aimed to understand sublethal contributions of urbanization and ARs on 65 biochemical markers of immune and organ function. Variance in immunological variables was primarily associated with AR exposure and secondarily with urbanization. Use of urban habitat and AR exposure has pervasive, complex and predictable effects on biochemical markers of immune and organ function in free-ranging bobcats that include impacts on neutrophil, lymphocyte and cytokine populations, total bilirubin and phosphorus. We find evidence of both inflammatory response and immune suppression associated with urban land use and rat poison exposure that could influence susceptibility to opportunistic infections. Consequently, AR exposure may influence mortality and has population-level effects, as previous work in the focal population has revealed substantial mortality caused by mange infection. The secondary effects of anticoagulant exposure may be a worldwide, largely unrecognized problem affecting a variety of vertebrate species in human-dominated environments.

Molecular analysis of stomach contents reveals important grass seeds in the winter diet of Baird's and Grasshopper sparrows, two declining grassland bird species

We analyzed the diet of Baird's Sparrow (Ammodramus bairdii) and Grasshopper Sparrow (A. savannarum) in three different sites and sampling periods across the Chihuahuan Desert in northern Mexico. DNA from seeds in regurgitated stomach contents was sequenced using NGS technology and identified with a barcoding approach using the P6 loop of the trnL intron as genetic marker. During each sampling period, we collected random soil samples to estimate seed availability in the soil seed bank. Due to the variability and size of the genetic marker, the resolution was limited to a family level resolution for taxonomic classification of seeds, but in several cases a genus level was achieved. Diets contained a high diversity of seeds but were dominated by a limited number of genera/families. Seeds from Panicoideae (from the genera Panicum, Setaria, Eriochloa, Botriochloa, and Hackelochloa) contributed for the largest part to the diets (53 ± 19%), followed by Bouteloua (10 ± 12%). Depending on the site and sampling period, other important seeds in the diets were Eragrostideae, Pleuraphis, Asteraceae, Verbena, and Amaranthus. The most abundant seeds were not always preferred. Aristida and Chloris were common in the soil seed bank but these seeds were avoided by both bird species. Baird's and Grasshopper sparrows did not differ in seed preferences. This work highlights the importance of range management practices that favor seed production of Panicoideae and Bouteloua grasses to enhance winter habitat use and survival of Baird's and Grasshopper sparrows in the Chihuahuan Desert.

Disturbance of a rare seabird by ship-based tourism in a marine protected area

Managers of marine protected areas (MPAs) must often seek ways to allow for visitation while minimizing impacts to the resources they are intended to protect. Using shipboard observers, we quantified the "zone of disturbance" for Kittlitz's and marbled murrelets (Brachyramphus brevirostris and B. marmoratus) exposed to large cruise ships traveling through Glacier Bay National Park, one of the largest MPAs in North America. In the upper reaches of Glacier Bay, where Kittlitz's murrelets predominated, binary logistic regression models predicted that 61% of all murrelets within 850 m perpendicular distance of a cruise ship were disturbed (defined as flushing or diving), whereas in the lower reaches, where marbled murrelets predominated, this percentage increased to 72%. Using survival analysis, murrelets in both reaches were found to react at greater distances when ships approached indirectly, presumably because of the ship's larger profile, suggesting murrelets responded to visual rather than audio cues. No management-relevant covariates (e.g., ship velocity, route distance from shore) were found to be important predictors of disturbance, as distance from ship to murrelet accounted for > 90% of the explained variation in murrelet response. Utilizing previously published murrelet density estimates from Glacier Bay, and applying an average empirical disturbance probability (68%) out to 850 m from a cruise ship's typical route, we estimated that a minimum of 9.8-19.6% of all murrelets in Glacier Bay are disturbed per ship entry. Whether these disturbance levels are inconsistent with Park management objectives, which include conserving wildlife as well as providing opportunities for visitation, depends in large part on whether disturbance events caused by cruise ships have impacts on murrelet fitness, which remains uncertain.

Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep

Landscape genetic studies based on neutral genetic markers have contributed to our understanding of the influence of landscape composition and configuration on gene flow and genetic variation. However, the potential for species to adapt to changing landscapes will depend on how natural selection influences adaptive genetic variation. We demonstrate how landscape resistance models can be combined with genetic simulations incorporating natural selection to explore how the spread of adaptive variation is affected by landscape characteristics, using desert bighorn sheep (Ovis canadensis nelsoni) in three differing regions of the southwestern United States as an example. We conducted genetic sampling and least-cost path modeling to optimize landscape resistance models independently for each region, and then simulated the spread of an adaptive allele favored by selection across each region. Optimized landscape resistance models differed between regions with respect to landscape variables included and their relationships to resistance, but the slope of terrain and the presence of water barriers and major roads had the greatest impacts on gene flow. Genetic simulations showed that differences among landscapes strongly influenced spread of adaptive genetic variation, with faster spread (1) in landscapes with more continuously distributed habitat and (2) when a pre-existing allele (i.e., standing genetic variation) rather than a novel allele (i.e., mutation) served as the source of adaptive genetic variation. The combination of landscape resistance models and genetic simulations has broad conservation applications and can facilitate comparisons of adaptive potential within and between landscapes.

Hypothermic stunning of green sea turtles in a western Gulf of Mexico foraging habitat

Texas waters provide one of the most important developmental and foraging habitats for juvenile green turtles (Chelonia mydas) in the western Gulf of Mexico, but hypothermic stunning is a significant threat and was the largest cause of green turtle strandings in Texas from 1980 through 2015; of the 8,107 green turtles found stranded, 4,529 (55.9%) were victims of hypothermic stunning. Additionally, during this time, 203 hypothermic stunned green turtles were found incidentally captured due to power plant water intake entrapment. Overall, 63.9% of 4,529 hypothermic stunned turtles were found alive, and 92.0% of those survived rehabilitation and were released. Numbers of green turtles recorded as stranded and as affected by hypothermic stunning increased over time, and were most numerous from 2007 through 2015. Large hypothermic stunning events (with more than 450 turtles documented) occurred during the winters of 2009–2010, 2010–2011, 2013–2014, and 2014–2015. Hypothermic stunning was documented between November and March, but peaked at various times depending on passage of severe weather systems. Hypothermic stunning occurred state-wide, but was most prevalent in South Texas, particularly the Laguna Madre. In the Laguna Madre, hypothermic stunning was associated with an abrupt drop in water temperatures strong northerly winds, and a threshold mean water temperature of 8.0°C predicted large turtle hypothermic stunning events. Knowledge of environmental parameters contributing to hypothermic stunning and the temporal and spatial distribution of turtles affected in the past, can aid with formulation of proactive, targeted search and rescue efforts that can ultimately save the lives of many affected individuals, and aid with recovery efforts for this bi-national stock. Such rescue efforts are required under the U.S. Endangered Species Act and respond to humanitarian concerns of the public.

Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison

Yellowstone National Park is home to one of the only plains bison populations that have continuously existed on their present landscape since prehistoric times without evidence of domestic cattle introgression. Previous studies characterized the relatively high levels of nuclear genetic diversity in these bison, but little is known about their mitochondrial haplotype diversity. This study assessed mitochondrial genomes from 25 randomly selected Yellowstone bison and found 10 different mitochondrial haplotypes with a haplotype diversity of 0.78 (± 0.06). Spatial analysis of these mitochondrial DNA (mtDNA) haplotypes did not detect geographic population subdivision (F_ST = -0.06, p = 0.76). However, we identified two independent and historically important lineages in Yellowstone bison by combining data from 65 bison (defined by 120 polymorphic sites) from across North America representing a total of 30 different mitochondrial DNA haplotypes. Mitochondrial DNA haplotypes from one of the Yellowstone lineages represent descendants of the 22 indigenous bison remaining in central Yellowstone in 1902. The other mitochondrial DNA lineage represents descendants of the 18 females introduced from northern Montana in 1902 to supplement the indigenous bison population and develop a new breeding herd in the northern region of the park. Comparing modern and historical mitochondrial DNA diversity in Yellowstone bison helps uncover a historical context of park restoration efforts during the early 1900s, provides evidence against a hypothesized mitochondrial disease in bison, and reveals the signature of recent hybridization between American plains bison (Bison bison bison) and Canadian wood bison (B. b. athabascae). Our study demonstrates how mitochondrial DNA can be applied to delineate the history of wildlife species and inform future conservation actions.

Modeled Tradeoffs between Developed Land Protection and Tidal Habitat Maintenance during Rising Sea Levels

Tidal habitats host a diversity of species and provide hydrological services such as shoreline protection and nutrient attenuation. Accretion of sediment and biomass enables tidal marshes and swamps to grow vertically, providing a degree of resilience to rising sea levels. Even if accelerating sea level rise overcomes this vertical resilience, tidal habitats have the potential to migrate inland as they continue to occupy land that falls within the new tide range elevations. The existence of developed land inland of tidal habitats, however, may prevent this migration as efforts are often made to dyke and protect developments. To test the importance of inland migration to maintaining tidal habitat abundance under a range of potential rates of sea level rise, we developed a spatially explicit elevation tracking and habitat switching model, dubbed the Marsh Accretion and Inundation Model (MAIM), which incorporates elevation-dependent net land surface elevation gain functions. We applied the model to the metropolitan Washington, DC region, finding that the abundance of small National Park Service units and other public open space along the tidal Potomac River system provides a refuge to which tidal habitats may retreat to maintain total habitat area even under moderate sea level rise scenarios (0.7 m and 1.1 m rise by 2100). Under a severe sea level rise scenario associated with ice sheet collapse (1.7 m by 2100) habitat area is maintained only if no development is protected from rising water. If all existing development is protected, then 5%, 10%, and 40% of the total tidal habitat area is lost by 2100 for the three sea level rise scenarios tested.

Bird Communities and Environmental Correlates in Southern Oregon and Northern California, USA

We examined avian community ecology in the Klamath Ecoregion and determined that individual bird species co-exist spatially to form 29 statistically distinguishable bird groups. We identified climate, geography, and vegetation metrics that are correlated with these 29 bird groups at three scales: Klamath Ecoregion, vegetation formation (agriculture, conifer, mixed conifer/hardwood, shrubland), and National Park Service unit. Two climate variables (breeding season mean temperature and temperature range) and one geography variable (elevation) were correlated at all scales, suggesting that for some vegetation formations and park units there is sufficient variation in climate and geography to be an important driver of bird communities, a level of variation we expected only at the broader scale. We found vegetation to be important at all scales, with coarse metrics (environmental site potential and existing vegetation formation) meaningful across all scales and structural vegetation patterns (e.g. succession, disturbance) important only at the scale of vegetation formation or park unit. Additionally, we examined how well six National Park Service units represent bird communities in the broader Klamath Ecoregion. Park units are inclusive of most bird communities with the exception of the oak woodland community; mature conifer forests are well represented, primarily associated with conifer canopy and lacking multi-layered structure. Identifying environmental factors that shape bird communities at three scales within this region is important; such insights can inform local and regional land management decisions necessary to ensure bird conservation in this globally significant region.

Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples

Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.

Tri-Variate Relationships among Vegetation, Soil, and Topography along Gradients of Fluvial Biogeomorphic Succession

This research investigated how the strength of vegetation-soil-topography couplings varied along a gradient of biogeomorphic succession in two distinct fluvial systems: a forested river floodplain and a coastal salt marsh creek. The strength of couplings was quantified as tri-variance, which was calculated by correlating three singular axes, one each extracted using three-block partial least squares from vegetation, soil, and topography data blocks. Within each system, tri-variance was examined at low-, mid-, and high-elevation sites, which represented early-, intermediate-, and late-successional phases, respectively, and corresponded to differences in ongoing disturbance frequency and intensity. Both systems exhibited clearly increasing tri-variance from the early- to late-successional stages. The lowest-lying sites underwent frequent and intense hydrogeomorphic forcings that dynamically reworked soil substrates, restructured surface landforms, and controlled the colonization of plant species. Such conditions led vegetation, soil, and topography to show discrete, stochastic, and individualistic behaviors over space and time, resulting in a loose coupling among the three ecosystem components. In the highest-elevation sites, in contrast, disturbances that might disrupt the existing biotic-abiotic relationships were less common. Hence, ecological succession, soil-forming processes, and landform evolution occurred in tight conjunction with one another over a prolonged period, thereby strengthening couplings among them; namely, the three behaved in unity over space and time. We propose that the recurrence interval of physical disturbance is important to-and potentially serves as an indicator of-the intensity and mechanisms of vegetation-soil-topography feedbacks in fluvial biogeomorphic systems.

A One Health Message about Bats Increases Intentions to Follow Public Health Guidance on Bat Rabies

Since 1960, bat rabies variants have become the greatest source of human rabies deaths in the United States. Improving rabies awareness and preventing human exposure to rabid bats remains a national public health priority today. Concurrently, conservation of bats and the ecosystem benefits they provide is of increasing importance due to declining populations of many bat species. This study used a visitor-intercept experiment (N = 521) in two U.S. national parks where human and bat interactions occur on an occasional basis to examine the relative persuasiveness of four messages differing in the provision of benefit and uncertainty information on intentions to adopt a rabies exposure prevention behavior. We found that acknowledging benefits of bats in a risk message led to greater intentions to adopt the recommended rabies exposure prevention behavior without unnecessarily stigmatizing bats. These results signify the importance of communicating benefits of bats in bat rabies prevention messages to benefit both human and wildlife health.

Effects of geolocators on hatching success, return rates, breeding movements, and change in body mass in 16 species of Arctic-breeding shorebirds

BACKGROUND

Geolocators are useful for tracking movements of long-distance migrants, but potential negative effects on birds have not been well studied. We tested for effects of geolocators (0.8-2.0 g total, representing 0.1-3.9 % of mean body mass) on 16 species of migratory shorebirds, including five species with 2-4 subspecies each for a total of 23 study taxa. Study species spanned a range of body sizes (26-1091 g) and eight genera, and were tagged at 23 breeding and eight nonbreeding sites. We compared breeding performance and return rates of birds with geolocators to control groups while controlling for potential confounding variables.

RESULTS

We detected negative effects of tags for three small-bodied species. Geolocators reduced annual return rates for two of 23 taxa: by 63 % for semipalmated sandpipers and by 43 % for the arcticola subspecies of dunlin. High resighting effort for geolocator birds could have masked additional negative effects. Geolocators were more likely to negatively affect return rates if the total mass of geolocators and color markers was 2.5-5.8 % of body mass than if tags were 0.3-2.3 % of body mass. Carrying a geolocator reduced nest success by 42 % for semipalmated sandpipers and tripled the probability of partial clutch failure in semipalmated and western sandpipers. Geolocators mounted perpendicular to the leg on a flag had stronger negative effects on nest success than geolocators mounted parallel to the leg on a band. However, parallel-band geolocators were more likely to reduce return rates and cause injuries to the leg. No effects of geolocators were found on breeding movements or changes in body mass. Among-site variation in geolocator effect size was high, suggesting that local factors were important.

CONCLUSIONS

Negative effects of geolocators occurred only for three of the smallest species in our dataset, but were substantial when present. Future studies could mitigate impacts of tags by reducing protruding parts and minimizing use of additional markers. Investigators could maximize recovery of tags by strategically deploying geolocators on males, previously marked individuals, and successful breeders, though targeting subsets of a population could bias the resulting migratory movement data in some species.

Implications of Harvest on the Boundaries of Protected Areas for Large Carnivore Viewing Opportunities

The desire to see free ranging large carnivores in their natural habitat is a driver of tourism in protected areas around the globe. However, large carnivores are wide-ranging and subject to human-caused mortality outside protected area boundaries. The impact of harvest (trapping or hunting) on wildlife viewing opportunities has been the subject of intense debate and speculation, but quantitative analyses have been lacking. We examined the effect of legal harvest of wolves (Canis lupus) along the boundaries of two North American National Parks, Denali (DNPP) and Yellowstone (YNP), on wolf viewing opportunities within the parks during peak tourist season. We used data on wolf sightings, pack sizes, den site locations, and harvest adjacent to DNPP from 1997–2013 and YNP from 2008–2013 to evaluate the relationship between harvest and wolf viewing opportunities. Although sightings were largely driven by wolf population size and proximity of den sites to roads, sightings in both parks were significantly reduced by harvest. Sightings in YNP increased by 45% following years with no harvest of a wolf from a pack, and sightings in DNPP were more than twice as likely during a period with a harvest buffer zone than in years without the buffer. These findings show that harvest of wolves adjacent to protected areas can reduce sightings within those areas despite minimal impacts on the size of protected wolf populations. Consumptive use of carnivores adjacent to protected areas may therefore reduce their potential for non-consumptive use, and these tradeoffs should be considered when developing regional wildlife management policies.