Biology Commons^™

The Venomous Rattlesnakes And New World Coral Snakes: Molecular Systematics, Biogeography And The Evolution Of Venom Systems, Jacobo Reyes Velasco

Biology Dissertations - Archive

Middle America is one of the most biologically diverse regions in the world, however it is also one with some of the highest rates of biodiversity loss. Reptiles are especially diverse in this region, and are a very important component of the area, from a biological as well as a cultural perspective. In Mexico and Central America venomous snakes are the most studied group of reptiles, as they are of great ecological and medical importance. Despite this, our understanding of the evolutionary relationships in many groups of venomous snakes is limited. Understanding these relationships is no ludicrous matter as it …

Plant Immune Defenses Against The Human Pathogens Escherichia Coli O157:H7 And Salmonella Enterica, Debanjana Roy

Biology Dissertations - Archive

Several pathogenic and non-pathogenic microorganisms reside on plant leaf surfaces while bacteria being the most abundant of them all. Often bacteria not only use the plant leaf surface as their habitat but also penetrate through stomatal pore on leaf epidermis to survive in the plant's intercellular space also known as the apoplast. To fight against infection caused by bacteria plants rely on their innate immunity system which consists of pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is considered to be the first line of defense response and it is effective against a broad range of pathogens. Nonetheless, some microbial …

Phylogenetic And Fossil Evidence For A Common Body Size Attractor In Marine Mammals, William Gearty, Jonathan Payne

School of Biological Sciences: Presentations

Evolutionary transitions between terrestrial and aquatic habitats are rare and often have large effects on the evolutionary trajectory of the clade making the transition. Following a single transition from the marine realm to the terrestrial realm, tetrapods have subsequently re-evolved a marine lifestyle at least 30 separate times. At least six of these re-invasions of the water occurred within crown-group mammals and four [sirenians (Sirenia), whales (Cetacea), pinnipeds (Pinnipedia), and otters (Lutrinae)] clades are extant. Although marine mammals are widely known to be larger than their terrestrial sister groups, the extent to which the body size evolution of these clades …

Genetically Based Low Oxygen Affinities Of Felid Hemoglobins: Lack Of Biochemical Adaptation To High-Altitude Hypoxia In The Snow Leopard, Jan E. Janecka, Simone S. E. Nielsen, Sidsel D. Andersen, Federico G. Hoffmann, Roy E. Weber, Trevor Anderson, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

Genetically based modifications of hemoglobin (Hb) function that increase blood–O₂ affinity are hallmarks of hypoxia adaptation in vertebrates. Among mammals, felid Hbs are unusual in that they have low intrinsic O₂ affinities and reduced sensitivities to the allosteric cofactor 2,3-diphosphoglycerate (DPG). This combination of features compromises the acclimatization capacity of blood–O2 affinity and has led to the hypothesis that felids have a restricted physiological niche breadth relative to other mammals. In seeming defiance of this conjecture, the snow leopard (Panthera uncia) has an extraordinarily broad elevational distribution and occurs at elevations above 6000 m in the Himalayas. Here, …

How Fast Is Fast? Eco-Evolutionary Dynamics And Rates Of Change In Populations And Phenotypes, John Delong, Valery E. Forbes, Nika Galic, Jean P. Gibert, Robert G. Laport, Joseph S. Phillips, Janna M. Vavra

School of Biological Sciences: Faculty Publications

It is increasingly recognized that evolution may occur in ecological time. It is not clear, however, how fast evolution – or phenotypic change more generally – may be in comparison with the associated ecology, or whether systems with fast ecological dynamics generally have relatively fast rates of phenotypic change. We developed a new dataset on standardized rates of change in population size and phenotypic traits for a wide range of species and taxonomic groups. We show that rates of change in phenotypes are generally no more than 2/3, and on average about 1/4, the concurrent rates of change in population …

Females Sample More Males At High Nesting Densities, But Ultimately Obtain Less Attractive Mates, Robin M. Tinghitella, Chelsea Stehle, Janette W. Boughman

School of Biological Sciences: Faculty Publications

Background: Sexual selection is largely driven by the availability of mates. Theory predicts that male competition and female choice should be density-dependent, with males competing more intensely at relatively high density, and females becoming increasingly discriminating when there are more males from whom to choose. Evidence for flexible mating decisions is growing, but we do not understand how environmental variation is incorporated into mate sampling strategies. We mimicked threespine stickleback (Gasterosteus aculeatus) breeding conditions in pools with high and low densities of nesting males and allowed females to search for mates to determine whether 1) mate search strategies change with …

Epistasis Constrains Mutational Pathways Of Hemoglobin Adaptation In High-Altitude Pikas, Danielle M. Tufts, Chandrasekhar Natarajan, Inge G. Revsbech, Joana Projecto- Garcia, Federico G. Hoffmann, Roy E. Weber, Angela Fago, Hideaki Moriyama, Jay F. Storz

School of Biological Sciences: Faculty Publications

A fundamental question in evolutionary genetics concerns the roles of mutational pleiotropy and epistasis in shaping trajectories of protein evolution. This question can be addressed most directly by using site-directed mutagenesis to explore the mutational landscape of protein function in experimentally defined regions of sequence space. Here, we evaluate how pleiotropic trade-offs and epistatic interactions influence the accessibility of alternative mutational pathways during the adaptive evolution of hemoglobin (Hb) function in high-altitude pikas (Mammalia: Lagomorpha). By combining ancestral protein resurrection with a combinatorial protein-engineering approach, we examined the functional effects of sequential mutational steps in all possible pathways that produced …

Contribution Of A Mutational Hot Spot To Hemoglobin Adaptation In High-Altitude Andean House Wrens, Spencer C. Galen, Chandrasekhar Natarajan, Hideaki Moriyama, Roy E. Weber, Angela Fago, Phred M. Benham, Andrea N. Chavez, Zachary A. Cheviron, Jay F. Storz, Christopher C. Witt

School of Biological Sciences: Faculty Publications

A key question in evolutionary genetics is why certain mutations or certain types of mutation make disproportionate contributions to adaptive phenotypic evolution. In principle, the preferential fixation of particular mutations could stem directly from variation in the underlying rate of mutation to function-altering alleles. However, the influence of mutation bias on the genetic architecture of phenotypic evolution is difficult to evaluate because data on rates of mutation to function-altering alleles are seldom available. Here, we report the discovery that a single point mutation at a highly mutable site in the βA-globin gene has contributed to an evolutionary change in hemoglobin …

Complete Genome Sequence Of Sulfolobus Solfataricus Strain 98/2 And Evolved Derivatives, Samuel Mccarthy, Julien Gradnigo, Tyler Johnson, Sophie Payne, Anna Lipzen, Joel Martin, Wendy Schackwitz, Etsuko Morlyama, Paul H. Blum

School of Biological Sciences: Faculty Publications

Sulfolobus solfataricus strain 98/2 is a thermoacidophilic chemoheterotrophic crenarcheote that grows optimally at 80°C and pH3.0 (1). The S. solfataricus 98/2 genome reported in 2009 (Gen- Bank accession no. CP001800.1, RefSeq NC_017274.1, GI: 261600703) is a deletion derivative of strain 98/2 called PBL2025 (2). It is often misconstrued as the wild-type strain 98/2, yet lacks a 50-kb region encoding numerous genes involved in sugar metabolism. A new closed and complete genome sequence for wildtype strain 98/2 referred to as SULA is presented here as GenBank accession no. CP011057 using locus tag SULA. This strain has been deposited at the Japan …

Complete Genome Sequence Of An Evolved Thermotoga Maritima Isolate, Raghuveer Singh, Julien Gradnigo, Derrick White, Anna Lipzen, Joel Martin, Wendy Schackwitz, Estuko N. Moriyama, Paul H. Blum

School of Biological Sciences: Faculty Publications

Thermotoga maritima MSB8 genomovar DSM3109 is a hyperthermophilic

anaerobic bacterium (1) that grows at 80°C, producing

a maximum of 4 mol of H2 per mol of glucose (2). There

are a variety of duplicated genes and direct repeats in its genome,

suggesting the potential for genome instability. Genome resequencing

of T. maritima MSB8 genomovar DSM3109 in 2011 and

2013 (3, 4) indicated that the earlier sequenced T. maritima MSB8

reported by Nelson et al. (NC_000853.1) (5) was an evolved laboratory

variant with an approximately 8-kb deletion located between

TM1847 and TM1848 (annotation according to reference

5). The 8-kb deletion may …

First Record On Secondary Pollen Presentation In The Cucurbitaceae Family, Shivani Jadeja

School of Biological Sciences: Faculty Publications

Aim – Secondary pollen presentation in flowers has been described only in a few species across about 25 plant families. The first report of secondary pollen presentation in the Cucurbitaceae family is given here.

Key result – Sechium talamancensis, endemic to high elevations in Costa Rica, presents nearly 39% of its pollen secondarily on the distal ends of its petals. The remaining pollen is presented on the anthers, the primary pollen presenters.

Significance – Closely related and commercially important congeners of S. talamancensis do not show secondary pollen presentation. Potential selective advantages of the phenomenon that differentiates S. talamancensis …

Membrane Association And Catabolite Repression Of The Sulfolobus Solfataricus Α-Amylase, Edith Soo, Deepak Rudrappa, Paul H. Blum

School of Biological Sciences: Faculty Publications

Sulfolobus solfataricus is a thermoacidophilic member of the archaea whose envelope consists of an ether-linked lipid monolayer surrounded by a protein S-layer. Protein translocation across this envelope must accommodate a steep proton gradient that is subject to temperature extremes. To better understand this process in vivo, studies were conducted on the S. solfataricus glycosyl hydrolyase family 57 α-Amylase (AmyA). Cell lines harboring site specific modifications of the amyA promoter and AmyA structural domains were created by gene replacement using markerless exchange and characterized by Western blot, enzyme assay and culture-based analysis. Fusion of amyA to the malAp promoter overcame amyAp …

Intraspecific Polymorphism, Interspecific Divergence, And The Origins Of Function-Altering Mutations In Deer Mouse Hemoglobin, Chandrasekhar Natarajan, Federico G. Hoffmann, Hayley C. Lanier, Cole J. Wolf, Zachary A. Cheviron, Matthew L. Spangler, Roy E. Weber, Angela Fago, Jay F. Storz

School of Biological Sciences: Faculty Publications

Major challenges for illuminating the genetic basis of phenotypic evolution are to identify causative mutations, to quantify their functional effects, to trace their origins as new or preexisting variants, and to assess the manner in which segregating variation is transduced into species differences. Here, we report an experimental analysis of genetic variation in hemoglobin (Hb) function within and among species of Peromyscus mice that are native to different elevations. A multilocus survey of sequence variation in the duplicated HBA and HBB genes in Peromyscus maniculatus revealed that function-altering amino acid variants are widely shared among geographically disparate populations

from different …

Gene Turnover In The Avian Globin Gene Families And Evolutionary Changes In Hemoglobin Isoform Expression, Juan C. Opazo, Federico G. Hoffmann, Chandrasekhar Natarajan, Christopher C. Witt, Michael Berenbrink, Jay F. Storz

School of Biological Sciences: Faculty Publications

The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the α- and β-type subunits of hemoglobin (Hb), the tetrameric α₂β₂ protein responsible for blood-O₂ transport. A comparative genomic analysis of 52 bird species revealed that the size and membership composition of the α- and β-globin gene families have remained remarkably constant during …

The Complexities Of Female Mate Choice And Male Polymorphisms: Elucidating The Role Of Genetics, Age, And Mate-Choice Copying, Kasey D. Fowler-Finn, Laura Sullivan-Beckers, Amy M. Runck, Eileen A. Hebets

Eileen Hebets Publications

Genetic, life history, and environmental factors dictate patterns of variation in sexual traits within and across populations, and thus the action and outcome of sexual selection. This study explores patterns of inheritance, diet, age, and mate-choice copying on the expression of male sexual signals and associated female mate choice in a phenotypically diverse group of Schizocosa wolf spiders. Focal spiders exhibit one of two male phenotypes: ‘ornamented’ males possess large black brushes on their forelegs, and ‘non-ornamented’ males possess no brushes. Using a quantitative genetics breeding design in a mixed population of ornamented/non-ornamented males, we found a strong genetic basis …

Octopamine Levels Relate To Male Mating Tactic Expression In The Wolf Spider Rabidosa Punctulata, Eileen A. Hebets, Matthew Hansen, Thomas C. Jones, Dustin J. Wilgers

Eileen Hebets Publications

In the wolf spider Rabidosa punctulata, upon encountering a female, males use one of two distinct strategies: (1) they court the female in an attempt to elicit a mating, or (2) they engage in a direct-mount tactic that involves extensive grappling with the female until a mating is achieved. The latter tactic appears more sexually aggressive, and both tactics come with the risk of being cannibalized. We explored the physiological mechanisms underlying this behavioral variation by assessing the relationship between circulating levels of the biogenic amine octopamine (OA), a neuromodulator suggested to play a role in “fight or flight” responses …

Functional Approach To Condition, Dustin J. Wilgers, Eileen A. Hebets

Eileen Hebets Publications

Animal signaling is commonly thought to be costly. Signaling costs can arise via a variety of avenues, including energy expenditure, predator attraction, and so on (reviews in Zuk and Kolluru, 1998; Kotiaho, 2001), and are predicted to increase with signal expression (e.g., size, amplitude, and intensity; Johnstone, 1997). Due to these costs, signaler condition, which is hypothesized to be a reflection of a signaler’s genetic quality, is expected to influence the level of signal expression one can afford (Zahavi, 1975), resulting in a positive correlation between signaler condition and signal expression – that is, condition-dependent signaling (Zahavi, 1977; West-Eberhard, 1979; …

Extreme Features Of The Galdieria Sulphuraria Organellar Genomes: A Consequence Of Polyextremophily?, Kanika Jain, Kirsten Krause, Felix Grewe, Gaven F. Nelson, Andreas P. M. Weber, Alan C. Christensen, Jeffrey P. Mower

School of Biological Sciences: Faculty Publications

Nuclear genome sequencing from extremophilic eukaryotes has revealed clues about the mechanisms of adaptation to extreme environments, but the functional consequences of extremophily on organellar genomes are unknown. To address this issue, we assembled the mitochondrial and plastid genomes from a polyextremophilic red alga, Galdieria sulphuraria strain 074W, and performed a comparative genomic analysis with other red algae andmore broadly across eukaryotes. The mitogenomeis highly reduced in size and genetic content and exhibits the highest guanine–cytosine skew of any known genome and the fastest substitution rate among all red algae. The plastid genomecontains a large number of intergenic stem-loop structures …

Genome-Wide Gene Expression In Relation To Age In Large Laboratory Cohorts Of Drosophila Melanogaster, Kimberly A. Carlson, Kylee Gardner, Anjeza Pashaj, Darby J. Carlson, Fang Yu, James D. Eudy, Chi Zhang, Lawrence G. Harshman

School of Biological Sciences: Faculty Publications

Aging is a complex process characterized by a steady decline in an organism’s ability to perform life-sustaining tasks. In the present study, two cages of approximately 12,000 mated Drosophila melanogaster females were used as a source of RNA from individuals sampled frequently as a function of age. A linear model for micro array data method was used for the micro array analysis to adjust for the box effect; it identified 1,581 candidate aging genes.Cluster analyses using a self-organizing map algorithm on the 1,581 significant genes identified gene expression patterns across different ages. Genes involved in immune system function and regulation, …

Site-Specific Differences In T Cell Frequencies And Phenotypes In The Blood And Gut Of Hivuninfected And Art-Treated Hiv+ Adults, Steven A. Yukl, Amandeep K. Shergill, Valerie Girling, Qingsheng Li, Maudi Killian, Lorrie Epling, Peilin Li, Philipp Kaiser, Ashley Haase, Diane V. Havlir, Kenneth Mcquaid, Elizabeth Sinclair, Joseph K. Wong

School of Biological Sciences: Faculty Publications

Gastrointestinal T lymphocytes are critical for mucosal immunity and HIV pathogenesis, yet little is known about normal T cell numbers and phenotypes in different regions of the gut, or the degree to which ART can restore levels to those of HIV-uninfected individuals. To investigate these questions, we measured T cell frequencies and markers of memory, activation, anergy, and homing in the blood, ileum, and rectum of HIV- and ART-suppressed HIV+ adults. In HIV- individuals, T cell frequencies and phenotypes differed significantly between sites. Compared to HIV- adults, HIV+ adults had lower absolute CD4+T cell counts in the ileal lamina propria …

Complete Genome Sequences Of Evolved Arsenate-Resistant Metallosphaera Sedula Strains, Chenbing Ai, Samuel Mccarthy, Wendy Schackwitz, Joel Martin, Anna Lipzen, Paul H. Blum

School of Biological Sciences: Faculty Publications

Metallosphaera sedula is a thermoacidophilic crenarchaeote with a 2.19-Mb genome. Here, we report the genome sequences of several evolved derivatives of M. sedula generated through adaptive laboratory evolution for enhanced arsenate resistance.

What Drives Masting? The Phenological Synchrony Hypothesis, Walter D. Koenig, Johannes M.H. Knops, William J. Carmen, Ian S. Pearse

School of Biological Sciences: Faculty Publications

Annually variable and synchronous seed production, or masting behavior, is a widespread phenomenon with dramatic effects on wildlife populations and their associated communities. Proximally, masting is often correlated with environmental factors and most likely involves differential pollination success and resource allocation, but little is known about how these factors interact or how they influence seed production. We studied masting in the valley oak (Quercus lobata Nee), a California endemic tree, and report evidence that phenological synchrony in flowering driven by microclimatic variability determines the size of the acorn crop through its effects on pollen availability and fertilization success. These …

Pollen Limitation And Flower Abortion In A Wind-Pollinated, Masting Tree, Ian S. Pearse, Walter D. Koenig, Kyle A. Funk, Mario B. Pesendorfer

School of Biological Sciences: Faculty Publications

Pollen limitation is a key assumption of theories that explain mast seeding, which is common among wind-pollinated and woody plants. In particular, the pollen coupling hypothesis and pollination Moran effect hypothesis assume pollen limitation as a factor that synchronizes seed crops across individuals. The existence of pollen limitation has not, however, been unambiguously demonstrated in wind-pollinated, masting trees. We conducted a two-year pollen supplementation experiment on a masting oak species, Quercus lobata. Supplemental pollen increased acorn set in one year but not in the other, supporting the importance of pollen coupling and pollination Moran effect models of mast seeding. …

Transgenic Virus Resistance In Crop-Wild Cucurbita Pepo Does Not Prevent Vertical Transmission Of Zucchini Yellow Mosaic Virus, H. E. Simmons, H. R. Prendeville, J. P. Dunham, M. J. Ferrari, J. D. Earnest, Diana Pilson, G. P. Munkvold, E. C. Holmes, A. G. Stephenson

School of Biological Sciences: Faculty Publications

Zucchini yellow mosaic virus (ZYMV) is an economically important pathogen of cucurbits that is transmitted both horizontally and vertically. Although ZYMV is seed-transmitted in Cucurbita pepo, the potential for seed transmission in virus-resistant transgenic cultivars is not known. We crossed and backcrossed a transgenic squash cultivar with wild C. pepo, and determined whether seed-to-seedling transmission of ZYMV was possible in seeds harvested from transgenic backcrossed C. pepo.We then compared these transmission rates to those of non-transgenic (backcrossed and wild) C. pepo. The overall seed-to-seedling transmission rate in ZYMV was similar to those found in previous studies …

A Five Million Year Old Experiment: The Evolutionary Dynamics Of A Cave Environment, Tyler Bussian 15

Honor Scholar Theses

No abstract provided.

Analysis Of A Coupled N-Patch Population Model With Ceiling Density Dependence, Jason Callahan, Richard Rebarber, Eva Strawbridge, Brigitte Tenhumberg, Shenglan Yuan

School of Biological Sciences: Faculty Publications

We consider a system of difference equations with ceiling density dependence to model the dynamics of a coupled population on an arbitrary, finite number of distinct patches where migration between all patches is possible. In this model, each patch possesses a separate carrying capacity, and the dynamics of the coupled population is governed by a linear model until the population of a patch reaches its capacity, after which it remains at this maximum value. Further, we analyze the global attractors of this model and apply these results to an Arabian oryx metapopulation model with some patches protected and others unprotected …

Assessing Pesticide Risks To Threatened And Endangered Species Using Population Models: Findings And Recommendations From A Croplife America Science Forum, V. E. Forbes, R. Brain, D. Edwards, N. Galic, T. Hall, J. Honegger, C. Meyer, D.R.J. Moore, D. Nacci, R. Pastorok, T. G. Preuss, S. F. Railsback, C. Salice, R. M. Sibly, B. Tenhumberg, P. Thorbek, M. Wang

School of Biological Sciences: Faculty Publications

This brief communication reports on the main findings and recommendations from the 2014 Science Forum organized by CropLife America. The aim of the forum was to gain a better understanding of the current status of population models and how they could be used in ecological risk assessments for threatened and endangered species potentially exposed to pesticides in the United States. The forum panelists' recommendations are intended to assist the relevant government agencies with implementation of population modeling in future endangered species risk assessments for pesticides. The forum included keynote presentations that provided an overview of current practices, highlighted the findings …

Clues To Aquatic Beetle Research In Southeast Asia: A Multitude Of Ecological Niches, Microhabitats And Deduced Field Sampling Techniques, Hendrik Freitag

Biology Faculty Publications

The basic ecological classification of Southeast Asian beetle families that are associated with aquatic habitats is reviewed. The microhabitat preferences of the taxa are examined on family level with generic examples. Suitable collection methods for quantitative and qualitative sampling are suggested which take into account the different ecological adaptation patterns and microhabitat preferences.

Hearing Loss From Traumatic Brain Injury, Nathan Young

A with Honors Projects

Traumatic brain injury to the parts of the brain responsible for processing auditory information can result in hearing loss that is difficult to assess and treat. Symptoms can include difficulty in filtering background noises or filtering out specific sounds, confusion, and disorientation or nausea. Treatment of this type of hearing loss varies, but primarily consists of psychological treatment focused around rehabilitation and coping.

Adaptive Plasticity And Epigenetic Variation In Response To Warming In An Alpine Plant, Adrienne B. Nicotra, Deborah L. Segal, Gemma L. Hoyle, Aaron W. Schrey, Koen J. Verhoeven, Christina L. Richards

Integrative Biology Faculty and Staff Publications

Environmentally induced phenotypic plasticity may be a critical component of response to changing environments. We examined local differentiation and adaptive phenotypic plasticity in response to elevated temperature in half-sib lines collected across an elevation gradient for the alpine herb, Wahlenbergia ceracea. Using Amplified Fragment Length Polymorphism (AFLP), we found low but significant genetic differentiation between low- and high-elevation seedlings, and seedlings originating from low elevations grew faster and showed stronger temperature responses (more plasticity) than those from medium and high elevations. Furthermore, plasticity was more often adaptive for plants of low-elevation origin and maladaptive for plants of high elevation. With …