Ad hoc Smoothing Parameter Performance in Kernel Estimates of GPS-derived Home Ranges

Accuracy of home-range estimates in animals is influenced by a variety of factors, such as method of analysis and number of locations, but animal space use is less often considered and frequently over-generalized through simulations. Our objective was to assess effect of an ad hoc (h_ad hoc)smoothing parameter in kernel analysis from two species that were predicted to have different patterns of utilization distributions across a range of sample sizes. We evaluated variation in home-range estimates with location data collected from GPS collars on two species: mule deer Odocoileus hemionus and coyotes Canis latrans. We calculated home ranges using 95% and 50% kernel contours using reference (h_ref and h ad hoc smoothing parameters. To evaluate the influence of sample size, we calculated home ranges using both smoothing parameters for random subsamples of 5, 10, 25 and 50% of GPS locations and compared area estimates to estimates for 100% of GPS locations. On mule deer, we also conducted visual relocations using conventional radiotelemetry, which resulted in fewer locations than GPS collars. Area was overestimated at smaller sample sizes, but an interesting pattern was noted with higher relative bias at 60–100 locations than at sample sizes \u3c 50 locations. Relative bias was most likely due to increased smoothing of outer data points. Subsampling allowed us to examine relative bias across a range of samples sizes for the two smoothing parameters. Minimum number of points to obtain a consistent home range estimates varied by smoothing method, species, study duration, and volume contour (95% or 50%). While h_ad hoc performed consistently better over most sample sizes, there may not be a universal recommendation for all studies and species. Behavioral traits resulting in concentrated or disparate space use complicates comparisons among and between species. We suggest researchers examine their point distribution, justify their choice of smoothing parameter, and report their choices for home-range analysis based on their study objectives

How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species

Restoration of depleted populations is an important method in biological conservation. Reintroduction strategies frequently aim to restore stable, increasing, self-sustaining populations. Knowledge of asymptotic system dynamics may provide advantage in selecting reintroduction strategies. We introduce interactive software that is designed to identify strategies for release of females that are immediately aligned with stable population dynamics from species represented by 2-, 3-, 4-, and 5-stage life history strategies. The software allows managers to input a matrix of interest, the desired number of breeding females, and the desired management timeline, and calls upon stable population theory to give release strategies that are in concert with both stable population status and the management goals. We demonstrate how the software can aid in assessing various strategies ahead of a hypothetical restoration. For the purpose of demonstration of the tool only, we use published vital rates of an ungulate species, but remark that the selection of species for demonstration is not central to the use of this tool. Adaption of this tool to real-life restorations of any 2-, 3-, 4-, or 5-stage iteroparous species may aid in understanding how to minimize undesirable recovery complications that may naturally arise from transient population dynamics. The software is freely available at: https//cwhl.vet.cornell.edu/tools/stapopd

A review of episodes of zinc phosphide toxicosis in wild geese (Branta spp.) in Oregon (2004–2011)

Epizootic mortality in several geese species, including cackling geese (Branta hutchinsii) and Canada geese (Branta canadensis), has been recognized in the Willamette Valley of Oregon for over a decade. Birds are generally found dead on a body of water or are occasionally observed displaying neurologic clinical signs such as an inability to raise or control the head prior to death. Investigation of these epizootic mortality events has revealed the etiology to be accidental poisoning with the rodenticide zinc phosphide (Zn₃ P₂ ). Gross and histologic changes are restricted to acute pulmonary congestion and edema, sometimes accompanied by distension of the upper alimentary tract by fresh grass. Geese are unusually susceptible to this pesticide; when combined with an epidemiologic confluence of depredation of specific agricultural crops by rodents and seasonal avian migration pathways, epizootic toxicosis may occur. Diagnosis requires a high index of suspicion, appropriate sample collection and handling, plus specific test calibration for this toxicant. Interagency cooperation, education of farmers regarding pesticide use, and enforcement of regulations has been successful in greatly decreasing these mortality events since 2009.Keywords: Neurologic disease, Pulmonary edema, Branta, Toxicosis, Rodenticide, Geese, Zinc phosphide, Epizootic mortalit

Monitoring for Chronic Wasting Disease in Mule Deer and White-Tailed Deer at Wind Cave National Park: Investigating an Emerging Epizootic

Chronic wasting disease (CWD) has emerged as a disease of concern in cervid populations. Testing, transmission, and detection of CWD are areas of interest for managing populations of North American deer (Odocoileus). This dissertation addresses these areas with research from data collected on mule deer (O. hemionus) and white-tailed deer (O. virginanus) in Wind Cave National Park, South Dakota, USA, between February 2003 and December 2005. The objectives for this research were to: 1) assess performance of 2 sampling approaches with tonsillar biopsy for CWD testing; 2) evaluate home-range overlap and direct contacts for potential transmission of CWD; 3) determine probabilities of detection and death related to CWD from deer mortalities; and 4) examine sample size and smoothing parameters on home ranges from GPS collars on home ranges for mule deer and coyotes (Canis latrans). For objective 1, we collected data between January 2003 and January 2005 on white-tailed deer in southeast and southwest Minnesota and white-tailed and mule deer in Wind Cave National Park, South Dakota through biopsy sampling with dorso-lateral and ventral-medial approaches for collecting tonsillar follicles. We obtained significantly more follicles using the dorsolateral (median number of follicles = 19) than the ventral-medial (median number of follicles = 5.5) approach. No differences were observed in collection of tonsillar follicles that were related to sex, age class, or species of deer. We recommend the dorso-lateral approach for assessing CWD prevalence in deer populations. Regarding objective 2, horizontal transmission (i.e., transmission between potentially unrelated animals) is suspected of serving as the predominate source of infection for CWD epizootics. An indirect form of horizontal infection includes environmental contamination, which has recently been confirmed experimentally to be a source of infection. We radiocollared and tested 4 white-tailed deer and 60 mule deer for CWD in Wind Cave National Park, South Dakota, USA. Our study determined if home-range overlap was an accurate predictor of contact rates between deer. We examined contact and home-range parameters between species, mule deer sexes, and CWD-infected versus non-infected mule deer. Home-range overlap was not a good predictor of contact between deer pairs unless home ranges overlapped by ≥70%. Moreover, interspecific contact was unlikely despite home-range overlap. Intraspecific contact between mule deer resulted from same-sex associations for most of the year, but reproductive status (e.g., lactation, rut) influenced association of sexes. Deer infected with CWD had slightly decreased contact rates and increased home-range overlap compared with non-infected deer. We hypothesize that indirect transmission through environmental contamination is a more likely route of interspecific disease spread than direct horizontal contact because of overlapping home ranges with limited social contact. Thus, models of CWD transmission in deer should include home-range overlap because of the possibility of environmental contamination. For objective 3, estimates of mortality rates are essential for understanding population dynamics of ungulates. Currently, there are few data on how CWD affects deer populations or the likelihood that CWD-infected deer are tested. Detection rates for CWD are important because in some instances, deer positive with CWD at time of death cannot be tested for the disease because of availability or condition of appropriate tissues. We evaluated survival, mortality, transition, and detection rates for deer infected with CWD residing in Wind Cave National Park. We included 34 monthly encounters of deer resightings and mortalities for 67 deer (4 white-tailed deer, 63 mule deer). Mortalities were tested for CWD and resulted in prevalence rates of 2.9% in 2003, 9.1% in 2004, and 15.0% in 2005 for a pooled prevalence rate of 9.0% over 3 years. We assessed survival and influence of covariates, such as age, sex, species, collar type, and capture, using known-fate analysis in Program MARK as a precursory evaluation for multi-state modeling. We created multi-state models within Program MARK using a capture-recapture framework with 3 states: 1) 1= alive; 2) A = dead with CWD; and 3) B = dead, non-CWD. Transition probabilities were fixed to 0 for nonsensical transitions. We performed a suite of models and determined that mortality for non-infected deer was 2 times higher than CWD-infected deer, but non-infected deer were 7 times more likely to be tested. As many as 24% of infected deer may not be tested, indicating failures in detection that may be related to mortality from predators. Our multistate model with constant encounters over time and time-dependent transitions indicated CWD did not function as a fully additive source of mortality in this deer population. Nevertheless, there may be deer on the landscape infected with CWD that are being removed by predators and thereby go undetected. For our last objective, estimation of home ranges of animals is a common practice in wildlife science, but a variety of factors, such as choice of smoothing parameter and number of locations necessary for an accurate estimate, are under debate. Methods of data collection, such as the use of global positioning system (GPS) collars versus traditional radiotelemetry, can influence estimates as a result of sampling protocols. We evaluated effect of sample size and smoothing parameter on 2 species (coyotes and mule deer) that likely have variable utilization distributions using location data collected from GPS collars. Data were collected from GPS collars on mule deer in Wind Cave National Park and coyotes in Badlands National Park. We calculated home ranges using 95% and 50% adaptive kernel contours using reference (h_ref) and ad hoc (h_ad hoc) smoothing parameters using ArcGIS 9.1 with Home Range Tools . The ad hoc approach was designed to reduce bias commonly associated with reference bandwidths that use a bivariate normal distribution. We calculated home ranges with both smoothing parameters for random subsamples of 5, 10, 25, and 50% of GPS locations to evaluate necessary sample size and compared area estimates with those obtained for 100% GPS locations. For mule deer, we also conducted visual relocations using conventional radiotelemetry, which resulted in fewer locations than from GPS collars (\u3c 20%). Area was overestimated at smaller sample sizes, but an interesting pattern was noted with greater bias at 60-100 locations than at sample sizes \u3c50 locations. This bias may have resulted from increasing autocorrelation, but it was most likely a result of random sampling error. Examining relative differences produced from home ranges created through subsampling provided a means to estimate variability by smoothing parameter and sample size. Minimum number of points to obtain bias \u3c10% varied by smoothing method, species, study duration, and volume contour (95% or 50%), indicating there may not be a universal recommendation for all studies and species. While h_ad hoc performed consistently better over most sample sizes, we suggest researchers examine point distributions, choose smoothing parameters with the least bias variance, justify and report choices for home-range analysis based on study objectives

NYPlastiPOPdV2 Web Interactive: Software to investigate the population scale impacts of lead in New York State from 1990-2018

This software is shared under a MIT License. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.We assessed the population scale impacts of lead (Pb) toxicosis in free-ranging bald eagles (Haliaeetus leucocephalus) in New York State, USA from 1990-2018. The NYPlastiPOPdV2 repeats the comparison in PlastiPOPd (https://doi.org/10.7298/7rxf-ee77) for a region specific to New York State. Statistical medians used for comparison arise from the NYCounterPOPdV2 software (https://doi.org/10.7298/rsse-e634.2), which are themselves generated using data collected between 1990 and 2018 by the Wildlife Health Unit of the New York State Department of Environmental Conservation.This study was funded in part by the Morris Animal Foundation under Grant # D18ZO-103 and in part by the New York State Department of Environmental Conservation. This software has not been reviewed nor endorsed by the Foundation nor the Department, and the views expressed in this software do not necessarily reflect the views of the funders, their officers, directors, affiliates, or agents

NYClosedCounterPOPd V2 Web Interactive: Software to investigate the population scale impacts of lead in New York State from 1990-2018

This software is shared under a MIT License. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.The NYClosedCounterPOPdV2 software is an interactive application used to explore the differences in population dynamics in the presence and absence of lead (Pb) in bald eagles in New York State between 1990 and 2018 under conditions closed to dispersal. Comparisons include a factual Pb scenario (“Actual”), a counter factual scenario where Pb poisoning cases did not exist (“Pb-reduced”), and counter factual scenario where Pb exposure cases did not exist (“Pb-free”). All data was collected by the New York State Department of Environmental Conservation, and these data collapse via an algorithm into several comparative population scale properties, including the life tables, annual abundances (January – December), bi-annual abundances (January – June and July – December), bi-annual hatchling abundances, bi-annual immature and non-breeder adult abundances, bi-annual breeder abundances, abundances during the breeding periods (January – June), abundances during the non-breeding periods (July – December), migration and dispersal values, lambda values, survival rates, stable stage distributions, reproductive values, elasticities, cumulative growth rates, stochastic growth rates, transient growth rates, reactivity, maximum amplifications, and maximum attenuations (Caswell 2001). The summarized data appears for immediate use in this packet. The raw data may be obtained by contacting the Wildlife Health Unit at the New York State Department of Environmental Conservation [[email protected] or (518) 478-2203].This study was funded in part by the Morris Animal Foundation under Grant # D18ZO-103 and in part by the New York State Department of Environmental Conservation. This software has not been reviewed nor endorsed by the Foundation nor the Department, and the views expressed in this software do not necessarily reflect the views of the funders, their officers, directors, affiliates, or agents