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At least 325 records · Page 18Linked to original sources

USGS1983

Structure and petrology of the La Perouse gabbro intrusion, Fairweather Range, southeastern Alaska

The middle Tertiary La Perouse gabbro intrusion occurs in a Mesozoic metamorphic terrane (Chugach terrane) in the Fairweather Range, southeastern Alaska. The intrusion is 12 km wide and 27 km long, and has an exposed cumulate layering thickness of about 6000 m. The contact consists of biotite and hornblende gneiss of the granulite facies, which forms a discontinuous belt as much as 200 m wide. The outer contact of the zone is a fault, along which it is in contact with regionally metamorphosed biotite schist and amphibolite of the amphibolite facies. This fault seems to be a peripheral fault along which the intrusion was uplifted to its present level. The layering in the intrusion forms an asymmetrical funnel that is elongate northwestward and is structurally deepest at the southeast end near Mount La Perouse where the layering has inward dips of as much as 85°. Although the region was probably under compression at the time the gabbro was intruded, there is evidence that the intrusion's extremely sunken form is due not to tectonism but instead to subsidence from magmatic loading at high temperatures that continued after solidification. This tectonism was probably related to the interaction between the north-moving Pacific oceanic plates and the North American continent during the Tertiary. This interaction, which involved long-term right-lateral movement with a compressional component, and possibly minor subduction, on the site of the Fairweather fault, may have controlled the mode of magmatic intrusion and possibly the production of magma at depth, but does not appear to have significantly deformed the intrusion.

Journal of Petrology↗

USGS1962

Stability relations of the ferruginous biotite, annite

Annite , KFe 3 AISi 3 O 10 (OH) 2 a member of the iron biotites and the ferrous analogue of phlogopite, has been synthesized and its phase relations have been determined as functions of temperature, fugacity of oxygen (fo 2 ), and total pressure (P total ≈PH 2 O+PH 2 ). A method for controlling fo 2 at high total pressures is described, and data for the 'oxygen buffers' used are given. Buffers range from quartz+iron+fayalite assemblages (low fo 2 ) to magnetite-hematite assemblages (high fo 2 ). Optical properties and unit-cell dimensions of synthetic annites depend on the conditions of synthesis.By recalculating published analyses of natural iron-rich biotites it can be shown that one cannot assume a constant hydrogen content for such biotites. Oxidation may have occurred by drying at 115°C. Octahedral occupancy therefore cannot be calculated from such data.Phase relations of annite are presented in 2,070 and 1,035 bar sections. Depending on fo 2 -T values annite was found to decompose to one of the following assemblages: hematite+ sanidine, magnetite+sanidine, fayalite+leucite+kalsilite, iron+sanidine. All decompositions are dehydration and redox reactions and are sensitive to changes in fH 2 0 and fo 2 (or fH 2 0 and fH 2 ). At 2, 070 bars total pressure annite +magnetite+sanidine can coexist between 425°C and 825° C, depending upon the magnitude of fo 2 .In the presence of quartz the stability field of annite is more restricted. Phase equilibria in the system KAlSiO 4 -SiO 2 -Fe-O 2 -H 2 have been summarized schematically.Wherever possible, thermodynamic extrapolations are made to test the internal consistency of the data. Enthalpies of formation are calculated for both annite and phlogopite. Ranges of fo 2 values in nature as well as mechanisms for changes in fo 2 are investigated. It is useful to distinguish between assemblages which are internally buffered with respect to fo 2 changes and those which are not buffered. The applications of individual reactions involving annite to specific geologic problems are discussed with respect to igneous, metamorphic, and sedimentary rocks.

Journal of Petrology↗

USGS1990

Calc-alkaline, shoshonitic, and primitive tholeiitic lavas from monogenetic volcanoes near Crater Lake, Oregon

Quaternary monogenetic volcanism in the High Cascades of Oregon is manifested by cinder cones, lava fields, and small shields. Near Crater Lake caldera, monogenetic lava compositions include: low-K (as low as 0·09% K 2 O) high-alumina olivine tholeiite (HAOT); medium-K. calc-alkaline basalt, basaltic andesite, and andesite; and shoshonitic basaltic andesite (2·1% K 2 O, 1750 ppm Sr at 54% SiO 2 ). Tholeiites have MORB-like trace element abundances except for elevated Sr, Ba, and Th and low high field strength elements (HFSE), and they represent near-primary liquids. They are similar to HAOTs from the Cascades and adjacent Basin and Range, and to many primitive basalts from intraoceanic arcs. Calc-alkaline lavas show a well-developed arc signature of high large-ion lithophile elements (LILE) and low HFSE. Their Zr and Hf concentrations are at least partly decoupled from those of Nb and Ta; HREE are low relative to HAOT. Incompatible element abundances and ratios vary widely among basaltic andesites. Some calc-alkaline lavas vented near Mount Mazama contain abundant gabbroic microxcnoliths, and are basaltic andesitic magmas contaminated with olivine gabbro. A calc-alkaline basalt and a few basaltic andesites have MgO and compatible trace element contents that suggest only minor fractionation. There appears to be a compositional continuum between primitive tholeiitic and calc-alkaline lavas. Compositional variation within suites of comagmatic primitive lavas, both tholeiitic and calc-alkaline, mainly results from different degrees of partial melting. Sources of calc-alkaline primary magmas were enriched in LILE and LREE by a subduction component and contained residual garnet, whereas sources of HAOTs had lower LILE and LREE concentrations and contained residual clinopyroxene. High and variable LILE and LREE contents of calc-alkaline lavas reflect variations in fluid-transported subduction component added to the mantle wedge, degree of partial melting, and possibly also interaction with rocks or partial melts in the lower crust. Andesites were derived from calc-alkaline basaltic andesites by fractionation of plagioclase+augite+magnetite+apatite ± orthopyroxene or olivine, commonly accompanied by assimilation. Many andesites are mixtures of andesitic or dacitic magma and a basaltic or basaltic andesitic component, or are contaminated with gabbroic material. Mingled basalt, andesite, and dacite of Williams Crater formed by multi-component, multi-stage mixing of basaltic andesitic magma, gabbro, and dacitic magma. The wide range of compositions vented from monogenetic volcanoes near Crater Lake is a result of the thick crust coupled with mild tectonic extension superimposed on a subduction-related magmatic arc.

Oregon↗

USGS2001

Eruptive stratigraphy of the Tatara-San Pedro complex, 36°S, sourthern volcanic zone, Chilean Andes: Reconstruction method and implications for magma evolution at long-lived arc volcanic centers

The Quaternary Tatara–San Pedro volcanic complex (36°S, Chilean Andes) comprises eight or more unconformity-bound volcanic sequences, representing variably preserved erosional remnants of volcanic centers generated during ∼930 ky of activity. The internal eruptive histories of several dominantly mafic to intermediate sequences have been reconstructed, on the basis of correlations of whole-rock major and trace element chemistry of flows between multiple sampled sections, but with critical contributions from photogrammetric, geochronologic, and paleomagnetic data. Many groups of flows representing discrete eruptive events define internal variation trends that reflect extrusion of heterogeneous or rapidly evolving magma batches from conduit–reservoir systems in which open-system processes typically played a large role. Long-term progressive evolution trends are extremely rare and the magma compositions of successive eruptive events rarely lie on precisely the same differentiation trend, even where they have evolved from similar parent magmas by similar processes. These observations are not consistent with magma differentiation in large long-lived reservoirs, but they may be accommodated by diverse interactions between newly arrived magma inputs and multiple resident pockets of evolved magma and/or crystal mush residing in conduit-dominated subvolcanic reservoirs. Without constraints provided by the reconstructed stratigraphic relations, the framework for petrologic modeling would be far different. A well-established eruptive stratigraphy may provide independent constraints on the petrologic processes involved in magma evolution—simply on the basis of the specific order in which diverse, broadly cogenetic magmas have been erupted. The Tatara–San Pedro complex includes lavas ranging from primitive basalt to high-SiO 2 rhyolite, and although the dominant erupted magma type was basaltic andesite (∼52–55 wt % SiO 2 ) each sequence is characterized by unique proportions of mafic, intermediate, and silicic eruptive products. Intermediate lava compositions also record different evolution paths, both within and between sequences. No systematic long-term pattern is evident from comparisons at the level of sequences. The considerable diversity of mafic and evolved magmas of the Tatara–San Pedro complex bears on interpretations of regional geochemical trends. The variable role of open-system processes in shaping the compositions of evolved Tatara–San Pedro complex magmas, and even some basaltic magmas, leads to the conclusion that addressing problems such as arc magma genesis and elemental fluxes through subduction zones on the basis of averaged or regressed reconnaissance geochemical datasets is a tenuous exercise. Such compositional indices are highly instructive for identifying broad regional trends and first-order problems, but they should be used with extreme caution in attempts to quantify processes and magma sources, including crustal components, implicated in these trends.

Andes Mountains, Tatara-San Pedro Volcanic Complex↗

USGS2020

Petrologic insights into rift zone magmatic interactions from the 2011 eruption of Kīlauea Volcano, Hawaiʻi

The high frequency of historical eruptions at Kīlauea Volcano presents an exceptional opportunity to address fundamental questions related to the transport, storage, and interaction of magmas within rift zones. The Nāpau Crater area on Kīlauea’s East Rift Zone (ERZ) experienced nine fissure eruptions within 50 years (1961–2011). Most of the magma intruded during these frequent eruptions remained stored within the rift zone, creating a potential magma mixing depot within the ERZ. The superbly monitored and sampled 2011 eruption (Puʻu ʻŌʻō episode 59) presents an extraordinary opportunity to evaluate magma mixing processes within the ERZ. Whole-rock, glass, and olivine compositions were determined, not only for lava from the 2011 eruption, but also for a new suite of Nāpau Crater area samples from the 1963, 1965, 1968, 1983, and 1997 eruptions, as well as the previously undocumented 1922 eruption. Whole-rock XRF data revealed two geochemically distinct magma batches for episode 59: one less evolved (∼6·6 wt % MgO, 0·46 wt % K2O) than the other (∼6·2 wt % MgO, 0·58 wt % K2O). Episode 59 lava is remarkably aphyric (∼0·1 vol. % phenocrysts), making use of mineralogy to identify parent magma affinities problematic. Linear compositional trends of whole-rock major and trace elements, and reversely zoned olivine crystals indicate episode 59 lavas underwent magma mixing. Least squares regression calculations and plots of major and trace element data, were used to evaluate whether the episode 59 samples are products of mixing summit-derived magma with residual magma from previous Nāpau Crater area eruptions. The regression results and trace element ratios are inconsistent with previously proposed mixing scenarios, but they do support mixing between summit-derived magma and residual magma from the 1983 and 1997 Nāpau Crater area eruptions. These magmas were stored in physically and chemically distinct pods at depths of 1·6–3·0 km prior to mixing with new magma intruded from the summit to produce the episode 59 lava. One pod contained a fractionated equivalent of 1983 lava, and the other a hybrid of compositions similar to 1983 and 1997 lavas. The petrology of episode 59 lava demonstrates that magmas from two previous eruptions (1983 and 1997) were available to mix with magma intruded from the summit region. This study clarifies the pre-eruptive history of the mixed episode 59 lava, and elucidates the evolution of the volcano's magmatic system in a region of frequent eruptions.

Hawaii↗

USGS2012

Genetic analysis of a novel nidovirus from fathead minnows

A bacilliform virus was isolated from diseased fathead minnows ( Pimephales promelas ). Analysis of the complete genome coding for the polyprotein (pp1ab), spike (S), membrane (M) and nucleocapsid (N) proteins revealed that the virus was most like white bream virus (WBV), another bacilliform virus isolated from white bream ( Blicca bjoerkna L.) and the type species of the genus Bafinivirus within the order Nidovirales . In addition to similar gene order and size, alignment of deduced amino acid sequences of the pp1ab, M, N and S proteins of the fathead minnow nidovirus (FHMNV) with those of WBV showed 46, 44, 39 and 15 % identities, respectively. Phylogenetic analysis using the conserved helicase domain of the replicase showed FHMNV was distinct from WBV, yet the closest relative identified to date. Thus, FHMNV appears to represent a second species in the genus Bafinivirus . A PCR assay was developed for the identification of future FHMNV-like isolates.

Journal of General Virology↗

USGS2004

Isolation and characterization of a rhabdovirus from starry flounder (Platichthys stellatus) collected from the northern portion of Puget Sound, Washington, USA

The initial characterization of a rhabdovirus isolated from a single, asymptomatic starry flounder (Platichthys stellatus) collected during a viral survey of marine fishes from the northern portion of Puget Sound, Washington, USA, is reported. Virions were bullet-shaped and approximately 100 nm long and 50 nm wide, contained a lipid envelope, remained stable for at least 14 days at temperatures ranging from -80 to 5 degrees C and grew optimally at 15 degrees C in cultures of epithelioma papulosum cyprini (EPC) cells. The cytopathic effect on EPC cell monolayers was characterized by raised foci containing rounded masses of cells. Pyknotic and dark-staining nuclei that also showed signs of karyorrhexis were observed following haematoxylin and eosin, May-Grunwald Giemsa and acridine orange staining. PAGE of the structural proteins and PCR assays using primers specific for other known fish rhabdoviruses, including Infectious hematopoietic necrosis virus, Viral hemorrhagic septicemia virus, Spring viremia of carp virus, and Hirame rhabdovirus, indicated that the new virus, tentatively termed starry flounder rhabdovirus (SFRV), was previously undescribed in marine fishes from this region. In addition, sequence analysis of 2678 nt of the amino portion of the viral polymerase gene indicated that SFRV was genetically distinct from other members of the family Rhabdoviridae for which sequence data are available. Detection of this virus during a limited viral survey of wild fishes emphasizes the void of knowledge regarding the diversity of viruses that naturally infect marine fish species in the North Pacific Ocean.

Journal of General Virology↗

USGS1999

GIXAFS study of Fe3+ sorption and precipitation on natural quartz surfaces

Grazing-incidence EXAFS has been used to characterize the structure of Fe 3+ sorbed onto natural single crystal quartz surfaces. Fe 3+ sorption at ca. 5% monolayer coverage on a natural crystal allowed to equilibrate in air resulted in formation of hematite nuclei with strong texturing on r-and m-planes. EXAFS calculations suggests that both O and Fe backscattering is necessary to yield acceptable structural models, that about 50% of the sorbed iron resides in nuclei, and that the approximate dimensions of the nuclei can be estimated via Feff 7.0 calculations of various nuclei sizes and shapes.

Journal of Synchrotron Radiation↗

USGS2017

Effects of host species and environment on the skin microbiome of Plethodontid salamanders

The amphibian skin microbiome is recognized for its role in defence against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (35 Plethodon cinereus , 17 Plethodon glutinosus , 10 Plethodon cylindraceus ) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient ( n = 50, 700–1,000 m a.s.l.) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% ( SD ± 8.5) per salamander. All salamanders tested negative for Bd. We conclude that environment is more influential in shaping skin microbiome structure than host differences in these congeneric species, and suggest that environmental characteristics that covary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.

Journal of Animal Ecology↗

USGS2020

A test of the Niche Variation Hypothesis in a ruminant herbivore

Despite the shared prediction that the width of a population's dietary niche expands as food becomes limiting, the Niche Variation Hypothesis (NVH) and Optimal Foraging Theory (OFT) offer contrasting views about how individuals alter diet selection when food is limited. Classical OFT predicts that dietary preferences do not change as food becomes limiting, so individuals expand their diets as they compensate for a lack of preferred foods. In contrast, the NVH predicts that among-individual variation in cognition, physiology or morphology create functional trade-offs in foraging efficiency, thereby causing individuals to specialize on different subsets of food as food becomes limiting. To evaluate (a) the predictions of the NVH and OFT and (b) evidence for physiological and cognitive-based functional trade-offs, we used DNA microsatellites and metabarcoding to quantify the diet, microbiome and genetic relatedness (a proxy for social learning) of 218 moose Alces alces across six populations that varied in their degree of food limitation. Consistent with both the NVH and OFT, dietary niche breadth increased with food limitation. Increased diet breadth of individuals—rather than increased diet specialization—was strongly correlated with both food limitation and dietary niche breadth of populations, indicating that moose foraged in accordance with OFT. Diets were not constrained by inheritance of the microbiome or inheritance of diet selection, offering support for the little-tested hypothesis that functional trade-offs in food use (or lack thereof) determine whether populations adhere to the predictions of the NVH or OFT. Our results indicate that both the absence of strong functional trade-offs and the digestive physiology of ruminants provide contexts under which populations should forage in accordance with OFT rather than the NVH. Also, because dietary niche width increased with increased food limitation, OFT and the NVH provide theoretical support for the notion that plant–herbivore interaction networks are plastic rather than static, which has important implications for understanding interspecific niche partitioning. Lastly, because population-level dietary niche breadth and calf recruitment are correlated, and because calf recruitment can be a proxy for food limitation, our work demonstrates how diet data can be employed to understand a populations' proximity to carrying capacity.

Colorado, Utah, Wyoming↗

USGS2021

Age-related reproductive performance of the Adélie penguin, a long-lived seabird exhibiting similar outcomes regardless of individual life-history strategy

Age-related variation in reproductive performance in long-lived iteroparous vertebrate species is common, with performance being influenced by within-individual processes, such as improvement and senescence, in combination with among-individual processes, such as selective appearance and disappearance. Few studies of age-related reproductive performance have compared the role of these drivers within a metapopulation, subject to varying degrees of resource competition. We accounted for within- and among-individual changes among known-aged Adélie penguins Pygoscelis adeliae during 17 years (1997-2013), at three clustered colonies of disparate size, to understand patterns in age-related reproductive success during early and late adulthood. Age at first reproduction (AFR) was lowest, and number of breeding attempts highest, at the largest colony. Regardless of AFR, success improved with early post-recruitment experience. For both oldest and youngest recruitment groups, peak performance occurred at the end of their reproductive life span indicating a possible cost of reproduction. Intermediate recruitment groups reached peak performance in their mid-reproductive life span and with intermediate breeding experience, before decreasing. Breeding success was lowest for the initial breeding attempt regardless of AFR, but we observed subsequent variation relative to recruitment age. Gaining experience by delaying recruitment positively influenced reproductive performance early in the reproductive life span and was most evident for the youngest breeders. Oldest recruits had the highest initial and peak breeding success. Differences in AFR resulted in trade-offs in reproductive life span or timing of senescence but not in the overall number of breeding attempts. Patterns differed as a function of colony size, and thus competition for resources. Early life improvement in performance at the larger colonies was primarily due to within-individual factors and at the largest colony, AFR. Regardless of colony size late-life performance was positively related to the age at last reproduction, indicating selective disappearance of lower performing individuals. These results highlight that different life-history strategies were equally successful, indicating that individuals can overcome potential trade-offs associated with early- and late-life performance. These results have important implications for understanding the evolution of life-history strategies responsible for driving population change.

Beaufort Island ,Ross Island↗

USGS2022

Behavioural adjustments in the social associations of a precocial shorebird mediate the costs and benefits of grouping decisions

Animals weigh multiple costs and benefits when making grouping decisions. The cost-avoidance grouping framework proposes that group density, information quality and risk affect an individual’s preference for con or heterospecific groups. However, this assumes the cost–benefit balance of a particular grouping is constant spatiotemporally, which may not always be true. Investigating how spatiotemporal context influences grouping choices is therefore key to understanding how animals contend with changing conditions. Changes in body size during development lead to variable conditions for individuals over short time-scales that can influence their ecological interactions. Hudsonian godwits Limosa haemastica , for instance, form a protective nesting association with a major predator of young godwit chicks, colonial short-billed gulls Larus brachyrhynchus . Godwit broods may avoid areas of higher gull densities when chicks are susceptible to gull predation but likely experience higher risk from alternative predators as a result. Associating with conspecifics could allow godwits to buffer these costs but requires enough other broods with whom to group. To determine how age-dependent predation risk and conspecific density influence godwit grouping behaviours, we first quantified the time-dependent effects of con- and heterospecific interactions on the mortality risk for godwit chicks throughout development. We then determined how godwit density and chick age affected their associations with con- and heterospecific. We found that younger godwit chicks' survival improved with closer association with conspecifics, earlier hatch dates and lower gull densities, whereas older chicks survived better with earlier hatch dates, though this effect was less clear. Concomitantly, godwit broods avoided gulls early in development and when godwit densities were high but maintained loose associations with conspecifics throughout development. We identified how individuals can optimally shift with whom they group according to risks that vary spatially and temporally. Investigating the effects of a species' ecological interactions across spatiotemporal contexts in this way can shed light on how animals adjust their associations according to the costs and benefits of each association.

Journal of Animal Ecology↗

USGS2022

Using piecewise regression to identify biological phenomena in biotelemetry datasets

1. Technological advances in the field of animal tracking have greatly expanded the potential to remotely monitor animals, opening the door to exploring how animals shift their behavior over time or respond to external stimuli. A wide variety of animal-borne sensors can provide information on an animal’s location, movement characteristics, external environmental conditions, and internal physiological status. 2. Here, we demonstrate how piecewise regression can be used to identify the presence and timing of potential shifts in a variety of biological responses using GPS telemetry and other biologging data streams. Different biological latent states can be inferred by partitioning a time-series into multiple segments based on changes in modeled responses (e.g., their mean, variance, trend, degree of autocorrelation) and specifying a unique model structure for each interval. 3. We provide six example applications highlighting a variety of taxonomic species, data streams, timescales and biological phenomena. These examples include a short-term behavioural response (flee and return) by a trumpeter swan Cygnus buccinator following a GPS collar deployment; remote identification of parturition based on movements by a pregnant moose Alces alces ; a physiological response (spike in heart-rate) in a black bear Ursus americanus to a stressful stimulus(presence of a drone); a mortality event of a trumpeter swan signalled by changes in collar temperature and overall dynamic body acceleration; an unsupervised method for identifying the onset, return, duration and staging use of sandhill crane Antigone canadensis migration; and estimation of the transition between incubation and brood-rearing (i.e. hatching) for a breeding trumpeter swan. 4. We implement analyses using the MCP package in R, which provides functionality for specifying and fitting a wide variety of user-defined model structures in a Bayesian framework and methods for assessing and comparing models using information criteria and cross-validation measures.

Journal of Animal Ecology↗

USGS2024

A ‘how-to’ guide for estimating animal diel activity using hierarchical models

Animal diel activity patterns can aid understanding of (a) how species behaviourally adapt to anthropogenic and natural disturbances, (b) mechanisms of species co-existence through temporal partitioning, and (c) community or ecosystem effects of diel activity shifts. Activity patterns often vary spatially, a feature ignored by the kernel density estimators (KDEs) currently used for estimating diel activity. Ignoring this source of heterogeneity may lead to biased estimates of uncertainty and misleading conclusions regarding the drivers of diel activity. Thus, there is a need for more flexible statistical approaches for estimating activity patterns and testing hypotheses regarding their biotic and abiotic drivers. We illustrate how trigonometric terms and cyclic cubic splines combined with hierarchical models can provide a valuable alternative to KDEs. Like KDEs, these models accommodate circular data, but they can also account for site-to-site and other sources of variability, correlation amongst repeated measures, and variable sampling effort. They can also more readily quantify and test hypotheses related to the effects of covariates on activity patterns. Through empirical case studies, we illustrate how hierarchical models can quantify changes in activity levels due to seasonality and in response to biotic and abiotic factors (e.g. anthropogenic stressors and co-occurrence). We also describe frequentist and Bayesian approaches for quantifying site-specific (conditional) and population-averaged (marginal) activity patterns. We provide guidelines and tutorials with detailed step-by-step instructions for fitting and interpreting hierarchical models applied to time-stamped data, such as those recorded by camera traps and audio recorders. We conclude that this approach offers a viable, flexible, and effective alternative to KDEs when modelling animal activity patterns.

Journal of Animal Ecology↗

USGS2015

Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction

The reintroduction of a species into its historic range is a critical component of conservation programmes designed to restore extirpated metapopulations. However, many reintroduction efforts fail, and the lack of rigorous monitoring programmes and statistical models have prevented a general understanding of the factors affecting metapopulation viability following reintroduction. Spatially explicit metapopulation theory provides the basis for understanding the dynamics of fragmented populations linked by dispersal, but the theory has rarely been used to guide reintroduction programmes because most spatial metapopulation models require presence–absence data from every site in the network, and they do not allow for observation error such as imperfect detection. We develop a spatial occupancy model that relaxes these restrictive assumptions and allows for inference about metapopulation extinction risk and connectivity. We demonstrate the utility of the model using six years of data on the Chiricahua leopard frog Lithobates chiricahuensis , a threatened desert-breeding amphibian that was reintroduced to a network of sites in Arizona USA in 2003. Our results indicate that the model can generate precise predictions of extinction risk and produce connectivity maps that can guide conservation efforts following reintroduction. In the case of L. chiricahuensis , many sites were functionally isolated, and 82% of sites were characterized by intermittent water availability and high local extinction probabilities (0·84, 95% CI: 0·64–0·99). However, under the current hydrological conditions and spatial arrangement of sites, the risk of metapopulation extinction is estimated to be <3% over a 50-year time horizon. Low metapopulation extinction risk appears to result from the high dispersal capability of the species, the high density of sites in the region and the existence of predator-free permanent wetlands with low local extinction probabilities. Should management be required, extinction risk can be reduced by either increasing the hydroperiod of existing sites or by creating new sites to increase connectivity. Synthesis and applications . This work demonstrates how spatio-temporal statistical models based on ecological theory can be applied to forecast the outcomes of conservation actions such as reintroduction. Our spatial occupancy model should be particularly useful when management agencies lack the funds to collect intensive individual-level data.

Arizona, New Mexico↗

USGS2016

Habitat drives dispersal and survival of translocated juvenile desert tortoises

1.In spite of growing reliance on translocations in wildlife conservation, translocation efficacy remains inconsistent. One factor that can contribute to failed translocations is releasing animals into poor quality or otherwise inadequate habitat. 2.Here we used a targeted approach to test the relationship of habitat features to post-translocation dispersal and survival of juvenile Mojave desert tortoises Gopherus agassizii . 3.We selected three habitat characteristics—rodent burrows, substrate texture (prevalence and size of rocks), and washes (ephemeral river beds)–that are tied to desert tortoise ecology. At the point of release, we documented rodent burrow abundance, substrate texture, and wash presence and analysed their relationship to maximum dispersal. We also documented relative use by each individual for each habitat characteristic and analysed their relationships with survival and fatal encounters with a predator in the first year after release. 4.In general, the presence of refugia or other areas that enabled animals to avoid detection, such as burrows and substrate, decreased overall mortality as well as predator-mediated mortality. The presence of washes and substrate that enhanced the tortoises’ ability to avoid detection also associated with reduced dispersal away from the release site. These results indicate an important role for all three measured habitat characteristics in driving dispersal, survival, or fatal encounters with a predator in the first year after translocation. 5. Synthesis and applications . Resource managers using translocations as a conservation tool should prioritize acquiring data linking habitat to fitness. In particular, for species that depend on avoiding detection, refuges such as burrows and habitat that improved concealment had notable ability to improve survival and dispersal. Our study on juvenile Mojave desert tortoises showed that refuge availability or the distributions of habitat appropriate for concealment are important considerations for identifying translocation sites for species highly dependent on crypsis, camouflage, or other forms of habitat matching.

Journal of Applied Ecology↗

USGS2018

Decision making for mitigating wildlife diseases: From theory to practice for an emerging fungal pathogen of amphibians

Conservation science can be most effective in its decision‐support role when seeking answers to clearly formulated questions of direct management relevance. Emerging wildlife diseases, a driver of global biodiversity loss, illustrate the challenges of performing this role: in spite of considerable research, successful disease mitigation is uncommon. Decision analysis is increasingly advocated to guide mitigation planning, but its application remains rare. Using an integral projection model, we explored potential mitigation actions for avoiding population declines and the ongoing spatial spread of the fungus Batrachochytrium salamandrivorans ( Bsal ). This fungus has recently caused severe amphibian declines in north‐western Europe and currently threatens Palearctic salamander diversity. Available evidence suggests that a Bsal outbreak in a fire salamander ( Salamandra salamandra ) population will lead to its rapid extirpation. Treatments such as antifungals or probiotics would need to effectively interrupt transmission (reduce probability of infection by nearly 90%) in order to reduce the risk of host extirpation and successfully eradicate the pathogen. Improving the survival of infected hosts is most likely to be detrimental as it increases the potential for pathogen transmission and spread. Active removal of a large proportion of the host population has some potential to locally eradicate Bsal and interrupt its spread, depending on the presence of Bsal reservoirs and on the host's spatial dynamics, which should therefore represent research priorities. Synthesis and applications . Mitigation of Batrachochytrium salamandrivorans epidemics in susceptible host species is highly challenging, requiring effective interruption of transmission and radical removal of host individuals. More generally, our study illustrates the advantages of framing conservation science directly in the management decision context, rather than adapting to it a posteriori .

Journal of Applied Ecology↗

USGS2022

Primary production responses to extreme changes in North American Monsoon precipitation vary by elevation and plant functional composition through time

Primary production in dryland ecosystems is limited by water availability and projected to be strongly affected by future shifts in seasonal precipitation. Warm-season precipitation derived from the North American Monsoon contributes 40% of annual precipitation to dryland ecosystems in the southwestern U.S. and is projected to become more variable. However, there is large uncertainty on whether this variability will be expressed as either extreme wet or dry years and how primary production of different plant functional types will respond across widespread elevation gradients in this region. We experimentally imposed extreme drought and water addition treatments from 2016 – 2020, during which ambient warm-season precipitation declined to reach historic lows, to understand production sensitivity of dominant plant functional types along a 1,000 m elevation gradient. We found that the production responses of plant functional types to monsoon precipitation extremes were dependent on the number of treatment years that occurred across sites along the elevation gradient. C 4 perennial grasses were most responsive to precipitation manipulation treatments, followed by C 3 perennial grasses and annuals, while perennial forbs and shrubs had weak or no responses. C 4 perennial grass reductions due to extreme drought were generally stronger or occurred earlier at low elevation sites, while multi-year extreme drought extended negative effects to C 3 perennial grasses at high elevation, and all sites showed delayed responses to multi-year water addition. We found that the sensitivity of C 3 perennial grass production differed for extreme drought and water addition compared to ambient precipitation at one site, but other sites and plant functional types had similar sensitivities to the different treatment types. Synthesis . The upward advance of primary production responsiveness from single- to multi-year extreme changes in warm-season precipitation suggests more immediate shifts in functional composition and carbon cycling at low elevation, while high elevation ecosystems may become less resistant as the effects of extreme precipitation compound through time.

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