Source: UNIVERSITY OF ARKANSAS submitted to NRP
ECOLOGY, CONSERVATION, AND MANAGEMENT OF LARGE MAMMALS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
1013315
Grant No.
(N/A)
Cumulative Award Amt.
(N/A)
Proposal No.
(N/A)
Multistate No.
(N/A)
Project Start Date
Oct 1, 2017
Project End Date
Sep 30, 2022
Grant Year
(N/A)
Program Code
[(N/A)]- (N/A)
Recipient Organization
UNIVERSITY OF ARKANSAS
(N/A)
FAYETTEVILLE,AR 72703
Performing Department
Forestry And Natural Resources
Non Technical Summary
The purpose of this project is to outline my research plan to investigate the ecology, conservation, and management of large, forest-dwelling mammals in Arkansas beginning 1 October 2017 and ending 30 September 2022. Seven research projects scheduled under the scope of this project will be described. Each project has specific measurable objectives that will be accomplished within the time frames indicated. The 7 project objectives are as follows: 1) Determine elk and cattle diet composition and overlap, and elk depredation of standing forage crops in Arkansas, 2) Estimate elk abundance, density, and distribution in Arkansas, 3) Estimate survival and causes of mortality of elk calves, and female birth-site selection in Tennessee, 4) Genetically assign white-tailed deer and elk from Arkansas that have chronic wasting disease (CWD) to family groups, 5) Genotype CWD-positive and CWD-negative white-tailed deer and elk from Arkansas, 6) Determine the economic impacts of CWD in Arkansas, and 7) Estimate abundance and density of black bears in the Mississippi River Alluvial Plain and West Gulf Coastal Plain, Arkansas.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
13508301070100%
Knowledge Area
135 - Aquatic and Terrestrial Wildlife;

Subject Of Investigation
0830 - Wild animals;

Field Of Science
1070 - Ecology;
Goals / Objectives
Determine elk and cattle diet composition and overlap, and elk depredation of standing forage crops in Arkansas;Estimate elk abundance, density, and distribution in Arkansas;Estimate survival and causes of mortality of elk calves, and female birth-site selection in Tennessee.Genetically assign white-tailed deer and elk from Arkansas that have chronic wasting disease (CWD) to family groups;Genotype CWD-positive and CWD-negative white-tailed deer and elk from Arkansas;Determine the economic impacts of CWD in Arkansas;Estimate abundance and density of black bears in the Mississippi River Alluvial Plain and West Gulf Coastal Plain, Arkansas.
Project Methods
Project: Elk and Cattle Diet Composition and Overlap, and Elk Depredation of Standing Forage Crops in the Buffalo River Watershed, ArkansasMicrohistological analysis will be used to quantify vegetation composition of elk and cattle diets from fecal pellet collections. Plant identification and percentage composition will be determined by examining 2 slides of 25 views per pellet sample. Plants contained within the pellets will be identified to species when possible. I will measure the niche breadth of elk and cattle using Levin's normalized index and use Ivlev's electivity index to evaluate elk and cattle forage selection. I will analyze diet overlap between elk and cattle using the simplified Morisita index. I will analyze differences in the proportion of plant categories or individual key plant species across herbivore species using a Kruskal-Wallis H-test.Project: Elk Abundance, Density, and Distribution in ArkansasA Jet Ranger helicopter and professional wildlife capture crew will be employed to capture 75 elk (50 cows and 25 bulls) of all age classes within the Buffalo River watershed. Thiafentanil oxalate will be used to anesthetize elk. Elk will be fitted with VHF radiocollars. I will divide the Buffalo River watershed into Elk Population Zones (EPZ) based, at least in part, on drainage basin topography. Using a helicopter, I will fly each EPZ and count and classify all elk observed. The most difficult aspect of developing the detection model will be obtaining accurate measurements of covariates for elk groups that are not detected in the preliminary surveys. I will use a fixed-wing aircraft to monitor the location of collared elk with telemetry before and during each survey. As soon as possible after it is clear that the survey crew has not detected a collared elk in an area they have covered, the telemetry crew will find the elk and record the associated covariates.Project: Survival and Causes of Mortality of Elk Calves, and Female Birth-Site Selection in TennesseeI will capture 40-45 adult female elk in baited corral traps. After capture, adult female elk will be anesthetized using a combination of carfentanil and xylazine. Immediately after anesthesia, each pregnant female will be fitted with either a satellite GPS or VHF radio-collar and vaginal implant transmitter. Pregnancy will be verified with ultrasonography. VITs will be programmed with a temperature-sensitive switch, set at 95oF, to be triggered on expulsion (i.e., at parturition) and, thus, allow me to begin my search for calves in the area they were born. When a VIT radio signal is detected, i.e., when the female gives birth to a calf, I will immediately search the birth area on foot. I will hand capture approximately 30 neonatal calves <6 days old. All calves will be aged, weighed, measured (hind foot and head length), and examined for ticks. General body condition will be subjectively determined as poor, moderate, or good based on behavior, presence or absence of inflammation of the umbilicus and anus, and level of ectoparasite infestation. Calves will be fitted with expandable, releasable radio-collars. Each calves' radio signal will be monitored each day at dawn from mid-May through mid-August, when the risk of mortality to calves is relatively high. Beginning in mid-August, calves will be monitored less intensively: 3 times per week until mid-November, then once or twice per week until mid-May. I will develop models of calf survival using the known-fate models in program MARK. Weekly, preweaning, seasonal, and annual calf survival will be estimated. I will examine up to 90 birth site locations and evaluate birth site-specific habitat selection at macro- and microhabitat scales using a resource selection function modeling approach.Project: Family Group Assignment and Genotyping White-tailed Deer in Arkansas Using DNA extracted from the ear tissues of the 266 deer collected for CWD testing in the CWD focus area and the 52 deer collected from southwestern Pope County (N = 318 ear tissue samples), I intend to address the question of whether or not the CWD-positive male found dead in Pope County can be genetically assigned to the deer subherd in Newton County. DNA will be extracted from ear tissue collected from each deer (N = 318) and genotyped using 2,000 Single Nucleotide Polymorphism (SNP) DNA markers.Project: Family Group Assignment and Genotyping Elk in ArkansasDNA samples will be collected from as many elk in the Pruitt herd as possible. While the animals are still warm, 25 guard hairs will be collected from the dorsal and ventral neck region. Hair samples will be supplemented with scat samples from Pruitt, Boxley Valley, and Gene Rush WMA, to assure we have a good genetic representation of elk in and surrounding the Pruitt subherd. For each hair and scat sample, WGI will conduct 16-locus microsatellite genotyping followed by analysis of individual origins (specifically, statistical testing with GeneClass 2 to establish whether the genotype from the CWD-positive cow could have been drawn from the local population).Project: Economic Impacts of Chronic Wasting Disease in ArkansasThis project consists of a statewide telephone survey conducted in cooperation with the UALR Survey Research Center to study the awareness, attitudes, and experiences of licensed hunters regarding CWD.Project: Estimate Abundance and Density of Black Bears in the Mississippi River Alluvial Plain and West Gulf Coastal Plain, ArkansasThe study area is too large to adequately survey with typical uniformly-spaced hair trap configurations. I will, therefore, employ a clustered hair trapping grid and utilize spatially explicit capture-mark-recapture (secr) population abundance and density estimation techniques. Each trapping cluster will consist of 9 (3x3) hair traps. Each trap within each cluster will be 2 km apart. Each hair trap will consist of an enclosure comprised of 2 strands of 4-pronged barbed wire stretched around 3-5 trees and positioned 50 and 25 cm above ground level. We will hang bait and scent attractants such as bakery products, fish carcasses, molasses, and/or candy flavoring from a line above the enclosure. Different lures will be employed after each trapping session to provide a novel scent to previously "captured" bears. Each trap will be checked and rebaited weekly for 7 consecutive weeks, beginning in June 2017. Hair samples that may have originated from different animals, i.e., hair collected from different barbs, will be collected and stored separately. We will remove hair samples from the barbed-wire wearing sterile latex gloves to avoid contamination of the DNA. Each hair sample will be placed in small paper envelopes, sealed, and the location, date, session number, and trap number will be recorded on the envelope. A flame will be passed under each barb to remove any missed hairs before the wire is reused. All hair samples will be stored in ZiplocĀ® plastic bags containing granular silica and stored in a dry, cool, dark environment until analysis. Silica is a desiccant, which minimizes DNA degradation. Following standard protocols, DNA will be extracted and analyzed based on 12 microsatellite markers and a gender marker. Once the hair samples are genotyped and individual bears identified, we will create capture histories and use the secr package for program R to model population abundance and density.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Members of the general public, hunters, private forestland owners, and state and federal wildlife biologists and managers. Changes/Problems:Project Goal 7: Estimate abundance and density of black bears in the Mississippi River Alluvial Plain and West Gulf Coastal Plain, Arkansas, was scheduled for completion in 2020. High water issues in many of my study areas, however, prohibited access. Therefore, the final field season for this project goal has been rescheduled for 2021. What opportunities for training and professional development has the project provided?DNA extraction using the QIAamp Fast DNA Tissue Kit protocol. Amplify a coding section of the PRNP gene. Reconstruct haplotypes using a probabilistic model of linkage disequilibrium. How have the results been disseminated to communities of interest?Primary research journal article. What do you plan to do during the next reporting period to accomplish the goals?Project Goal 7: Estimate abundance and density of black bears in the Mississippi River Alluvial Plain and West Gulf Coastal Plain, Arkansas. My objectives are to estimate population abundance and density of bears in eastern and southern Arkansas from late June through mid-August 2021. Study areas will be centered in White River and Felsenthal but also include areas adjacent to public and private land in both the LMAP and WGCP. At White River, I will evaluate the effects of harvest by comparing bear population density estimates produced in this study to those estimated by Clark et al. (2010). Based on the population abundance estimates produced in this study and the known number of bears originally reintroduced to Felsenthal, I will estimate the annual population growth rate for that region. Equipped with these data, wildlife managers will be in a much better position to judge the success of the Felsenthal bear reintroduction program and can take the next steps toward wise management of this resource. Finally, data from this project will be used to predict the potential role of bear populations in White River and Felsenthal and adjacent areas in bear metapopulation dynamics across the LMAV.

Impacts
What was accomplished under these goals? Project Goals 4 and 5: Chronic-wasting disease (CWD) is a prion-derived fatal neurodegenerative disease that has affected wild cervid populations on a global scale. Susceptibility has been linked unambiguously to several amino acid variants within the prion protein gene (PRNP). Quantifying their distribution across landscapes can provide critical information for agencies attempting to adaptively manage CWD. In this project my coauthors and I attempted to further define management implications of PRNP polymorphism by quantifying the contemporary geographic distribution (i.e., phylogeography) of PRNP variants in hunter-harvested white-tailed deer (WTD; Odocoileus virginianus, N = 1433) distributed across Arkansas (USA), including a focal spot for CWD since detection of the disease in February 2016. Of these, PRNP variants associated with the well-characterized 96S non-synonymous substitution showed a significant increase in relative frequency among older CWD-positive cohorts. We interpreted this pattern as reflective of a longer life expectancy for 96S genotypes in a CWD-endemic region, suggesting either decreased probabilities of infection or reduced disease progression. Other variants showing statistical signatures of potential increased susceptibility, how-ever, seemingly reflect an artefact of population structure. We also showed marked heterogeneity across the landscape in the prevalence of "reduced susceptibility" genotypes. This may indicate, in turn, that differences in disease susceptibility among WTD in Arkansas are an innate, population- level characteristic that is detectable through phylogeographic analysis.

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Tyler K. Chafin, Marlis R. Douglas, Bradley T. Martin, Zachery D. Zbinden, Christopher R. Middaugh, Jennifer R. Ballard, M. Cory Gray, Don White, Jr., and Michael E. Douglas. 2020. Age structuring and spatial heterogeneity in prion protein gene (PRNP) polymorphism in white-tailed deer. Prion 14:238-248.


Progress 10/01/18 to 09/30/19

Outputs
Target Audience:Arkansas private landowners. Wildlife biologists and natural resource managers.State, regional, national, and international scientific communities. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?I trained 5 biologists and 1 Administrator from the Arkansas Game and Fish Commission to use a spreadsheet model I developed to evaluate management actions aimed at understanding hunter population dynamics, recruiting hunters, and increasing license sales. I trained 12 foresters from the US Forest Service to agewhite-tailed deer and wild pigs using tooth wear and eruption characteristics. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?I plan to accomplish project goal 7: estimate abundance and density of black bears in the Mississippi River Alluvial Plain and West Gulf Coastal Plain, Arkansas. I have 1 field season left in this study. That work will be accomplish during summer 2019.

Impacts
What was accomplished under these goals? Project goal 4: genetically assign white-tailed deer from Arkansas that have chronic wasting disease (CWD) to family groups; and project goal 5: genotype CWD-positive and CWD-negative white-tailed deer from Arkansas, were accomplished in 2019. These studies represent an initial genetic evaluation of population connectivity in white-tailed deer in Arkansas and an assessment of genetic variation at the PRNP gene that codes for the prion protein, the disease-causing agent of Chronic Wasting Disease (CWD). Genetic patterns reflect dispersal of organisms through complex environments, and hence can be informative about potential disease spread and risk in wildlife populations. The objectives of this study were to: 1) assess genetic population structure to infer dispersal of deer among herds and hence the potential for spread of CWD from the initial CWD Focal Area, and 2) quantify distribution and frequency of PRNP gene variants among deer herds in the CWD Management Zone to evaluate potential for reduced susceptibility to CWD. My research group and I employed a novel genomic approach that is more effective at detecting subtle population connectivity, and more efficient and cost-effective at screening hundreds of samples than traditional genetic screening methods and used sequence analysis to identify variants of the PNRP gene. We evaluated a total of 384 ear tissues sampled from 19 counties in Arkansas, with the majority stemming from the CWD Management Zone. Key project findings include: 1) variants of the prion-coding PRNP gene exist among white-tailed deer in Arkansas, including haplotypes (alleles) identified as being associated in other states with reduced susceptibility to CWD, 2) distribution and frequencies of PRNP gene variants differ among counties, and also show a trend towards differences in CWD-negative vs CDW-positive deer, 3) analysis of genome-wide genetic variation using a novel genomic approach (i.e., analysis of 38,424 single nucleotide polymorphism) revealed subtle population structure among 375 white-tailed deer from the CWD Management Zone, indicating the potential for reduced population connectivity among deer in Arkansas, 4) detection of four slightly differentiated subpopulations (gene pools) associated with geographic areas in the CWD Management Zone suggests that major landscape features such as rivers and topography modulate deer dispersal, 5) findings of this study provide an initial landscape genetics baseline from which to gauge future spread of CWD in the state.

Publications

  • Type: Other Status: Published Year Published: 2019 Citation: Meeker, R., J. Brown, B. Carner, K. Stephens, G. Dugger, B. Groves, M. Mourot, M. Barbee, E. Horrell, J. Mitchell, J. Lawson, J. Abernathy, K. Key, J. Smith, and D. White, Jr. 2019. 2019 White-tailed Deer Strategic Management Plan, Arkansas Game and Fish Commission, Little Rock, Arkansas, USA.


Progress 10/01/17 to 09/30/18

Outputs
Target Audience:Arkansas private landowners; state, regional, national, and international scientific communities; professional wildlife biologists and managers. Changes/Problems:I had major surgery in late December 2017. Although recovery required more time than expected, I have recoved completely. Time spent recovering from surgery delayed progress for some of my research projects in 2018. Those projects will be completed in 2019. What opportunities for training and professional development has the project provided?I provided training in chronic wasting disease at the Ouachita Society of American Foresters annual meeting on 9 April 2018. I provided training in chronic wasting disease to attendees to students of the US Forest Service National Advanced Silviculture Programon 28 April 2018. How have the results been disseminated to communities of interest?Reports, publications, conference presentations, media (radio and television) interviews, social media, webinars. What do you plan to do during the next reporting period to accomplish the goals?Continue and complete data analysis. Publish articles in primary research journals. Present research results and state, regional, national, and international wildlife conferences.

Impacts
What was accomplished under these goals? Goal 1: Data collection completed. Analysis and report writing in progress. Knowledge of diet selection is an integral component to an understanding of ungulate ecology and is basic to planning and evaluating habitat improvement programs.Although food habits of elk have been extensively studied in the Rocky Mountain region, only 7 studies have been conducted in the eastern North America. Istudied seasonal forage availability and diet of elk in Arkansas from January 2015 to December 2017. Based upon microhistological examinations of >500 elk feces, I found that elk exhibited an annual diet of grasses (24%), forbs (27%), and browse (32%).Perhaps due to availability and palatability, diets shifted seasonally: forbs dominated the summer diet (34%), whereas grasses, forbs, and woody browse accounted for approximately equal proportions in the fall diet.Grasses (40%) and browse (46%) dominated the diet during winter and spring, respectively. Goal 4: Data collection completed. Analysis and report writing in progress. Chronic Wasting Disease (CWD) is a highly infectious, fatal, neurological prion disease affecting deer, elk, and moose. In Arkansas, CWD has been found in 580 white-tailed deer and 16 elk since first detected in autumn 2015. Because the disease is transmitted via direct and indirect contact between uninfected and infected hosts, major factors affecting the potential for CWD spread across the landscape are: 1) rate of dispersal between herds and 2) rate of disease penetration within herds. This study addresses both of these issues by combining next-generation genomic methods with traditional genetic screening approaches to understand how patterns of dispersal and disease susceptibility covary with landscape features across Arkansas. To infer population structure and connectivity, my team and I have sequenced >50,000 SNP markers for 896 white-tailed deer, and applied landscape genetic methods to understand patterns of population differentiation and landscape resistance statewide. We then assayed the same individuals for certain known variants that have been associated with differential disease susceptibility in other states using targeted sequencing of the PRNP gene. Understanding the landscape features modulating dispersal and the distribution of susceptibility-linked PRNP variants across Arkansas will allow stakeholders to more effectively gauge potential risk for disease spread. Goal 5: Data collection completed. Analysis and report writing in progress. This study represents an initial genetic evaluation of population connectivity in white-tailed deer in Arkansas and an assessment of genetic variation at the PRNP gene that codes for the prion protein, the disease-causing agent of Chronic Wasting Disease (CWD). Genetic patterns reflect dispersal of organisms through complex environments, and hence can be informative about potential disease spread and risk in wildlife populations. We employed a novel genomic approach that is more effective at detecting subtle population connectivity, and more efficient and cost-effective at screening hundreds of samples than traditional genetic screening methods and used sequence analysis to identify variants of the PNRP gene. We evaluated a total of 384 ear tissues sampled from 19 counties in Arkansas, with the majority stemming from the CWD Management Zone. Variants of the prion-coding PRNP gene exist among white-tailed deer in Arkansas, including haplotypes (alleles) identified as being associated in other states with reduced susceptibility to CWD. Distribution and frequencies of PRNP gene variants differ among counties, and also show a trend towards differences in CWD-negative vs CWD positive deer. Detection of four slightly differentiated subpopulations (gene pools) associated with geographic areas in the CWD Management Zone suggests that major landscape features such as rivers and topography modulate deer dispersal. Goal 7: Year 1 data collected. Year 2 data will be collected in 2019. Hair collection and DNA extraction represent breakthroughs for estimating bear population abundance and density. Individual bears can be identified from DNA extracted from hair samples. The method functions like a typical mark-recapture study in that bear hair samples are collected from barbed wire at bait sites and the bears identified genetically, or "trapped," are treated as marked animals. Advantages of this technique are that it minimizes biases due to trap response, is cost effective, and can be used over an extensive area. I collected 571 hair samples were inJuly and August 2018. Most of thehair samples were collected in the Felsenthal National Wildlife Refuge (29.6%) and from areas east of Monticello, AR (29.4%). Most (42%) of the hair samples were bear hair; 26% of the hair samples were feral hoghair.The remaining 32% of the hair collected in this study are currently unidentified. Based on the population abundance estimates produced in this study and known number of bears originally reintroduced to the Felsenthal Refuge from 2000 to 2010, I will estimate the annual population growth rate for that region. Equipped with these data, wildlife managers will be in a much better position to judge the success of the Felsenthal Refuge bear reintroduction program and can take the next steps toward wise management of this resource. Data from this project will also be used to predict the potential role of bear populations within the White River Refuge and Felsenthal Refuge and adjacent areas in bear metapopulation dynamics across the Lower Mississippi Alluvial Plain.

Publications

  • Type: Journal Articles Status: Accepted Year Published: 2018 Citation: Kristensen, T., M. Means, L.S. Eggert, K.G. Smith, and Don White, Jr. 2018. Demographics of American black bear (Ursus americanus) populations following changes in harvest policy. Ursus. In Press Kristensen, T., D. White, Jr., E.E. Puckett, E.L. Landguth, J.T. Hast, C. Carpenter, J.L. Sajecki, J.L. Belant, J. Beringer, M. Means, J.J. Cox, R.A. Van Den Bussche, L.S. Eggert, and K.G. Smith. 2018. Variability in sex-biased philopatry and dispersal in American black bears (Ursus americanus). Heredity 120:329-341.