Ecology and Evolutionary Biology Commons^™

2matrix: A Utility For Indel Coding And Phylogenetic Matrix Concatenation, Nelson R. Salinas, Damon P. Little

Publications and Research

Premise of the study: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets.

Methods and Results: A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs.

Conclusions: 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open …

The Longhorn Beetles (Coleoptera: Cerambycidae) Of Nebraska, Usa: New State Records, A Checklist Of Known Species, And Distribution Maps, Stephen M. Spomer

University of Nebraska State Museum: Entomology Papers

One hundred eighty-three species/subspecies of longhorn beetles are recorded from Nebraska, an increase of 19 species since 1971. The greatest number of recent discoveries have come from sites along the Missouri River, especially Indian Cave State Park in southeastern Nebraska, as well as the Pine Ridge at Chadron, Nebraska.

Using Indicators Of Biotic Integrity For Assessment Of Stream Condition, Stephanie A. Ogren

Dissertations, Master's Theses and Master's Reports - Open

Multiple indices of biotic integrity and biological condition gradient models have been developed and validated to assess ecological integrity in the Laurentian Great Lakes Region. With multiple groups such as Tribal, Federal, and State agencies as well as scientists and local watershed management or river-focused volunteer groups collecting data for bioassessment it is important that we determine the comparability of data and the effectiveness of indices applied to these data for assessment of natural systems. We evaluated the applicability of macroinvertebrate and fish community indices for assessing site integrity. Site quality (i.e., habitat condition) could be classified differently depending on …

Variation In Setal Micromechanics And Performance Of Two Gecko Species, Travis J. Hagey, Jonathan B. Puthoff, Madisen Holbrook, Luke J. Harmon, Kellar Autumn

Biology

Biomechanical models of the gecko adhesive system typically focus on setal mechanics from a single gecko species, Gekko gecko. In this study, we compared the predictions from three mathematical models to experimental observations considering an additional gecko species Phelsuma grandis, to quantify interspecific variation in setal micromechanics. We also considered the accuracy of our three focal models: the frictional adhesion model, work of detachment model, and the effective modulus model. Lastly, we report a novel approach to quantity the angle of toe detachment using the Weibull distribution. Our results suggested the coupling of frictional and adhesive forces in isolated setal …

Patch Burn‐Grazing: An Annotated Bibliography, Rajeeva Voleti, Stephen L. Winter, Sherry Leis

School of Natural Resources: Faculty Publications

Patch burn‐grazing is a rangeland management strategy that exploits the attraction of grazing animals to recently burned areas in order to achieve management objectives. When fire is applied to a landscape in a patchy manner, leaving some patches unburned, the resulting grazing animal activity, forage utilization, and animal impact are patchily distributed within that landscape as well. Areas that have been recently burned tend to be characterized by the highest levels of grazing animal activity while areas that have gone the longest without burning tend to be characterized by the lowest levels of grazing animal activity. This can be advantageous …

Proceedings Of The Twelfth North American Crane Workshop, David A. Aborn, Richard Urbanek

Proceedings of the North American Crane Workshop

CONTENTS

PREFACE iii

RESEARCH PAPERS

DISTRIBUTION, ABUNDANCE, AND MIGRATION TIMING OF GREATER AND LESSER SANDHILL CRANES WINTERING IN THE SACRAMENTO-SAN JOAQUIN RIVER DELTA REGION OF CALIFORNIA - . Gary L. Ivey, Bruce D. Dugger, Caroline P. Herziger, Michael L. Casazza, and Joseph P. Fleskes 1

CHARACTERISTICS OF SANDHILL CRANE ROOSTS IN THE SACRAMENTO-SAN JOAQUIN DELTA OF CALIFORNIA - . Gary L. Ivey, Bruce D. Dugger, Caroline P. Herziger, Michael L. Casazza, and Joseph P. Fleskes 12

EFFECTS OF WIND FARMS ON SANDHILL CRANE PLAYA OCCUPANCY ON THE TEXAS HIGH PLAINS - Laura Navarrete and Kerry L. Griffis-Kyle 20

EVALUATION OF …

An Illustrated Id Guide To The Crayfishes Found In Nebraska Native And Non-Native, Steve Schainost

Nebraska Invasive Species Program

There are five crayfishes native to Nebraska. These are:

Orconectes immunis (papershell crayfish)

Orconectes virilis (northern crayfish)

Orconectes neglectus neglectus (ringed crayfish)

Cambarus diogenes (Devil crayfish)

Procambarus gracilis (prairie crayfish)

Three additional non-native crayfishes have also been found here:

Orconectes rusticus (rusty crayfish) [bait tanks and established in two ponds in Omaha]

Procambarus clarkii (red swamp crayfish) [bait tanks]

Procambarus acutus (White River crayfish) [bait tanks]

I will attempt here to provide a photographic guide to field identification, one species per page.

Evaluating Trends In Valve Shape In Eunotia By Comparing Fossil And Modern Species, Jordan Bishop-Genovesi

Environmental Studies Honors Papers

No abstract provided.

Regional And Scale-Specific Effects Of Land Use On Amphibian Diversity [Poster], James R. Vonesh, David Marsh, J. J. Apodaca, Karen H. Beard, Jane M. Bell, Christine Bozarth, Derrick Carper, Julie Charbonnier, Bradley J. Cosentino, Andreia Dantas, Elizabeth A. Forys, Miranda Foster, Jaquelyn General, Kristen S. Genet, Macie Hanneken, Kyle Hess, Shane Hill, Faisal Iqbal, Kara Jones, Nancy E. Karraker, Eran Kilpatrick, Tom A. Langen, James Langford, Katherine Lauer, Alison J. Mccarthy, Joseph Neale, Saumya Patel, Austin Patton, Cherie Southwick, Nathaniel Stearrett, Nick Steijn, Mohammad Tasleem, Joseph Taylor

Biology Presentations

Background/Question/Methods

Habitat loss and degradation influence amphibian distributions and are important drivers of population declines. Our previous research demonstrated that road disturbance, development and wetland area consistently influence amphibian richness across regions of the U.S. Here, we examined the relative importance of these factors in different regions and at multiple spatial scales. Understanding the scales at which habitat disturbance may be affecting amphibian distributions is important for conservation planning. Specifically, we asked: 1) Over what spatial scales do distinct landscape features affect amphibian richness? and 2) Do road types (non-rural and rural) have similar effects on amphibian richness? This is …

Stream Restoration Project: Creating A Wetland, Rochelle Dymond, Lukas Bernhardt, Alec Bates

Plum Run Water Quality Study Documents

No abstract provided.

Using Ailuropoda Melanoleuca As A Model Species For Studying The Ecomorphology Of Paranthropus, Ryan Andrew King

Theses, Dissertations and Capstones

Giant pandas (Ailuropoda melanoleuca) have cranial morphology similar to the extinct hominin genus Paranthropus which makes them an excellent model species when studying Paranthropus diet. Both species have wide skulls with flared zygomatic arches adapted for chewing. To gain insight into possible food sources of Paranthropus, I investigated the giant panda’s specialized diet of bamboo. The toughness, hardness, and stiffness of various bamboo species was determined to assess mechanical challenges facing giant pandas during feeding. Bamboo is thought to be tough, but studies on such properties and how they apply to mastication of giant pandas are largely …

The Natural Life History Of Cambarus (Puncticambarus) Smilax, The Greenbrier Crayfish, Paul William Hughes

Theses, Dissertations and Capstones

The natural life history of Cambarus (Puncticambarus) smilax, the Greenbrier Crayfish, was studied in West Fork of the Greenbrier River and in Thorny Creek, a tributary of the main stem of the Greenbrier River. The Greenbrier Crayfish gets its name from the Greenbrier River watershed where it is thought to occur exclusively. Among described members of the subgenus Puncticambarus, C. smilax is a sister taxon most similar to Cambarus (Puncticambarus) robustus. Monthly collections were made within the two study sites, from August 2010 to July 2011. Collecting techniques included dip-netting, seine-netting, and hand collecting. Cambarus smilax and all other species …

Ecology, Information Literacy And Bernard Lonergan: A Librarian Immersed., Lisa Rose-Wiles

Praxis Presentations

No abstract provided.

"Over The River And Through The Woods": An Analysis Of Understory And Canopy Plant Diversity In Urban Riparian Forests, Carlisle R. Evans Peck

Urban Forest Project

As population growth explodes and urban areas expand, studying the ecology of urban areas has become increasingly important. Urban development has been shown to drastically alter native habitats and to severely degrade biodiversity. However, urban landscapes also hold the potential to harbor and support valuable biodiversity especially if managed correctly. We studied the understory herbaceous plant and overstory tree canopy diversity of eight forested ravines in the small cities of Rock Island and Moline IL surrounded by a range of urban development intensity. The goal of the project was to determine whether or not the composition of the plant communities …

Risk Assessments For New Bioinvasions For The North Sea Region, Josefin Madjidian

NSBWO

This deliverable is a compilation of summaries of four scientific papers that cover different aspects of risks connected to marine bioinvasions in the North Sea Region. One of the papers looks deeper into global shipping and adds several factors to shipping density to describe hotspots for potential invasions and invasion routes. Two of the papers dig into concerns of regional perspective (the Wadden Sea), one developing a model of a specific kind of water body’s vulnerability to non-native, the other dealing with questions related to when a species should be stated as a non-native and when it has become part …

Male-Male Mounting And The Unreliability Of Body Size As A Character For Mate Choice In Male Japanese Beetles (Popillia Japonica Newman), Paul Switzer, Patrick Forsythe, Kipp Kruse

Faculty Research & Creative Activity

Background: Same-sex pairing is common in many animal species. In many insects, same-sex pairing is often thought to be a result of poor sexual discrimination (i.e., a mistake), but few detailed studies of the mechanisms underlying the mistaken pairing have been conducted. Previous studies have found that in the field, a small proportion of Japanese beetle (Popillia japonica) mating pairs consist of two males instead of a male and a female. In the current study, we investigated the relationship between body size, the tendency to mount other males, and the duration of these mounts, in laboratory experiments on male Japanese …

On The Challenges Of Modeling The Net Radiative Forcing Of Wetlands: Reconsidering Mitsch Et Al. 2013, Scott C. Neubauer

Biology Publications

Wetlands play a role in regulating global climate by removing carbon dioxide (CO2) from the atmosphere and sequestering it as soil carbon, and by emitting methane (CH4) and nitrous oxide (N2O) to the atmosphere. In a recent article in this journal (Mitsch et al. Landscape Ecol 28:583–597, 2013), CO2 sequestration and CH4 emissions were modeled for several freshwater wetlands that vary in vegetation type, climate, and hydrology. The authors of that study made significant errors that caused them to underestimate the importance of wetland CH4 emissions on climate dynamics. Here, I reanalyze the Mitsch et al. dataset and show that …

Lack Of Quantitative Training Among Early-Career Ecologists: A Survey Of The Problem And Potential Solutions, F. Barraquand, T. G. Ezard, P. Søgaard Jørgensen, Naupaka B. Zimmerman, S. Chamberlain, R. Salguero-Gómez, T. J. Curran, T. Poisot

Biology Faculty Publications

Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75% were not satisfied with their understanding of mathematical models; 75% felt that the level of mathematics was “too low” in their ecology classes; 90% wanted more mathematics classes for ecologists; and 95% more statistics classes. Respondents thought that 30% of classes in ecology-related degrees should be …

Impacts Of Climate Change On Soil Microorganisms In Northern Hardwood Forests, Carley Jane Kratz

Dissertations, Master's Theses and Master's Reports - Open

As global climate continues to change, it becomes more important to understand possible feedbacks from soils to the climate system. This dissertation focuses on soil microbial community responses to climate change factors in northern hardwood forests. Two soil warming experiments at Harvard Forest in Massachusetts, and a climate change manipulation experiment with both elevated temperature and increased moisture inputs in Michigan were sampled. The hyphal in-growth bag method was to understand how soil fungal biomass and respiration respond to climate change factors. Our results from phospholipid fatty acid (PLFA) analyses suggest that the hyphal in-growth bag method allows relatively pure …

Big Manistee River Tributaries As Potential Arctic Grayling Habitat, Brian M. Danhoff

Dissertations, Master's Theses and Master's Reports - Open

The Big Manistee River was one of the most well known Michigan rivers to historically support a population of Arctic grayling (Thymallus arctics). Overfishing, competition with introduced fish, and habitat loss due to logging are believed to have caused their decline and ultimate extirpation from the Big Manistee River around 1900 and from the State of Michigan by 1936. Grayling are a species of great cultural importance to Little River Band of Ottawa Indian tribal heritage and although past attempts to reintroduce Arctic grayling have been unsuccessful, a continued interest in their return led to the assessment of environmental conditions …

Impacts And Management Of Hemlock Woolly Adelgid In National Parks Of The Eastern United States, Scott R. Abella

Life Sciences Faculty Research

No abstract provided.

Assessing Perceived And Documented Crop Damage In A Tanzanian Village Impacted By Human-Elephant Conflict (Hec), Rebekah R. Hoffmeier-Karimi, Bruce A. Schulte

Biology Faculty Publications

In sub-Saharan Africa human-wildlife conflict (HWC) is a growing conservation issue and human-elephant conflict (HEC) is of special concern. Crop loss to wildlife comprises a main component of HWC. Deterrent methods for crop loss are numerous and such schemes could be more effective by an improved understanding of how farmers’ perceptions align with actual causes of crop loss. Our objective was to compare the perception by farmers of the causes and extent of crop damage to the measured crop damage in fields of maize (Zea mays) using different deterrent methods. We interviewed agriculturalists in the farming village of Miti Mirefu …

Impacts Of Environmental Pressures On The Reproductive Physiology Of Subpopulations Of Black Rhinoceros (Diceros Bicornis Bicornis) In Addo Elephant National Park, South Africa, Elizabeth Freeman, Jordana Meyer, Jed Bird, John Adendorff, Bruce A. Schulte, Rachel Santymire

Biology Faculty Publications

Black rhinoceros are an icon for international conservation, yet little is known about their physiology due to their secretive nature. To overcome these challenges, non-invasive methods were used to monitor rhinoceros in two sections of Addo Elephant National Park, South Africa, namely Addo and Nyathi. These sections were separated by a public road, and the numbers of elephants, predators and tourists were higher in Addo. Faecal samples (n = 231) were collected (from July 2007 to November 2010) from known individuals and analysed for progestagen and androgen metabolite (FPM and FAM, respectively) concentrations. As biotic factors could impact reproduction, …

Natural History Of A Population Of Wood Turtles (Glyptemys Insculpta) In West Virginia, Jessica Curtis

Theses, Dissertations and Capstones

The Wood Turtle (Glyptemys insculpta) is listed as vulnerable in West Virginia and only occurs in the Eastern Panhandle. The study population is unique in West Virginia because it occurs at a much higher mean elevation than other Wood Turtle populations in the state. The primary objective of this study was to determine if, and to what extent, altitude affected this population’s ecology. Turtles were located with opportunistic surveys and captured by hand. I located 31 turtles: 18 males, and 13 females. Turtles were captured a total of 68 times. Ratio of males to females did not differ significantly from …

Effectiveness Of Hand Removal For Small-Scale Management Of Japanese Beetles (Coleoptera: Scarabaeidae), Paul V. Switzer, Ryan M. Cumming

Faculty Research & Creative Activity

Hand removal is often recommended as a method for small-scale control of Japanese beetles (Popillia japonica Newman). In this study, we investigated the effectiveness of daily hand removal for controlling damage by Japanese beetles on grape plants. We also investigated whether the timing of the removal (at 0800, 1400, or 1900 hours, or at all 3 periods) inßuenced the effectiveness of the technique. We found that hand removal signiÞcantly lowered the number of beetles on, and consequently the damage to, grape plants relative to nonremoval controls. Of the single removal treatments, removal of beetles at 1900 hours was most effective, …

Male-Male Mounting And The Unreliability Of Body Size As A Character For Mate Choice In Male Japanese Beetles (Popillia Japonica Newman), Paul V. Switzer, Patrick S. Forsythe, Kipp C. Kruse

Faculty Research & Creative Activity

Background: Same-sex pairing is common in many animal species. In many insects, same-sex pairing is often thought to be a result of poor sexual discrimination (i.e., a mistake), but few detailed studies of the mechanisms underlying the mistaken pairing have been conducted. Previous studies have found that in the field, a small proportion of Japanese beetle (Popillia japonica) mating pairs consist of two males instead of a male and a female. In the current study, we investigated the relationship between body size, the tendency to mount other males, and the duration of these mounts, in laboratory experiments on male Japanese …

Effectiveness Of Hand Removal For Small-Scale Management Of Japanese Beetles (Coleoptera: Scarabaeidae), Paul Switzer, Ryan Cumming

Faculty Research & Creative Activity

Hand removal is often recommended as a method for small-scale control of Japanese beetles (Popillia japonica Newman). In this study, we investigated the effectiveness of daily hand removal for controlling damage by Japanese beetles on grape plants. We also investigated whether the timing of the removal (at 0800, 1400, or 1900 hours, or at all 3 periods) inßuenced the effectiveness of the technique. We found that hand removal signiÞcantly lowered the number of beetles on, and consequently the damage to, grape plants relative to nonremoval controls. Of the single removal treatments, removal of beetles at 1900 hours was most effective, …

Landmark Ruling On Whaling From The International Court Of Justice, Mark P. Simmonds

Laws and Legislation Collection

On 31 March 2014, the International Court of Justice (ICJ) ruled that Japan’s whaling activities in Antarctica did not comply with Article VIII of the International Convention for the Regulation of Whaling (ICRW), which permits whaling for scientific purposes. Copious and confusing media commentary followed the decision. This included seemingly conflicting reports from within Japan, which initially indicated whole-hearted compliance with the ruling, which required this whaling to cease, but later suggested that implementation by Japan might be limited to a brief halt followed by a launch of a new Antarctic ‘research’ programme including lethal take.

Marine Noise Pollution - Increasing Recognition But Need For More Practical Action, Mark P. Simmonds, Sarah J. Dolman, Michael Jasny, E. C. M. Parsons, Lindy Weilgart, Andrew J. Wright, Russell Leaper

Ecology Collection

Over the last two decades, marine noise pollution has become increasingly recognized as an issue of major significance. The issue has become a primary focus of marine mammal research, but is also of concern to the public and policy makers. The result has been efforts involving a variety of disciplines, and relevant legislation and associated guidance are now in place in many parts of the world. Most current mitigation efforts are directed at reducing the risk of injury from exposure to intense noise, although the effectiveness of such mitigation measures in terms of risk reduction has rarely been quantified. Longer-term …

Hatching Success Of Rainbowfish Eggs Following Exposure To Air, Lois J. Oulton, Penelope Carbia, Culum Brown

Aquaculture Collection

Translocation of fishes within and between drainage basins is widely recognised as a threatening process to Australian native fishes. While many translocations are deliberate, for example for fisheries enhancement, it is possible that translocation can occur naturally. In the Wet Tropic region of Australia, the widespread eastern rainbowfish, Melanotaenia splendida, has begun to colonise the Atherton tablelands. This is of particular concern because the area is home to several endangered endemic species such as the Lake Eacham rainbowfish, M. eachamensis, and its allies. It is likely that some of the translocations have occurred through the use of this species as …