Life Sciences Commons^™

Simulating Detection-Censored Movement Records For Home Range Analysis Planning, Lyndsie S. Wszola, Victoria L. Simonsen, Lucía Corral, Christopher J. Chizinski, Joseph J. Fontaine

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Home range estimation is an important analytical method in applied spatial ecology, yet best practices for addressing the effects of spatial variation in detection probability on home range estimates remain elusive. We introduce the R package “DiagnoseHR,” simulation tools for assessing how variation in detection probability arising from landscape, animal behavior, and methodological processes affects home range inference. We demonstrate the utility of simulation methods for home range analysis planning by comparing bias arising from three home range estimation methods under multiple detection scenarios. We simulated correlated random walks in three landscapes that varied in detection probability and constructed home …

Comparing Strategies For Selection Of Low-Density Snps For Imputation-Mediated Genomic Prediction In U.S. Holsteins, Jun He, Jiaqi Xu, Xiao-Lin Wu, Stewart Bauck, Jungjae Lee, Gota Morota, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

SNP chips are commonly used for genotyping animals in genomic selection but strategies for selecting low-density (LD) SNPs for imputation-mediated genomic selection have not been addressed adequately. The main purpose of the present study was to compare the performance of eight LD (6K) SNP panels, each selected by a different strategy exploiting a combination of three major factors: evenly-spaced SNPs, increased minor allele frequencies, and SNP-trait associations either for single traits independently or for all the three traits jointly. The imputation accuracies from 6K to 80K SNP genotypes were between 96.2 and 98.2%. Genomic prediction accuracies obtained using imputed 80K …

The Effects Of Sample Storage Conditions On The Microbial Community Composition In Hydraulic Fracturing Produced Water, Daniel Lipus, Amit Vikram, Richard Hammack, Kyle Bibby, Djuna Gulliver

Roman L. Hruska U.S. Meat Animal Research Center: Reports

The petroleum industry has an increasing interest in understanding the microbial communities driving biofouling and biocorrosion in reservoirs, wells, and infrastructure. However, sampling of the relevant produced fluids from subsurface environments for microbiological analyses is often challenged by high liquid pressures, workplace regulations, operator liability concerns, and remote sampling locations. These challenges result in infrequent sampling opportunities and the need to store and preserve the collected samples for several days or weeks. Maintaining a representative microbial community structure from produced fluid samples throughout storage and handling is essential for accurate results of downstream microbial analyses. Currently, no sample handling or …

Impact Of Ethanol Process Changes On Distillers Grains For Beef Cattle, Shelby Garland

Department of Animal Science: Dissertations, Theses, and Student Research

Distillers grains plus solubles (DGS) have been widely utilized in beef cattle diets. Fractionation of the corn kernel pre- and post-fermentation has changed the composition of DGS and allowed for the production of other feed byproducts over time. The use of fractionated DGS and other feed byproducts from the ethanol industry has not been heavily researched in beef cattle diets. Three experiments were conducted to evaluate the effect of feeding high protein distillers grains (HiPro DDG) and corn bran plus solubles (Bran + Solubles) in beef cattle diets. Experiment 1 evaluated the effect of byproduct type on finishing performance and …

Relationships Among Biodiversity Dimensions Of Birds In Nebraska, Nadejda Mirochnitchenko

School of Natural Resources: Dissertations, Theses, and Student Research

Biological diversity, or biodiversity, is a multi-dimensional concept that can be decomposed to measure information about taxonomic, phylogenetic, and functional variation within communities. Although the dimensions of biodiversity are interrelated, the assumption that measuring one dimension of diversity can inform about patterns in another dimension does not necessarily follow from theory or empirical study. The relationships among biodiversity dimensions is not well understood, nor how differences among dimensions could influence conservation decision making. Using the avian community as a study system, we explored the relationships of breadth metrics from the taxonomic, phylogenetic, and functional dimensions among each other and across …

Safety, Stephen M. Vantassel, Brenda K. Osthus

Wildlife Damage Management Technical Series

Wildlife damage management (WDM) is an exciting field with many opportunities to provide solutions to the complex issues involved in human-wildlife interactions. In addition, WDM wildlife control operators (WCO) face a variety of threats to their physical well-being. Injuries can result from misused (Figure 1), faulty, or poorly maintained equipment, inexperience, mishandled wildlife, harsh weather, and dangerous situations, such as electrical lines. The goals of this publication are to: * Develop an awareness of safety issues and adopt a mindset of “Safety First”, * Review the major safety threats that WCOs face, * Provide basic information for WCOs to protect …

Implications Of Spatially Variable Costs And Habitat Conversion Risk In Landscape-Scale Conservation Planning, Max Post Van Der Burg, Neil Chartier, Ryan Drum

USGS Northern Prairie Wildlife Research Center

‘‘Strategic habitat conservation’’ refers to a process used by the U.S. Fish and Wildlife Service to develop cost-efficient strategies for conserving wildlife populations and their habitats. Strategic habitat conservation focuses on resolving uncertainties surrounding habitat conservation to meet specific wildlife population objectives (i.e., targets) and developing tools to guide where conservation actions should be focused on the landscape. Although there are examples of using optimization models to highlight where conservation should be delivered, such methods often do not explicitly account for spatial variation in the costs of conservation actions. Furthermore, many planning approaches assume that habitat protection is a preferred …

Northern Saw-Whet Owl (Aegolius Acadicus) Nest Box Project: The First Seven Years, Wayne J. Mollhoff

Nebraska Bird Review

This report summarizes the first seven years of the nest box project for the Northern Saw-whet Owl in Nebraska. The project was initiated with several goals in mind: 1) to document breeding in Nebraska, 2) to get an idea of the breeding range of saw-whet owls, and 3) to establish their breeding phenology. The project started in 2012 with the placement of 29 boxes. Six boxes were added in 2015, four more in 2016, and eight in 2017.

This study, along with an ongoing study in South Dakota (Drilling 2015), makes it appear that we share an isolated breeding population. …

Sandhill Crane Activity In The Central Platte River Valley In Late May And Early June, Jenna M. Malzahn, Andrew J. Caven, Marin Dettweiler, Joshua D. Wiese

Nebraska Bird Review

In this report we discuss observations of Sandhill Cranes remaining in the Central Platte River Valley until early June 2018 and discuss potential explanations for this extended stay into the breeding season.

We detected two pairs of adult Sandhill Cranes in two different locations on 15 May 2018 (Table 1). We then detected three injured adult Sandhill Cranes in a third location on 16 May 2018 (Table 1). Two of the three Sandhill Cranes each had a missing leg and the third crane’s leg was broken above the tibiotarsal joint; however, all were still capable of foraging and flight. Later, …

Fall Field Report, August - November 2018, W. Ross Silcock

Nebraska Bird Review

As far as birds go, this was a relatively quiet season, but, as usual, there was much of interest to chew on. Most important in any report are range changes, major changes in expected numbers or early and late dates, all of which relate directly to the status, positive or negative, of a given species.

Waterfowl in general were only average in numbers; new high counts are rare these days compared with numbers 20 or so years ago. Two winter finches, Common Redpoll and Red Crossbill, that normally arrive in late fall, were virtually unreported. Notable range expansions are under …

2018 Fall Banding Migration Summary, Chadron State Park, Chris Murray

Nebraska Bird Review

In order to better understand wild birds and their migration, Bird Conservancy of the Rockies conducted bird monitoring for the 11th straight year at our fall migration banding station in Chadron State Park within the Pine Ridge Region of Nebraska. Operated in collaboration with the Nebraska Game and Parks Commission, this station is open to the public and visited by school groups to serve as an outdoor classroom. Among our goals are to enhance the public’s appreciation of birds as well as their understanding of threats to bird survival and the role of science in bird conservation. Serving as an …

The Nebraska Bird Review, Volume 86 December 2018 Number 4

Nebraska Bird Review

Fall Field Report, August - November 2018, by W. Ross Silcock …146-167

Northern Saw-whet Owl (Aegolius acadius) Nest Box Project: The First Seven Years, by Wayne J. Mollhoff …168-174

Sandhill Crane Activity in the Central Platte River Valley in Late May and Early June, by Jenna Malzahn, Andrew J. Caven, Marin Dettweiler, Joshua D. Wiese .... 175-180

2018 Fall Banding Migration Summary, Chadron State Park, by Chris Murray …181-185

Ainsworth Fall Field Days, Sept. 14-16, 2018, by Janis Paseka …186-190

Index to Volume 86 …191-206

Subscription and Organization Information … 207

Prairie Reconstruction Unpredictability And Complexity: What Is The Rate Of Reconstruction Failures?, Jack E. Norland, Cami Dixon, Diane Larson, Kristine Askerooth, Benjamin A. Geaumont

USGS Northern Prairie Wildlife Research Center

The outcomes of prairie reconstructions are subject to both unpredictability and complexity. Prairie, tallgrass, and mixed grass reconstruction is defined as the planting of a native herbaceous seed mixture composed of multiple prairie species (10 or more) in an area where the land has been heavily cultivated or anthropogenically disturbed. Because of the unpredictability and complexity inherent in reconstructions, some outcomes end up being failures dominated by exotic species. We propose that these failures follow a fat-tailed distribution as found in other complex systems. Fat-tailed distributions follow the Pareto principle, where 80% of the time reconstructions work as expected but …

Quality Effects On Beef From Cattle Fed High-Protein Corn Distillers Grains Or Other Ethanol By-Products, Kellen B. Hart

Department of Animal Science: Dissertations, Theses, and Student Research

The objective of this study was to evaluate the effects of feeding high protein corn distillers grains on fresh beef quality. Steers (n=300) were fed one of five diets (6 pens with 10 head/pen): a corn control, 40% high protein dry distillers grains plus solubles (HP-DDGS), 40% dry distillers grains plus solubles (DDGS), 40% wet distillers grains plus solubles (WDGS), or 40% bran plus solubles (Bran). Eighteen Choice carcasses (3 head/pen) were randomly selected within each treatment (n=88). Strip loins were aged for 2, 9, or 23 d, after which steaks were placed under retail display conditions for 0, 4, …

Surveillance And Evaluation Of Manure Treatment Practices For Mitigation Of The Porcine Epidemic Diarrhea Virus (Pedv) In A Commercial Swine Farm Setting, Erin Boyles

Department of Animal Science: Dissertations, Theses, and Student Research

The emergence of the porcine epidemic diarrhea virus (PEDv) in the United States in 2013 resulted in billions of dollars in annual losses for the U.S. swine industry. Infection with PEDv causes severe diarrhea and vomiting in pigs, spreads rapidly through ingestion of infected manure, and produces nearly 100% mortality in pre-weaned piglets. Because swine manure slurry is a valuable crop nutrient source, concerns about virus persistence in stored manure remain a major barrier to proper manure management. Proper manure handling and application practices are necessary to control the risk of pathogen re-infection at affected production sites or infecting new …

Risk Of Nitrate Toxicity When Grazing Annual Forages, Mary Lenz

Department of Animal Science: Dissertations, Theses, and Student Research

Annual forages provide a valuable grazing resource for producers; however, annuals are prone to accumulating nitrate and toxicity can be a potential challenge. There are multiple publications regarding nitrate toxicity, but few, if any, address grazing high nitrate forages. There is variability on what amount of nitrate is considered toxic to cattle, and information is not available on the frequency producers experience toxicity when feeding annual forages. To understand the incidence of nitrate toxicity in the North Central Region of the U.S., a survey was distributed through the “UNL BeefWatch” newsletter to producers. Though producers appeared concerned about nitrates in …

Bats Of Saint Lucia, Lesser Antilles, Scott C. Pedersen, Gary G. Kwiecinski, Hugh H. Genoways, Roxanne J. Larsen, Peter A. Larsen, Carleton J. Phillips, Robert J. Baker

University of Nebraska State Museum: Mammalogy Papers

Eight species of bat have been previously recorded from the island of Saint Lucia: Noctilio leporinus, Monophyllus plethodon, Artibeus jamaicensis, Brachyphylla cavernarum, Ardops nichollsi, Sturnira paulsoni, Molossus molossus, and Tadarida brasiliensis. Herein, we add a ninth species to the fauna—Pteronotus davyi. These nine species represent nine genera from four families: Noctilionidae, Mormoopidae, Phyllostomidae, and Molossidae. This fauna includes four trophic guilds: N. leporinus (piscivore/insectivore), M. plethodon (nectarivore/pollenivore), A. jamaicensis × schwartzi, B. cavernarum, A. nichollsi, and S. paulsoni (frugivores), and P. davyi, M. molossus, and …

Assessing The Effects Of Genetic Selection For Porcine Circovirus Type 2 Resistance Or Feed Additives On Nursery And Grow-Finish Pig Performance, Dana Van Sambeek

Department of Animal Science: Dissertations, Theses, and Student Research

The swine industry is ever evolving as it strives to produce healthy, wholesome pork for consumers. As such, the industry is constantly looking for ways to improve production and reduce costs. This includes using novel feed ingredients to reduce cost and improve animal health, genetic selection for increased performance, and vaccines to attenuate or prevent illness. Research plays a significant role in assessing the effectiveness of these strategies. Overall, the objective of this thesis was to assess how genetic selection, vaccines, and feed additives may impact growth performance, health, nutrient digestibility, and the microbiome.

In Chapter 2, pigs were either …

Factors Affecting Trailer Thermal Environment Experienced By Market Pigs Transported In The Us, Y Xiong, Richard S. Gates, Angela R. Green-Miller

Department of Animal Science: Faculty Publications

Extreme weather conditions challenge pig thermoregulation during transport and are addressed by the National Pork Board (NPB) Transport Quality Assurance® (TQA) program that provides guidelines for trailer boarding, bedding, and misting. These guidelines are widely applied, yet very little is known about the microenvironment within the trailer. In this study, TQA guidelines (V4) were evaluated via extensive thermal environment measurements during transport in order to evaluate spatial variability and implications on ventilation pattern. Effects of trailer management strategies including bedding, boarding, and misting were examined and the trailer was monitored for interior temperature rise and THI responses within six separate …

Examining Patterns In Nest Predation Using Artificial Nests, Victoria L. Simonsen

School of Natural Resources: Dissertations, Theses, and Student Research

The use of artificial nests to study the predation of avian nests has faced disregard by ecologists due to inconsistencies found between the survival rates of real and artificial nests across studies and reviews. The negative perception of artificial nests providing an inconsistent assessment of survival has thus fostered the perception that artificial nests are a secondary option to be used to overcome logistical hurdles associated with achieving sufficient sample sizes in systems where study species are rare or elusive, or as merely a preliminary method to study predation across gradients. We argue that the greatest mistake ecologists have made …

13 Terrestrial Wetlands, Randall Kolka, Carl T Trettin

USGS Northern Prairie Wildlife Research Center

The objective of this chapter is to characterize the distribution of carbon stocks and fluxes in terrestrial wetlands within North America. The approach was to synthesize available literature from field measurements with analyses of resource inventory data to estimate wetland area, carbon stocks, and net ecosystem exchange (NEE) of carbon and methane (CH4) fluxes of terrestrial wetlands (see Appendices 13A, p. 547, and 13B, p. 557, for details1). Then, the findings employed from large-scale simulation studies provided additional context, with consideration given to the effects of disturbance regimes, restoration and creation of terrestrial wetlands, and the application of modeling tools …

The Impact Of Selective Genotyping On The Response To Selection Using Single-Step Genomic Best Linear Unbiased Prediction, Jeremy T. Howard, Thomas A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Across the majority livestock species, routinely collected genomic and pedigree information has been incorporated into evaluations using single-step methods. As a result, strategies that reduce genotyping costs without reducing the response to selection are important as they could have substantial economic impacts on breeding programs. Therefore, the objective of the current study was to investigate the impact of selectively genotyping selection candidates on the selection response using simulation. Populations were simulated to mimic the genome and population structure of a swine and cattle population undergoing selection on an index comprised of the estimated breeding values (EBV) for 2 genetically correlated …

Index To Volume 86

Nebraska Bird Review

16 pages, from Aguillon, Stepfanie 103, to Yungbluth, Linda 149

Museum Metabarcoding: A Novel Method Revealing Gut Helminth Communities Of Small Mammals Across Space And Time, Stephen E. Greiman, Joseph A. Cook, Vasyl V. Tkach, Eric P. Hoberg, Damian M. Menning, Andrew G. Hope, Sarah A. Sonsthagen, Sandra L. Talbot

Harold W. Manter Laboratory of Parasitology: Faculty and Staff Publications

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification …

Landscape Genetics Reveal Broad And Fine‐Scale Population Structure Due To Landscape Features And Climate History In The Northern Leopard Frog (Rana Pipiens) In North Dakota, Justin M. Waraniak, Justin D. L. Fisher, Kevin Purcell, David M. Mushet, Craig A. Stockwell

USGS Northern Prairie Wildlife Research Center

Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east–west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified …

Landscape Genetics Reveal Broad And Fine‐Scale Population Structure Due To Landscape Features And Climate History In The Northern Leopard Frog (Rana Pipiens) In North Dakota, Justin M. Waraniak, Justin D.L. Fisher, Kevin Purcell, David M. Mushet, Craig A. Stockwell

USGS Northern Prairie Wildlife Research Center

Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east–west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified …

Bats Of St. Vincent, Lesser Antilles, Gary G. Kwiecinski, Scott C. Pedersen, Hugh H. Genoways, Peter A. Larsen, Roxanne J. Larsen, Justin D. Hoffman, Fitzroy Springer, Carleton J. Phillips, Robert J. Baker

University of Nebraska State Museum: Mammalogy Papers

The chiropteran fauna of the island of Saint Vincent, represented by 12 species, is among the most complex in the Lesser Antilles, being represented by four families including Noctilionidae (1 species), Mormoopidae (1), Phyllostomidae (8), and Molossidae (2). This fauna includes four trophic guilds as represented by Noctilio leporinus (piscivore/insectivore); Glossophaga longirostris and Monophyllus plethodon (nectarivore/pollenivore); Artibeus lituratus, A. schwartzi, Brachyphylla cavernarum, Ardops nichollsi, and Sturnira paulsoni (frugivore); and Pteronotus fuscus, Micronycteris buriri, Molossus molossus, and Tadarida brasiliensis (insectivore). One species—Micronycteris buriri—and two subspecies—Sturnira paulsoni paulsoni and Ardops nichollsi vincentensis …

Multi-Element Fingerprinting Of Waters To Evaluate Connectivity Among Depressional Wetlands, Yuxiang Yuan, Xiaoyan Zhu, David M. Mushet, Marinus L. Otte

USGS Northern Prairie Wildlife Research Center

Establishing the connectivity among depressional wetlands is important for their proper management, conservation and restoration. In this study, the concentrations of 38 elements in surface water and porewater of depressional wetlands were investigated to determine chemical and hydrological connectivity of three hydrological types: recharge, flow-through, and discharge, in the Prairie Pothole Region of North America. Most element concentrations of porewater varied significantly by wetland hydrologic type (p < 0.05), and increased along a recharge to discharge hydrologic gradient. Significant spatial variation of element concentrations in surface water was observed in discharge wetlands. Generally, higher element concentrations occurred in natural wetlands compared to wetlands with known disturbances (previous drainage and grazing). Electrical conductivity explained 42.3% and 30.5% of the variation of all element concentrations in porewater and surface water. Non-metric multidimensional scaling analysis showed that the similarity decreased from recharge to flowthrough to discharge wetland in each sampling site. Cluster analysis confirmed that element compositions in porewater of interconnected wetlands were more similar to each other than to those of wetlands located farther away. Porewater and surface water in a restored wetland showed similar multi-element characteristics to natural wetlands. In contrast, depressional wetlands connected by seeps along a deactivated drain-tile path and a grazed wetland showed distinctly different multi-element characteristics compared to other wetlands sampled. Our findings confirm that the multi-element fingerprinting method can be useful for assessing hydro-chemical connectivity across the landscape, and indicate that element concentrations are not only affected by land use, but also by hydrological characteristics.

Checklist Of Bloodfeeding Mites (Acari: Spinturnicidae) From The Wings Of Bats (Mammalia: Chiroptera) In The Manú Biosphere Reserve, Peru, Donald D. Gettinger

MANTER: Journal of Parasite Biodiversity

A survey collection of mites of the family Spinturnicidae from Peruvian bats includes 11 species of Periglischrus (acutisternus, gameroi, grandisoma, herrerai, hopkinsi, iheringi, micronycteridis, ojasti, paracutisternus, paravargasi, and ramirezi) and 2 Spinturnix (americanus and bakeri); almost all represent new locality records. This survey collection is available for further study at the following repositories: The Harold W. Manter Laboratory of Parasitology, University of Nebraska–Lincoln; the Field Museum of Natural History, Chicago; and the Laboratório de Espeleobiologia y Acarologia, Universidad Nacional Autónoma de México. When spinturnicid mites are …

Effect Of Stocking Rate On Growing Juvenile Sunshine Bass, Morone Chrysops × M. Saxatilis, In An Outdoor Biofloc Production System, Bartholomew W. Green, Steven D. Rawles, Carl D. Webster, Matthew E. Mcentire

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The biofloc technology production system is a production intensifying management strategy used primarily for culturing tilapia and penaeid shrimp, both of which can consume the biofloc. Other fish can be grown in biofloc systems because the biofloc serves to maintain water quality, metabolizing the ammonia excreted by intensively fed fish. A dose-response study was conducted in an outdoor biofloc system to begin quantifying the stocking rate-production function for sunshine bass, Morone chrysops x M. saxatilis, advanced fingerlings. Sunshine bass (2.9 ± 0.2 g/fish) were stocked into tanks at 50 to 250 fish/m² in 50 fish/m² increments. After …