Life Sciences Commons^™

2015 Final Report: Status Of The Arizona Toad (Anaxyrus Microscaphus) In New Mexico, Mason J. Ryan, Ian M. Latella, Jacek Tomasz Giermakowski, Howard L. Snell

Biology Faculty & Staff Publications

In 2013, we initiated a field study to assess the status of the Arizona Toad (Anaxyrus microscaphus) in New Mexico. Herein we provide the results of three years (2013-2015) of range-wide population monitoring, a review of threat assessments, and several contributions to the basic ecology of the Arizona Toad in New Mexico. This work highlights the sensitivity of the species to abiotic factors and emphasizes the nature of annual population fluctuations in a variable environment. We provide analyses of environmental factors that influence toad reproductive behaviors, employ occupancy and detection modeling at breeding sites, and provide analyses of tadpole habitat …

Genomic Legacy Of The African Cheetah, Acinonyx Jubatus, Pavel Dobrynin, Shiping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergey Kliver, A. Schmidt-Kunzel, Klaus-Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel Garcia-Perez, Marc De Manuel, Ricardo Godinez, Aleksey Komissarov, Alexey Makunin, Vladimir Brukhin, Weilin Qiu, Long Zhou, Fang Li, Jian Yi, Carlos A. Driscoll, Agostinho Antunes, T. K. Oleksyk, Eduardo Eizirik, Polina Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O'Brien

Biology Faculty Articles

Background

Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.

Results

Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years …

Expansion Of The Chlorovirus Genus By Studies On Virus Natural History And Chlorella Host Metabolism, Cristian F. Quispe

School of Biological Sciences: Dissertations, Theses, and Student Research

Inland waters cover about 2.5 percent of our planet and harbor huge numbers of known and unknown microorganisms including viruses. Viruses likely play dynamic, albeit largely undocumented roles in regulating microbial communities and in recycling nutrients in the ecosystem. Phycodnaviruses are a genetically diverse, yet morphologically similar, group of large dsDNA-containing viruses (160- to 560-kb) that inhabit aquatic environments. Members of the genus Chlorovirus are common in freshwater. They replicate in eukaryotic, single-celled, chlorella-like green algae that normally exist as endosymbionts of protists in nature. Very little is known about the natural history of the chloroviruses and how they achieve …

Discovery & Born-Digital Archiving: Open Source Systems For Preservation And Access, L. Bryan Cooper, Margarita Perez-Martinez

Works of the FIU Libraries

The Everglades Explorer (EE) portal at http://ee.fiu.edu continues to evolve with the addition of the Internet Archive's Archive-It, and future planned alignment with the Digital Public Library of America (DPLA). The reasons for the development of the portal continue to exist, as originally perceived four years ago. Adaptations to ongoing change and system testing continues, and the use of Archive-It has broad institutional potential beyond EE. Cross-walking skills continue to grown, and will benefit future syndication and discovery system integration. The metadata normalization and harmonization will help save time for the end-user. Preservation and access to learning and research …

Occupancy Analysis And Density Estimation Of Kori Bustards (Ardeotis Kori) And Helmeted Guineafowl (Numida Meleagris) For Use In Landscape Conservation Planning In The Northern Tuli Game Reserve, Botswana, Kathryn R. Mccollum

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

For understudied species, more informed conservation planning and decision-making on both the local and landscape levels may be attained through the use of occupancy and abundance estimations. Here, we focus on two iconic bird species in eastern Botswana, kori bustards (Ardeotis kori) and helmeted guineafowl (Numida meleagris). The overall goal of this project was to better understand the hierarchy of factors that influence occupancy (ψ) and density of kori bustard and helmeted guineafowl populations within the Northern Tuli Game Reserve and how these factors may interact to affect landscape conservation and usage. We performed distance sampling …

Open Educational Resources: A Catalyst For Innovation, Dominic Orr, Michele Rimini, Dirk Van Damme

Concepts in Animal Parasitology Textbook

Foreword:

Open educational resources (OER) are rapidly becoming a major phenomenon in education across OECD countries and beyond. Initiated largely at the level of institutions by pioneers and technology advocates, the OER community has grown considerably over the past ten years and the impact of OER on educational systems has become an issue of public policy. The open education community is increasingly well organised and enjoys support from various institutions and foundations. National governments have developed, or are in the process of developing, open policies to support access to and use of OER.

It is the task of the OECD …

North Shore: A Natural History Of Minnesota’S Superior Coast, Janet R. Keough

The Prairie Naturalist

Many readers of The Prairie Naturalist have lived along or visited Lake Superior’s coast. Like me, you have probably wondered about the geology and history of this beautiful and dramatic feature of northeastern Minnesota. Chel Anderson and Adelheid Fischer have written an accessible book that comprehensively describes the history and geology of the coast, surrounding highlands, and Lake Superior itself. In addition, the authors have provided fascinating subchapters on some of the most interesting species that are key elements of the region.

This rather large but beautiful book is arranged in five major chapters that cover the dominant geological units …

Sage-Grouse Nests In An Active Conifer Mastication Site, Charles P. Sandford, David K. Dahlgren, Terry A. Messmer

The Prairie Naturalist

Greater sage-grouse (Centrocercus urophasianus; sage-grouse) have experienced long-term range-wide population declines and now may occupy less than 50% of their historic range (Schroeder et al. 2004). Conifer encroachment into sagebrush (Artemisia spp.) habitat was identified as a major conservation threat by the United States Fish and Wildlife Service (USFWS) as the agency reviewed the listing status of the species for possible protection under the Endangered Species Act of 1973 (USFWS 2013).

Conifer encroachment into sagebrush habitats negatively impacts sage-grouse at landscape scales (Doherty et al. 2008, Casazza et al. 2011, Baruch-Mordo et al. 2013). Sage-grouse will utilize …

North Shore: A Natural History Of Minnesota’S Superior Coast, Janet R. Koeugh

The Prairie Naturalist

Many readers of The Prairie Naturalist have lived along or visited Lake Superior’s coast. Like me, you have probably wondered about the geology and history of this beautiful and dramatic feature of northeastern Minnesota. Chel Anderson and Adelheid Fischer have written an accessible book that comprehensively describes the history and geology of the coast, surrounding highlands, and Lake Superior itself. In addition, the authors have provided fascinating subchapters on some of the most interesting species that are key elements of the region.

This rather large but beautiful book is arranged in five major chapters that cover the dominant geological units …

Remembering The Days Of Old: Data Exploration And Simple Statistics, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! By the time you read this editorial, most of you will probably be enjoying spectacular seasonal changes in the outdoors this autumn and a hint of winter in the air (for those of us in the northern Great Plains region). I write this editorial during my favorite time of year, deer hunting in the Midwest. Temperatures are finally start- ing to resemble the fall and the Christmas Holiday season is just around the corner. Much like my children have images of Santa dancing in their heads on Christmas Eve, each fall I replay images of a trophy …

Effects Of Short-Term Soil Conditioning By Cheatgrass And Western Wheatgrass, James J. O'Connor, Janet S. Prevey

The Prairie Naturalist

The exotic grass Bromus tectorum (cheatgrass) is a ubiquitous invader in the western USA. Cheatgrass is a proficient competitor, frequently displacing native plants, forming monotypic stands and reducing biodiversity in ecosystems it invades. Our experiment tested whether short-term soil modification by cheatgrass and a predominant native grass, Pascopyrum smithii (western wheatgrass), affected subsequent growth of both species. We compared productivity of cheatgrass and western wheatgrass by harvesting aboveground biomass of plants grown in either cheatgrass- or western wheatgrass-conditioned soils over two simulated growing seasons. Results indicated that cheatgrass soils do not inhibit the productivity of the native grass, but do …

Estimating Herbaceous Biomass Of Grassland Vegetation Using The Reference Unit Method, Eric D. Boyda, Jack L. Bulter, Lan Xu

The Prairie Naturalist

Aboveground net primary production provides valuable information on wildlife habitat, fire fuel loads, and forage availability. Aboveground net primary production in herbaceous plant communities is typically measured by clipping aboveground biomass. However, the high costs associated with physically harvesting plant biomass may prevent collecting sufficient data to account for natural spatial and temporal variability of vegetation at a landscape scale. Various double-sampling techniques have been developed to increase sample size while reducing cost. We applied a biomass estimation technique previously developed for estimating shrub biomass using representative samples or “reference units” to estimate herbaceous grassland biomass. Our reference units consisted …

Distribution And Occurrence Of Bat Species In North Dakota, Josiah J. Nelson, Paul R. Barnhart, Erin H. Gillam

The Prairie Naturalist

Prior to 2009, a detailed survey of occurrence and distribution of bats in North Dakota had not been conducted. Localized surveys, occurrence reports, and museum specimens provided the only records of bats in the state. Ongoing habitat loss, exploitation of natural resources, and the impending spread of white-nose syndrome to the western United States are major threats to bat populations of the region. The objective of this study was to document presence and distributions of bat species resident in North Dakota. From 2009 to 2012, multiple mist-netting and acoustic surveys were conducted to document species presence across North Dakota. A …

Variability In The Selection Patterns Of Pronghorn: Are They Really Native Prairie Obligates?, Paul F. Jones, Mike Grue, Mike Suitor, Darren J. Bender, Cormack Gates, Dale Eslinger, Julie Landry-Deboer

The Prairie Naturalist

In Canada, pronghorn (Antilocapra americana) are primarily considered a native prairie obligate because of their reliance on open grassland vegetation communities, although an assessment of local ecological knowledge suggests that pronghorn in Alberta select a variety of habitat from native prairie to cultivated lands. The primary objective of our study was to assess whether pronghorn in Alberta and Saskatchewan are native prairie obligates. Specifically, we addressed the following questions: 1) do individual pronghorn show similar selection patterns for native prairie and, therefore, support the notion that they are prairie obligates; 2) do pronghorn show consistent resource selection patterns …

Book Reviews: Bumble Bees Of North America. Paul H. Williams, Robbin W. Thorp, Leif L. Richardson, And Sheila R. Colla., Samuel O’Dell

The Prairie Naturalist

Bumblebee identification is generally considered straight- forward, yet mistakes often are made due to the degree of similarity between the color patterns of different species. Bumble Bees of North America aims to improve the accuracy of identifications by both casual observers and professionals through the use of intuitive diagrams, descriptions, and the more technical dichotomous keys. In addition to providing the first complete field guide to North American bumblebees, the authors make efficient use of the reader’s attention by summarizing taxonomic history, favored food plants, and environmental issues concerning bumblebees.

Bumble Bees of North America is organized into three distinct …

Remembering Paul B. Kannowski, Robert Seabloom

The Prairie Naturalist

I am saddened to report that Dr. Paul Kannowski passed away 3 September 2015, succumbing to cancer. He was 88. A native of Grand Forks, Paul attended the University of North Dakota for his B.S. and M.S. degrees, and the University of Michigan for his Ph.D. He joined the University of North Dakota Biology Department in 1957, retiring in 1990 after 33 years of service

Paul chaired UND’s Biology Department twice, totaling 13 years, considered to be a remarkable achievement by many of us who have been exposed to that task! His leadership was instrumental in the nearly exponential growth …

Notes: Woodpecker Forage Availability In Habi- Tat Disturbances Of The Black Hills, Brian E. Dickerson, Angie K. Ambourn, Mark A. Rumble, Kurt K. Allen, Chad P. Lehman

The Prairie Naturalist

Habitat disturbance events are critical to ecological systems in which some bird species have become specialized. The vegetation community, reduced competition, ability to avoid predators, nest-site characteristics, and forage opportunities within a disturbed ecosystem are all aspects that make it desirable for selection by particular species (Svärdson 1949, Cody 1981, Martin 1998). Specifically, avian species rely on the forest conditions created by fire, insects, and disease (Brawn et al. 2001, Hunter et al. 2001, Devictor et al. 2008). In the Black Hills National Forest (BHNF) of South Dakota,two major types of natural disturbances include wildfires and mountain pine beetle (Dendroctonus …

Regional Evolutionary Distinctiveness And Endangerment As A Means Of Prioritizing Protection Of Endangered Species, Emily K. Brantner

FIU Electronic Theses and Dissertations

Conservation is costly, and choices must be made about where to best allocate limited resources. I propose a regional evolutionary diversity and endangerment (RED-E) approach to prioritization of endangered species. It builds off of the evolutionary diversity and global endangerment (EDGE) approach, but will allow conservation agencies to focus their efforts on species in specific regions. I used the RED-E approach to prioritize mammal and bird species listed under the U.S. Endangered Species Act (ESA), as well as to make a ranking of species without ESA critical habitat (CH), as a practical application. Regional conservation approaches differ significantly from global …

Predicting Toucan Locations In Panama Using Arcgis, Daniel J. Herrera

Geography: Student Scholarship & Creative Works

Toucans are omnivorous birds native to southern Latin America and South America. They are non-migratory, and their range is disputed among experts. In an attempt to develop a better understanding of the range and behavior of toucans, correlations between toucan presence and geographic features of the area were analyzed to create a location probability map.

The First Whole Genome And Transcriptome Of The Cinereous Vulture Reveals Adaptation In The Gastric And Immune Defense Systems And Possible Convergent Evolution Between The Old And New World Vultures, Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, Jehoon Jun, Hyejin Lee, Alvin Chon, Junsu Ko, Jeremy Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O'Brien, Andrea Manica, Jong Bhak, Woon Kee Paek

Biology Faculty Articles

Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.

Results: We sequenced the genome of a cinereous vulture, and mapped it to the bald …

Traversing Swanton Road, 21st Ed., James A. West

Academic, Government & Associated Organizational Research Resources

Situated at the northwest end of Santa Cruz County and occupying circa 30 square miles of sharply contrasted terrain, the Scott Creek Watershed concentrates within its geomorphological boundaries, at least 10-12% of California's flora, both native and introduced. Paradoxically, the use/abuse that the watershed has sustained over the past 140+ years, has not necessarily diminished the biodiversity and perhaps parallels the naturally disruptive but biologically energizing processes (fire, flooding, landslides and erosion), which have also been historically documented for the area for +60 years. This is an early edition of an extensive document by James A. West. Please visit the …

Integrative Taxonomy, A New Tool For Fisheries Conservation, Adela Roa-Varon, Eric J. Hilton

Presentations

Species delimitation is becoming increasingly objective and integrative. Sequence capture approaches allow collection of 1000s of loci for 100s of individuals. New approaches address the computational challenges of large datasets and offer potential for genome-wide sampling of variation at different evolutionary scales. These new approaches also allow integration of genetic and non-genetic data in a unified framework. Despite these advances, few studies have attempted to combine genetic and morphological data for delimiting species. Hakes (Merluccius spp.) are an ideal group for an empirical test of the power and applicability of these new methods because they are morphologically conserved and …

Gene Loss, Adaptive Evolution And The Co-Evolution Of Plumage Coloration Genes With Opsins In Birds, Rui Borges, Imran Khan, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Agostinho Antunes

Biology Faculty Articles

Background: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems.

Results: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal …

Métodos Cuantitativos Para La Conservación De Los Vertebrados, Michael J. Conroy, John P. Carroll, Juan Carlos Senar, Jeffrey J. Thompson

School of Natural Resources: Faculty Publications

Este libro es destinado para el uso por biólogos del campo y otras personas, incluso biólogos de campo en el futuro que podrían estar en un curso de la universidad y trabajando en estudios y conservación de animales. Nuestro objetivo es que los biólogos usen este libro como (haciendo apología a nuestro colega Evan Cooch) una “introducción suave” al campo de la ecología cuantitativa. Esperamos convencer a los lectores que los métodos y aproximaciones del libro no son solo para los matemáticos, estadísticos y programadores de computadoras, sino que de hecho son herramientas esenciales para practicar la conservación en el …

When An Invasive Plant Fails To Invade, Stephen L. Young

West Central Research and Extension Center, North Platte

In 2012, much of the US Midwest was gripped in one of the most severe droughts on record. While conducting experimental fieldwork at a site in Nebraska during June of that year, I noticed a single musk thistle (Carduus nutans; Figure 1) that appeared to be in the bolt or early flowering stage, which is typical for the species at that time. Here, however, two things were unusual: this plant was less than 1 meter tall (with adequate moisture and light, musk thistle typically grows to heights of 1–2.5 meters before flowering), and was only 3 months old (the bolt …

The Rediscovery And Precarious Status Of Chihuahuan Dwarf Crayfish Cambarellus Chihuahuae, Evan W. Carson, Carlos Pedraza-Lara, María De Lourdes Lozano-Vilano, Gabino A. Rodríguez-Almaráz, Iris Banda-Villanueva, Lissette A. Sepúlveda-Hernández, Lilia Vela-Valladares, Andrea Cantú-Garza, Mauricio De La Maza-Benignos

Occasional Papers

We report rediscovery of the Chihuahuan Dwarf Crayfish Cambarellus chihuahuae at the desert spring Ojo Solo in Ejido Rancho Nuevo in Chihuahua, México. This species was reported to be extinct. Morphological evaluation of 12 voucher specimens confirmed the population as C. chihuahuae. Crayfish were abundant upon rediscovery in September 2012 and remained so throughout bimonthly monitoring from February 2014 to April 2015. Despite abundance at Ojo Solo, the species is critically imperiled, with four of its five native habitats dry and the remaining one in decline; however, a population was established at Ojo Caliente, a nearby natural refuge habitat we …

Metazoan Endoparasites Of The Gray Fox, Urocyon Cinereoargenteus From New Mexico, John E. Ubelaker, Bretton S. Griffin, Genevieve M. Konicke, Nora Abdullah, Aya Mouhaffel, Donald Duszynski, Robert L. Harrison

MANTER: Journal of Parasite Biodiversity

Metazoan gastrointestinal endoparasites were recovered from 10 of 14 (71.4%) gray foxes [Urocyon cinereoargenteus (Schreber, 1775)] collected in New Mexico from 1996 -1998. They include a pentastome Porocephalus sp., (n=1, 7.1%), a trematode: Fasciola hepatica Linnaeus, 1758 (n=1, 7.1%), the nematodes: Physaloptera rara Hall and Wigdor, 1918 (n=3, 14.3%), Physaloptera praeputialis Linstow, 1899 (n=2, 14.3%), an unidentified female Physaloptera sp. (n=1, 7.1%), Toxocara mystax (Zeder, 1800) (n=2, 14.3%), Toxocara canis (Werner, 1782) (n=1, 7.1%), Spirocerca lupi (Rudolphi, 1809) (n=6, 42.9%), and cestodes: Taenia pisiformis (Bloch, 1780) n=3, n=3, (21.4%), Taenia serialis (Gervais, 1847) (n=3, 21.4%), and Mesocestoides …

Sediment Loss Of Santa Rosa Island Slopes: An Erosional Study, Michael Perez

STAR Program Research Presentations

Ranching began on Santa Rosa Island in the 1840’s, consequently introducing nonnative megafauna that put novel selective grazing pressures on endemic plant species. Their movement patterns also altered sediment integrity as the land was denuded of any stabilizing vegetation. Dense groves of island oak (Q. tomentella) are known to aid in sediment deposition and retention. The groves also function to collect water during periods of intense fog that are common to the island. This experiment sought to quantify the volume of sediment that has been lost on a south facing slope in the middle of the island that …

Sustaining The Saco Estuary: Final Report 2015, Christine B. Feurt Ph D, Pamela A. Morgan, Mark D. O. Adams, Anna L. Bass, Carrie J. Byron, Michael C. Daley, Michael O. Esty, Noah G. Perlut, Kayla Smith, Tyler Spillane, Michelle M. Steen-Adams, James Sulikowski, Stephan I. Zeeman, Jacob Aman, Michele Dionne, Jeremy Miller, Kristin Wilson

Environmental Studies Faculty Publications

This study focuses on the Saco estuary, the tidal portion of the Saco River, which drains the largest watershed in southern Maine. With headwaters in the White Mountains of New Hampshire, the watershed encompasses more than 4,400 km², and provides clean healthy drinking water to over 100,000 people living and working in communities in southern Maine.

When the study began in 2009, very little was known about the ecology of the Saco estuary. Researchers at the University of New England and the Wells National Estuarine Research Reserve employed the process of collaborative learning to bring together people who …

Radiocarbon Isotopic Classification Of Deep Tropical Forest Soils, Brooke Butler, Karis J. Mcfarlane, Jennifer Pett-Ridge, Katherine A. Heckman

STAR Program Research Presentations

Tropical forest soils have an important role in global carbon (C) stocks. Small changes in the cycling of C could drastically affect atmospheric carbon dioxide (CO2) concentrations and active cycling of carbon in a forest community. Currently, little is understood of how tropical forest soils will respond to the increasing global temperatures. To examine the effects of warming/ drought on losses of older versus younger soil C pools, we implemented radiocarbon (14C) isotopic characterization of various soil plot samples and depths from the Luquillo Experimental Forest, Puerto Rico. 14C was measured using Accelerated Mass Spectrometry (AMS) from catalytically condensed carbon …