Biology Commons^™

Applying Marine Protected Area Design Models In Large Estuarine Systems, Roman Zajac, Amanda E. Neely

Biology and Environmental Science Faculty Publications

Several types of design models are currently being used to develop marine protected areas (MPAs) for conservation of coastal and pelagic ecosystems. However, few studies have applied these models in large estuaries which have unique characteristics that need to be considered in MPA design, including strong physical, chemical and biological gradients and significant human impacts. We explored how one design model, MARXAN, can be applied to estuarine systems by developing MPA design scenarios for Long Island Sound, an estuary in the northeastern USA. Using sedimentary texture as a proxy for habitats, we modeled and tested several scenarios where conservation goals …

Ngasp - The Nematode Genome Annotation Assessment Project, Avril Coghlan, Tristan J. Fiedler, Sheldon J. Mckay, Paul R. Flicek, Todd W. Harris, Darin Blasiar, Lincoln D. Stein

Biomedical Engineering and Sciences Faculty Publications

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. Results: The most accurate gene-finders were …

Ecology Of The Evening Bat (Nycticeius Humeralis) At The Northern Edge Of The Range, Olivia Maya Munzer

Master's Theses and Doctoral Dissertations

Only a single colony of evening bats (Nycticeius humeralis) is known to occur in Michigan, and it is the northernmost colony on the North American continent. In mid-May, only female evening bats migrate to Michigan to raise their pups, and in late August, evening bats migrate to southern portions of their range, where they are ubiquitous. I studied the roosting and dietary ecology of the evening bat in southeastern Michigan. Evening bats roosted in cavities, crevices, and under exfoliating bark of older trees located in a bottomland forest, interlaced with waterways and surrounded by agricultural fields. These habitats …

Changes In Biotic And Abiotic Processes Following Mangrove Clearing, Elise Granek, Benjamin I. Ruttenberg

Biological Sciences

Mangrove forests, important tropical coastal habitats, are in decline worldwide primarily due to removal by humans. Changes to mangrove systems can alter ecosystem properties through direct effects on abiotic factors such as temperature, light and nutrient supply or through changes in biotic factors such as primary productivity or species composition. Despite the importance of mangroves as transitional habitats between land and sea, little research has examined changes that occur when they are cleared. We examined changes in a number of biotic and abiotic factors following the anthropogenic removal of red mangroves (Rhizophora mangle) in the Panamanian Caribbean, including …

Clustering Neural Spike Trains With Transient Responses, John D. Hunter, Jianhong Wu, John Milton

WM Keck Science Faculty Papers

The detection of transient responses, i.e. nonstationarities, that arise in a varying and small fraction of the total number of neural spike trains recorded from chronically implanted multielectrode grids becomes increasingly difficult as the number of electrodes grows. This paper presents a novel application of an unsupervised neural network for clustering neural spike trains with transient responses. This network is constructed by incorporating projective clustering into an adaptive resonance type neural network (ART) architecture resulting in a PART neural network. Since comparisons are made between inputs and learned patterns using only a subset of the total number of available dimensions, …

The Impact Of Repeated Rounds Of Mass Drug Administration With Diethylcarbamazine Plus Albendazole On Bancroftian Filariasis In Papua New Guinea, Gary J. Weil, Will Kastens, Melinda Susapu, Sandra J. Laney, Steven A. Williams, Christopher L. King, James W. Kazura, Moses J. Bockarie

Biological Sciences: Faculty Publications

Background: This study employed various monitoring methods to assess the impact of repeated rounds of mass drug administration (MDA) on bancroftian filariasis in Papua New Guinea, which has the largest filariasis problem in the Pacific region.

Methodology/Principal Findings: Residents of rural villages near Madang were studied prior to and one year after each of three rounds of MDA with diethylcarbamazine plus albendazole administered per World Health Organization (WHO) guidelines. The mean MDA compliance rate was 72.9%. Three rounds of MDA decreased microfilaremia rates (Mf, 1 ml night blood by filter) from 18.6% pre-MDA to 1.3% after the third MDA (a …

Production Of Marine Trematode Cercariae: A Potentially Overlooked Path Of Energy Flow In Benthic Systems, David W. Thieltges, Xavier De Montaudouin, Brian L. Fredensborg, K. Thomas Jensen, Janet Koprivnikar, Robert Poulin

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Parasites, in particular trematodes, are unseen but ubiquitous components of marine intertidal ecosystems. Although parasites are known to affect population dynamics and food web structure, their potential function as an unrecognized path of energy flow in these ecosystems is yet to be quantified. We use published data on rates at which trematodes produce free-swimming infective larvae (cercariae) that are released from their gastropod intermediate hosts to investigate patterns in cercarial output as a function of different variables, and to calculate the annual production of cercariae in different marine benthic systems. Across 18 trematode species, cercarial output (no. cercariae shed snail–1 …

Does Shape Predict Performance? An Analysis Of Morphology And Swimming Performance In Great Basin Fishes, John R. Aedo

Theses and Dissertations

Swimming performance strongly influences fitness in aquatic organisms and is closely tied to external body morphology. Although this connection has been closely examined at the individual and species level, few studies have focused on this relationship as it pertains to functional group assemblages. Using functional groups based on similarities in habitat use and morphology, I tested the hypothesis that swimming performance can be reliably predicted by functional group composition. I measured swimming performance as burst speed using a simulated predator attack and as prolonged speed using a step-endurance test in a laboratory flume. I measured morphology using geometric morphometric techniques. …

Trichomycetes From Lentic And Lotic Aquatic Habitats In Ontario, Canada, D. B. Strongman, Merlin M. White

Biology Faculty Publications and Presentations

Fungi and protists make up an ecological group, trichomycetes, that inhabit the guts of invertebrates, mostly aquatic insects. Trichomycetes are reported herein from arthropods collected in lotic habitats (fast flowing streams) and lentic environments (ponds, ditches, seeps, and lakes) from 11 sites in Algonquin Park and 6 other sites in Ontario, Canada. Thirty-two trichomycete species were recovered, including 7 new species: Legeriomyces algonquinensis, Legeriosimilis leptocerci, Legeriosimilis whitneyi and Paramoebidium umbonatum are described from mayfly nymphs (Ephemeroptera); Pennella digitata and Glotzia incilis from black fly and midge larvae (Diptera), respectively; and Arundinula opeongoensis from a crayfish (Crustacea). Legeriomyces rarus Lichtw. & …

Does Light Control Algal Abundance In Large River Systems?, Amy Macdonald

Theses and Dissertations

A limited amount of research has been done to investigate the factors influencing algal abundance in large river systems. This study examines light as the primary factor that controls algal abundance in the Upper Mississippi, Missouri and Ohio Rivers. Data were collected for 2004 in conjunction with the Environmental Monitoring Assessment Program- Great River Ecosystems EMAP-GRE project using EPA approved methods. Chlorophyll a concentrations were 34.6 µg•L-1 in the Upper Mississippi, 19.8 µg•L-1 in Missouri River and 9 µg•L-1 in the Ohio River for 2004. Chlorophyll a concentrations were significantly different among the three rivers (p<0.0001) but not between years. Inter-river variation could be loosely correlated with light availability: mean Average Irradiance Dosages, which consider factors that affect light climate (depth, transparency, velocity, surface irradiance), by river corresponded with mean chlorophyll a levels by river. Intra-river variation seemed to be due to both the influence of light and nutrients.

Effects Of Olfactory And Visual Predators On Nest Success And Nest-Site Selection Of Waterfowl In North Dakota, Jennifer Borgo

Green Canyon Environmental Research Area, Logan Utah

No abstract provided.

The Biological Soil Crusts Of The San Nicolas Island: Enigmatic Algae From A Geographically Isolated Ecosystem, Valerie R. Flechtner, Jeffrey R. Johansen, Jayne Belnap

Biology

Composite soil samples front 7 sites on San Nieolas Island were evaluated quantitatively and qualitatively for the presence of cyanobacteria and enkaryotic microalgae. Combined data demonstrated a rich algal flora with 19 cyanobacterial and 19 eukaryotic microalgal genera being identified, for a total of 56 species. Nine new species were identified and described among the cyanobacteria and the enkaryotic microalgae that were isolated: Leibleinia edaphica, Aphanothece maritima, Chroococcidiopsis edaphica, Cyanosarcina atroceneta, Hassallia californica, Hassallia pseudo-ramosissima, Microchaete terrestre, Palmellopsis californicus, and Pseudotetracystis compactis. Distinct distributional patterns of algal taxa existed among sites on the island and among soil algal floras of …

Yellow Head Virus: Transmission And Genome Analyses, Hongwei Ma

Dissertations

Yellow head virus (YHV) is an important pathogen to shrimp aquaculture. Among 13 species of naturally YHV-negative crustaceans in the Mississippi coastal area, the daggerblade grass shrimp, Palaemonetes pugio, and the blue crab, Callinectes sapidus, were tested for potential reservoir and carrier hosts of YHV using PCR and real time PCR. The YHV replicated in the daggerblade grass shrimp, and was still detectable on 36 d post-inoculation, causing 8% mortality after injection. However, YHV did not replicate in the blue crab. These data suggest that the daggerblade grass shrimp could act as a reservoir host for YHV. Storage conditions of …

Biological Responses In A Dynamic Bouyant River Plume, Mark A. Moline, Thomas K. Frazer, Robert Chant, Scott Glenn, Charles A. Jacoby, John R. Reinfelder, Jennifer Yost, Meng Zhou, Oscar Schofield

Biological Sciences

Buoyant river plumes are highly dynamic and often characterized by marked physical and chemical gradients that interact to drive biological responses. For example, interactions among factors resulting in algal growth (e.g., nutrient and light availability) and algal loss (e.g., sinking and zooplankton grazing) vary with spatiotemporal changes in physics and chemistry. The nature of these interactions profoundly influences the transfer and transformation of materials carried by the plume, including nutrients and metals. In April 2005, during the Lagrangian Transport and Transformation Experiment (LaTTE), water from the Hudson River recirculated in a nearshore eddy before moving southward to mix with relatively …

An Analysis Of Illegal Bushmeat Availability In Local Restaurants Located In Voi, Kenya, Bridget A. Sutton

Masters Theses & Specialist Projects

The illegal bushmeat harvest has been identified as a reason for declining wildlife populations throughout much of Africa. For many years the trade was thought to exist primarily in Western Africa. The illegal use of bushmeat in Eastern Africa, including Kenya, went undocumented and unstudied. In 2004, the Born Free Foundation published a study which claimed illegal sale of wild game was substantial in butcheries throughout Nairobi, Kenya. In an effort to determine other markets of the commercial trade, the goal of this study was to analyze local restaurants in Voi, Kenya for illegal bushmeat sale. The town of Voi …

Recombination-Based In Vivo Expression Technology Identifies Helicobacter Pylori Genes Important For Host Colonization, Andrea Castillo, Andrew J. Woodruff, Lynn E. Connolly, William E. Sause, Karen M. Ottemann

Biology Faculty Publications

Here we undertook to identify colonization and gastric disease-promoting factors of the human gastric pathogen Helicobacter pylori as genes that were induced in response to the stomach environment. Using recombination-based in vivo expression technology (RIVET), we identified six promoters induced in the host compared to laboratory conditions. Three of these promoters, designated Pivi10, Pivi66, and Pivi77, regulate genes that H. pylori may use to interact with other microbes or the host. Pivi10 likely regulates the mobA, mobB, and mobD genes, which have potential roles in horizontal gene transfer through plasmid mobilization. Pivi66 occurs in the cytotoxin-associated gene pathogenicity island, a …

Dispersal Of The Hudson River Plume In The New York Bight: Synthesis Of Observational And Numerical Studies During Latte, Robert J. Chant, John Wilkin, Weifeng Zhang, Byoung-Ju Choi, Eli Hunter, Renato Castelao, Scott Glenn, Joe Jurisa, Oscar Schofield, Robert Houghton, Josh Kohut, Thomas K. Frazer, Mark A. Moline

Biological Sciences

Observations and modeling during the Lagrangian Transport and Transformation Experiment (LaTTE) characterized the variability of the Hudson River discharge and identified several freshwater transport pathways that lead to cross-shelf mixing of the Hudson plume. The plume’s variability is comprised of several different outflow configurations that are related to wind forcing, river discharge, and shelf circulation. The modes are characterized by coastal current formation and unsteady bulge recirculation. Coastal currents are favored during low-discharge conditions and downwelling winds, and represent a rapid downshelf transport pathway. Bulge formation is favored during high-discharge conditions and upwelling winds. The bulge is characterized by clockwise …

Dietary Exposure To 2,2´,4,4´-Tetrabromodiphenyl Ether (Pbde-47) Alters Thyroid Status And Thyroid Hormone–Regulated Gene Transcription In The Pituitary And Brain, Sean C. Lema, Jon T. Dickey, Irvin R. Schultz, Penny Swanson

Biological Sciences

No abstract provided.

Integrating Development And Evolution In Psychology: Looking Back, Moving Forward, David S. Moore

Pitzer Faculty Publications and Research

This work is the editorial for a special edition of New Ideas in Psychology titled Integrating Development and Evolution in Psychology.

Distribution Patterns Of Sciurus Niger (Eastern Fox Squirrel) Leaf Nests Within Woodlots Across A Suburban/Urban Landscape, Carmen M. Salsbury

Scholarship and Professional Work - LAS

To determine habitat characteristics that influence Sciurus niger (Eastern Fox Squirrel) abundance and distribution within a suburban/urban landscape in the midwestern United States, I documented the density and placement of fox squirrel leaf nests in 20 woodlots in the Indianapolis metropolitan area, Marion County, IN. The woodlots varied in size (0.94 to 19.5 ha), approximate age, shape, and degree of isolation from other woodlots and suitable squirrel habitat in the surrounding area. Only 8.0% of nests were located in a tree with another nest, and nests were randomly distributed in all but one woodlot, where they were uniformly dispersed. Nest …

Predator-Prey Relationships And Spatial Ecology Of Jaguars In The Southern Pantanal, Brazil: Implications For Conservation And Management, Sandra Maria Cintra Cavalcanti

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Pantanal wetland of Brazil is an important area for the conservation of jaguars (Panthera onca) and a stronghold for the species. Although our knowledge of jaguar ecology has increased since the first field studies in the mid 1980’s, a detailed study of this cryptic species remains challenging. In the following chapters, we investigated the ecology of jaguars in the southern Pantanal of Brazil. In Chapter II, we examined the foraging ecology of jaguars, documenting predation rates, patterns, and species killed. We found individual jaguars differed in the selection of their prey. There were differences in the proportion …

Diets Of Ladybird Beetles (Coleoptera: Coccinellidae) In Utah Alfalfa Fields, Lynette Nicole Davidson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Aphidophagous lady beetles rely on multiple sources of food in their environment. Alfalfa fields provide both aphids and many alternate foods, such as other arthropod prey, pollen, and fungi. Alfalfa fields (Medicago sativa L.) in Utah have low aphid densities, which may require lady beetles to consume alternative sources of food. Many methods can be used to determine these diets; frass analysis is used here to compare the diets of the introduced species Coccinella septempunctata L. with two native species, C. transversoguttata richardsoni Brown and Hippodamia convergens Guérin-Méneville, that occur in the Utah alfalfa habitat.

In initial laboratory experiments …

Reproductive Tactics Of Aphidophagous Lady Beetles: Comparison Of A Native Species And An Invasive Species That Is Displacing It, Yukie Kajita

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Coccinella septempunctata L. (Coleoptera: Coccinellidae) has been introduced to North America in recent decades, raising concerns of adverse impacts on native lady beetles, including the congeneric C. transversoguttata richardsoni (Brown). The central focus of my dissertation is to understand the importance of reproduction, in particular, in promoting invasion of C. septempunctata and its replacement of native lady beetles in alfalfa fields of western North America.

Studies were conducted to compare reproductive tactics of the invasive C. septempunctata and the native C. transversoguttata, by addressing: 1) maximum rate of reproduction of overwintered lady beetles, 2) population dynamics of the invasive …

The Genetics Of Colonization In Two Amphibian Species After The 1980 Eruption Of Mount St. Helens, Kristin Ann Bakkegard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The genetics of colonization is understudied in salamanders but has large conservation implications as new habitats are formed or restored to their previous condition. The 1980 eruption of Mount St. Helens provided a natural experiment to study the genetic effects of a large infrequent environmental disturbance on two species of salamander, Taricha granulosa (Rough-skinned newt) and Ambystoma gracile (Northwestern salamander). Both these species breed in ponds, and are thought to exhibit high breeding site fidelity and low vagility. I designated three treatments based on the effects of the eruption: new ponds (created by the eruption, immigrants only), recovery lakes (in …

Estimating Total Phosphorus And Total Suspended Solids Loads From High Frequency Data, Amber Spackman Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Frequently measured turbidity was examined as a surrogate for total phosphorus (TP) and total suspended solids (TSS) loads at two locations in the Little Bear River, Utah, USA. Using regression techniques, equations were developed for TP and TSS as functions of turbidity. The equations accounted for censored data, and additional explanatory variables to represent hydrological conditions were considered for inclusion in the equations. By using the resulting surrogate relationships with high frequency turbidity measurements, high frequency estimates of TP and TSS concentrations were calculated. To examine the effect of sampling frequency, reference loads were determined from the concentration records for …

Phenotypic Plasticity And The Post-Modern Synthesis: Integrating Evo-Devo And Quantitative Genetics In Theoretical And Empirical Studies, Alison G. Scoville

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Mainstream evolutionary biology lacks a mature theory of phenotype. Following from the Modern Synthesis, researchers tend to assume an unrealistically simple mapping of genotype to phenotype, or else trust that the complexities of developmental architecture can be adequately captured by measuring trait variances and covariances. In contrast, the growing field of evolutionary developmental biology (evo-devo) explicitly examines the relationship between developmental architecture and evolutionary change, but lacks a rigorous quantitative and predictive framework. In my dissertation, I strive to integrate quantitative genetics and evo-devo, using both theoretical and empirical studies of plasticity. My first paper explores the effect of realistic …

A Conceptual Framework For Understanding Effects Of Wildlife Water Developments In The Western United States, Randy T. Larsen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Free water can be a limiting factor to wildlife in arid regions of the world. In the western United States, management agencies have installed numerous, expensive wildlife water developments (e.g. catchments, guzzlers, wells) to: 1) increase the distribution or density of target species, 2) influence animal movements, and 3) mitigate for the loss of available free water. Despite over 50 years as an active management practice, water developments have become controversial for several species. We lack an integrated understanding of the ways free water influences animal populations. In particular, we have not meshed understanding of evolutionary adaptations that reduce the …

Disturbance As Restoration In The Intermountain Sagebrush Steppe: Effects On Non Target Bird Species, Russell Edward Norvell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Changes in shrubsteppe passerine bird habitat associations in response to disturbance were investigated at multiple temporal and spatial scales. Spatial measures incorporated the effects of area at different ecological scales (nest site, territory, and landscape) to include ecologically meaningful extents. Temporal measures included seasonal and annual effects, and were designed to detect lagged responses should they occur. Local-to-landscape scale effects of mechanical restoration treatments on local extirpation and abundances of nine species indicated most were insensitive to changes in habitat quality, while abundance models showed only broad declines. Changing the availability of nesting habitat on both the attractiveness and quality …

Mountain Pine Beetle Fecundity And Offspring Size Differ Among Lodgepole Pine And Whitebark Pine Hosts, Donovan Gross

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Whitebark pine (Pinus albicaulis Engelmann) is a treeline species in the central Rocky Mountains. Its occupation of high elevations previously protected whitebark pine from long-term mountain pine beetle outbreaks. The mountain pine beetle, however, is currently reaching outbreaks of record magnitude in high-elevation whitebark pine. We used a factorial laboratory experiment to compare mountain pine beetle (Dendroctonus ponderosae Hopkins) life history characteristics between a typical host, lodgepole pine (Pinus contorta Engelmann), and whitebark pine. We tested the effects of natal host and brood host on beetle fecundity, offspring size, and brood sex-ratio. We reared mountain pine beetles …

Sex-Biased Predation On Taricha By A Novel Predator In Annadel State Park, Amber Noelle Brouillette

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Newts of the genus Taricha have long been studied due to the powerful neurotoxin found in their skin. Tetrodotoxin (TTX) acts by blocking receptors in sodium channels, ultimately resulting in death via asphyxiation. The only documented predators of species in this genus have been snakes of the genus Thamnophis. Recently, predation on Taricha in Ledson Marsh in Annadel State Park, Santa Rosa, CA was discovered. Predation was in the form of laceration or evisceration, and tracking of predation from 1998-2008 showed that it was male-biased. Two species of Taricha were found living sympatrically at this location, the California newt …