Biology Commons^™

Defence Mitigation By Predators Of Chemically Defended Prey Integrated Over The Predation Sequence And Across Biological Levels With A Focus On Cardiotonic Steroids, Shabnam Mohammadi, Lu Yang, Matthew Bulbert, Hannah M. Rowland

School of Biological Sciences: Faculty Publications

Predator–prey interactions have long served as models for the investigation of adaptation and fitness in natural environments. Anti-predator defences such as mimicry and camouflage provide some of the best examples of evolution. Predators, in turn, have evolved sensory systems, cognitive abilities and physiological resistance to prey defences. In contrast to prey defences which have been reviewed extensively, the evolution of predator counter-strategies has received less attention. To gain a comprehensive view of how prey defences can influence the evolution of predator counter-strategies, it is essential to investigate how and when selection can operate. In this review we evaluate how predators …

Dynamic Energy Budget Models: Fertile Ground For Understanding Resource Allocation In Plants In A Changing World, Sabrina E. Russo, Glenn Ledder, Erik B. Muller, Roger M. Nisbet

School of Biological Sciences: Faculty Publications

Climate change is having dramatic effects on the diversity and distribution of species. Many of these effects are mediated by how an organism’s physiological patterns of resource allocation translate into fitness through effects on growth, survival and reproduction. Empirically, resource allocation is challenging to measure directly and so has often been approached using mathematical models, such as Dynamic Energy Budget (DEB) models. The fact that all plants require a very similar set of exogenous resources, namely light, water and nutrients, integrates well with the DEB framework in which a small number of variables and processes linked through pathways represent an …

Constraints On The Evolution Of Toxin-Resistant Na,K-Atpases Have Limited Dependence On Sequence Divergence, Shabnam Mohammadi, Santiago Herrera-Álvarez, Lu Yang, María Del Pilar Rodrı´Guez-Ordoñez, Karen Zhang, Jay F. Storz, Susanne Dobler, Andrew J. Crawford, Peter Andolfatto

School of Biological Sciences: Faculty Publications

A growing body of theoretical and experimental evidence suggests that intramolecular epistasis is a major determinant of rates and patterns of protein evolution and imposes a substantial constraint on the evolution of novel protein functions. Here, we examine the role of intramolecular epistasis in the recurrent evolution of resistance to cardiotonic steroids (CTS) across tetrapods, which occurs via specific amino acid substitutions to the α-subunit family of Na,K-ATPases (ATP1A). After identifying a series of recurrent substitutions at two key sites of ATP1A that are predicted to confer CTS resistance in diverse tetrapods, we then performed protein engineering experiments to test …

Circadian Rhythms Mediate Infection Risk In Daphnia Dentifera, Alaina C. Pfenning-Butterworth, David T. Nguyen, Jessica L. Hite, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera–Metschnikowia bicuspidata host–pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit …

Functional Traits’ Annual Variation Exceeds Nitrogen-Driven Variation In Grassland Plant Species, George R. Wheeler, Chad Brassil, Johannes M. H. Knops

School of Biological Sciences: Faculty Publications

Effective application of functional trait approaches to ecological questions requires understanding the patterns of trait variation within species as well as between them. However, few studies address the potential for intraspecific variation to occur on a temporal basis and, thus, for trait-based findings to be contingent upon sampling year. To quantify annual variation in the functional traits of grassland plant species, we measured specific leaf area, leaf dry matter content, plant height, and chlorophyll content in 12 shortgrass prairie plant species. We repeated these measurements across 4 years, both in long-term nitrogen addition plots and in corresponding control plots. Three …

Time Domains Of Hypoxia Responses And -Omics Insights, James J. Yu, Amy L. Non, Erica C. Heinrich, Wanjun Gu, Joe Alcock, Esteban A. Moya, Elijah S. Lawrence, Michael S. Tift, Katie A. O'Brien, Jay F. Storz, Anthony V. Signore, Jane I. Khudyakov, William K. Milsom, Sean M. Wilson, Cynthia M. Beall, Francisco C. Villafuerte, Tsering Stobdan, Colleen G. Julian, Lorna G. Moore, Mark M. Fuster, Jennifer A. Stokes, Richard Milner, John B. West, Jiao Zhang, John Y. Shyy, Ainash Childebayeva, José Pablo Vázquez-Medina, Luu V. Pham, Omar A. Mesarwi, James E. Hall, Zachary A. Cheviron, Jeremy Sieker, Arlin B. Blood, Jason X. Yuan, Tatum S. Simonson, Et Al.

School of Biological Sciences: Faculty Publications

The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context …

Circadian Rhythms Mediate Infection Risk In Daphnia Dentifera, Alaina C. Pfenning-Butterworth, David T. Nguyen, Jessica L. Hite, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera–Metschnikowia bicuspidata host–pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit …

Circadian Rhythms Mediate Infection Risk In Daphnia Dentifera, Alaina C. Pfenning-Butterworth, David T. Nguyen, Jessica L. Hite, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Biological rhythms mediate important within-host processes such as metabolism, immunity, and behavior which are often linked to combating disease exposure. For many hosts, exposure to pathogens occurs while feeding. However, the link between feeding rhythms and infection risk is unclear because feeding behavior is tightly coupled with immune and metabolic processes which may decrease susceptibility to infection. Here, we use the Daphnia dentifera–Metschnikowia bicuspidata host–pathogen system to determine how rhythms in feeding rate and immune function mediate infection risk. The host is known to have a nocturnal circadian rhythm in feeding rate, yet we found that they do not exhibit …

Genome Sequence Of Sn1, A Bacteriophage That Infects Sphaerotilus Natans And Pseudomonas Aeruginosa, K.M. Damitha Gunathilake, Denise M. Tremblay, Pier-Luc Plante, Ellen C. Jensen, Kenneth Nickerson, Sylvain Moineau

School of Biological Sciences: Faculty Publications

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.

Genome Sequence Of Sn1, A Bacteriophage That Infects Sphaerotilus Natans And Pseudomonas Aeruginosa, K.M. Damitha Gunathilake, Denise M. Trembly, Pier-Luc Plante, Ellen C. Jensen, Kenneth W. Nickerson, Sylvian Moineau

School of Biological Sciences: Faculty Publications

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.

Stabilization By Adaptive Feedback Control For Positive Difference Equations With Applications In Pest Management, J. Edholm, C. Guiver, Richard Rebarber, Brigitte Tenhumberg, S. Townley

School of Biological Sciences: Faculty Publications

An adaptive feedback control scheme is proposed for stabilizing a class of forced nonlinear positive difference equations. The adaptive scheme is based on so-called high-gain adaptive controllers and contains substantial robustness with respect to model uncertainty as well as with respect to persistent forcing signals, including measurement errors. Our results take advantage of the underlying positive systems structure and ideas from input-to-state stability from nonlinear control theory. Our motivating application is to pest or weed control, and in this context the present work substantially strengthens previous work by the authors. The theory is illustrated with examples.

Long-Distance Vocalizations Of Spotted Hyenas Contain Individual, But Not Group, Signatures, Kenna D.S. Lehmann, Frants H. Jensen, Andrew Gersick, Ariana Strandburg-Peshkin, Kay E. Holekamp

School of Biological Sciences: Faculty Publications

In animal societies, identity signals are common, mediate interactions within groups, and allow individuals to discriminate group-mates from out-group competitors. However, individual recognition becomes increasingly challenging as group size increases and as signals must be transmitted over greater distances. Group vocal signatures may evolve when successful in-group/out-group distinctions are at the crux of fitness-relevant decisions, but group signatures alone are insufficient when differentiated within-group relationships are important for decision-making. Spotted hyenas are social carnivores that live in stable clans of less than 125 individuals composed of multiple unrelated matrilines. Clan members cooperate to defend resources and communal territories from neighbouring …

Our Past Creates Our Present: A Brief Overview Of Racism And Colonialism In Western Paleontology, Pedro M. Monarrez, Joshua B. Zimmt, Annaka M. Clement, William Gearty, John J. Jacisin, Kelsey M. Jenkins, Kristopher M. Kusnerik, Ashley W. Poust, Selina V. Robson, Judith A. Sclafani, Kelsey T. Stilson, Shamindri D. Tennakoon, Carmi Milagros Thompson

School of Biological Sciences: Faculty Publications

As practitioners of a historical science, paleontologists and geoscientists are well versed in the idea that the ability to understand and to anticipate the future relies upon our collective knowledge of the past. Despite this understanding, the fundamental role that the history of paleontology and the geosciences plays in shaping the structure and culture of our disciplines is seldom recognized and therefore not acted upon sufficiently. Here, we present a brief review of the history of paleontology and geology in Western countries, with a particular focus on North America since the 1800s. Western paleontology and geology are intertwined with systematic …

Mutant Microorganisms And Methods Of Making And Using, Raghuveer Singh, Derrick White, Paul Blum

School of Biological Sciences: Faculty Publications

This disclosure describes methods that allow for the uncoupling of microbial growth from product formation, which allows for maximal use of raw material and optimal end product formation.

Quantifying Predator Functional Responses Under Field Conditions Reveals Interactive Effects Of Temperature And Interference With Sex And Stage, Kyle E. Coblentz, Amber Squires, Stella Uiterwaal, John Delong

School of Biological Sciences: Faculty Publications

1. Predator functional responses describe predator feeding rates and are central to predator–prey theory. Originally defined as the relationship between predator feeding rates and prey densities, it is now well known that functional responses are shaped by a multitude of factors. However, much of our knowledge about how these factors influence functional responses is based on laboratory studies that are generally logistically constrained to examining only a few factors simultaneously and that have unclear links to the conditions organisms experience in the field.
2. We apply an observational approach for measuring functional responses to understand how sex/stage differences, temperature and predator densities …

Using Quantitative Imaging For Personalized Medicine In Pancreatic Cancer: A Review Of Radiomics And Deep Learning Applications, Kiersten Preuss, Nate Thach, Xiaoying Liang, Michael Baine, Justin Chen, Chi Zhang, Huijing Du, Hongfeng Yu, Chi Lin, Michael A. Hollingsworth, Dandan Zheng

School of Biological Sciences: Faculty Publications

As the most lethal major cancer, pancreatic cancer is a global healthcare challenge. Personalized medicine utilizing cutting-edge multi-omics data holds potential for major breakthroughs in tackling this critical problem. Radiomics and deep learning, two trendy quantitative imaging methods that take advantage of data science and modern medical imaging, have shown increasing promise in advancing the precision management of pancreatic cancer via diagnosing of precursor diseases, early detection, accurate diagnosis, and treatment personalization and optimization. Radiomics employs manually-crafted features, while deep learning applies computer-generated automatic features. These two methods aim to mine hidden information in medical images that is missed by …

Instructional Models For Course-Based Research Experience (Cre) Teaching, David I. Hanauer, Mark J. Graham, Rachel J. Arnold, Mary A. Ayuk, Mitchell F. Balish, Andrea R. Beyer, Kristen A. Butela, Christine A. Byrum, Catherine P. Chia, Hui Min Chung, Kari L. Clase, Stephanie Conant, Roy J. Coomans, Tom D'Elia, Jason Diaz, Arturo Diaz, Jean A. Doty, Nicholas P. Edgington, Dustin C. Edwards, Elvira Eivazova, Christine B. Emmons, Kayla M. Fast, Viknesh Sivanathan, And About 50 Others

School of Biological Sciences: Faculty Publications

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert …

Exploring Higher-Order Conceptual Learning In An Arthropod With A Large Multisensory Processing Center, Kenna D. S. Lehmann, Fiona G. Shogren, Mariah Fallick, James Colton Watts, Daniel Schoenberg, Daniel D. Wiegmann, Verner P. Bingman, Eileen A. Hebets

School of Biological Sciences: Faculty Publications

Comparative cognition aims to understand the evolutionary history and current function of cognitive abilities in a variety of species with diverse natural histories. One characteristic often attributed to higher cognitive abilities is higher-order conceptual learning, such as the ability to learn concepts independent of stimuli—e.g., ‘same’ or ‘different’. Conceptual learning has been documented in honeybees and a number of vertebrates. Amblypygids, nocturnal enigmatic arachnids, are good candidates for higher-order learning because they are excellent associational learners, exceptional navigators, and they have large, highly folded mushroom bodies, which are brain regions known to be involved in learning and memory in insects. …

The Ecology Of Wealth Inequality In Animal Societies, Eli D. Strauss, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Individuals vary in their access to resources, social connections and phenotypic traits, and a central goal of evolutionary biology is to understand how this variation arises and influences fitness. Parallel research on humans has focused on the causes and consequences of variation in material possessions, opportunity and health. Central to both fields of study is that unequal distribution of wealth is an important component of social structure that drives variation in relevant outcomes. Here, we advance a research framework and agenda for studying wealth inequality within an ecological and evolutionary context. This ecology of inequality approach presents the opportunity to …

Integrating Tropical Research Into Biology Education Is Urgently Needed, Ann E. Russell, T. Mitchell Aide, Elizabeth Braker, Carissa N. Ganong, Rebecca D. Hardin, Karen D. Holl, Sara C. Hotchkiss, Jeffrey A. Klemens, Erin K. Kuprewicz, Deedra Mcclearn, George Middendorf, Rebecca Ostertag, Jennifer S. Powers, Sabrina E. Russo, Jennifer L. Stynoski, Ursula Valdez, Charles G. Willis

School of Biological Sciences: Faculty Publications

Understanding tropical biology is important for solving complex problems such as climate change, biodiversity loss, and zoonotic pandemics, but biology curricula view research mostly via a temperatezone lens. Integrating tropical research into biology education is urgently needed to tackle these issues.

The tropics are engines of Earth systems that regulate global cycles of carbon and water, and are thus critical for management of greenhouse gases. Compared with higher-latitude areas, tropical regions contain a greater diversity of biomes, organisms, and complexity of biological interactions. The tropics house the majority of the world’s human population and provide important global commodities from species …

Functional Response Of Harmonia Axyridis To The Larvae Of Spodoptera Litura: The Combined Effect Of Temperatures And Prey Instars, Yasir Islam, Farhan Mahmood Shah, Ali Güncan, John Paul Delong, Xingmiao Zhou

School of Biological Sciences: Faculty Publications

Functional responses are central to predator–prey dynamics and describe how predation varies with prey abundance. Functional responses often are measured without regard to prey size (i.e., body mass) or the temperature dependence of feeding rates. However, variation in prey size within populations is ubiquitous, and predation rates are often both size and temperature-dependent. Here, we assessed functional responses of larvae and adult Harmonia axyridis on the 1st, 2nd, and 3rd instars of the prey Spodoptera litura across a range of temperatures (i.e., 15, 20, 25, 30, and 35◦C). The type and parameters of the functional responses were determined using logistic …

Late Pleistocene Megafauna Extinction Leads To Missing Pieces Of Ecological Space In A North American Mammal Community, Felisa A. Smith, Emma A. Elliott Smith, Amelia Villaseñor, Catalina P. Tomé, S. Kathleen Lyons, Seth D. Newsome

School of Biological Sciences: Faculty Publications

The conservation status of large-bodied mammals is dire. Their decline has serious consequences because they have unique ecological roles not replicated by smaller-bodied animals. Here, we use the fossil record of the megafauna extinction at the terminal Pleistocene to explore the consequences of past biodiversity loss. We characterize the isotopic and body-size niche of a mammal community in Texas before and after the event to assess the influence on the ecology and ecological interactions of surviving species (>1 kg). Preextinction, a variety of C₄ grazers, C₃ browsers, and mixed feeders existed, similar to modern African savannas, with …

Fishing Regulations, Sexual Dimorphism, And The Life History Of Harvest, Lyndsie S. Wszola, Zachary S. Feiner, Christopher J. Chizinski, Jamilynn B. Poletto, John P. Delong

School of Biological Sciences: Faculty Publications

Freshwater recreational fisheries regulations are a vital tool for achieving social and ecological fisheries objectives. However, angler behavior and fish biology may interact to influence regulation efficacy in unexpected ways. We combined models of fish growth and angler behavior to explore how angler behavior interacts with fish life history to shape the probability of fish harvest given capture across ages, life stages, and sexes of walleye (Sander vitreus). Compared to females, males grew more quickly as juveniles, matured earlier, and reached smaller maximum sizes. Male walleye were therefore vulnerable to harvest for more of their reproductive lives than …

An Empiricist’S Guide To Using Ecological Theory, Tess N. Grainger, Athmanathan Senthilnathan, Po-Ju Ke, Matthew A. Barbour, Natalie T. Jones, John Delong, Sarah P. Otto, Mary I. O'Connor, Kyle E. Coblentz, Nikunj Goel, Jawad Sakarchi, Megan C. Szojka, Jonathan M. Levine, Rachel M. Germain

School of Biological Sciences: Faculty Publications

A scientific understanding of the biological world arises when ideas about how nature works are formalized, tested, refined, and then tested again. Although the benefits of feedback between theoretical and empirical research are widely acknowledged by ecologists, this link is still not as strong as it could be in ecological research. This is in part because theory, particularly when expressed mathematically, can feel inaccessible to empiricists who may have little formal training in advanced math. To address this persistent barrier, we provide a general and accessible guide that covers the basic, step-by-step process of how to approach, understand, and use …

Predator Functional Responses And The Biocontrol Of Aphids And Mites, John Delong, Stella Uiterwaal

School of Biological Sciences: Faculty Publications

Biocontrol with predators is a key tool for controlling agricultural pests and preserving the productive efficiency of crops. Determining which predators to use for biocontrol often involves measuring their functional response—the relationship between foraging rate and prey abundance, yet comparisons of functional responses across predators are complicated by differences in experimental procedures. Here we use a compilation of functional responses standardized for time and space units to illustrate key sources of variation in functional responses for predators being tested for control of aphids and mites. Our results show that arena size (as a proxy for habitat structure) is a crucial …

Forage Database: A Compilation Of Functional Responses For Consumers And Parasitoids, Stella Uiterwaal, Ian T. Lagerstrom, Shelby R. Lyon, John Delong

School of Biological Sciences: Faculty Publications

Functional responses, the relationships between consumer foraging rate and resource (prey) density, provide key insights into consumer–resource interactions while also being a major driver of population dynamics and food web structure. We present a global database of 2598 standardized functional responses and parameters extracted from the published literature. We refit the functional responses with a Type II model using standardized methods and report the fitted parameters along with data on experimental conditions, consumer and resource taxonomy and type, as well as the habitat and dimensionality of the foraging interaction. The consumer and resource species covered here are taxonomically diverse, from …

An Expert-Curated Global Database Of Online Newspaper Articles On Spiders And Spider Bites, Stefano Mammola, Laura Segura-Hernández, Et Al.

School of Biological Sciences: Faculty Publications

Mass media plays an important role in the construction and circulation of risk perception associated with animals. Widely feared groups such as spiders frequently end up in the spotlight of traditional and social media. We compiled an expert-curated global database on the online newspaper coverage of human-spider encounters over the past ten years (2010– 2020). This database includes information about the location of each human-spider encounter reported in the news article and a quantitative characterisation of the content—location, presence of photographs of spiders and bites, number and type of errors, consultation of experts, and a subjective assessment of sensationalism. In …

Revisiting Clickers: In-Class Questions Followed By At-Home Reflections Are Associated With Higher Student Performance On Related Exam Questions, Dana L. Kirkwood-Watts, Emily K. Bremers, Emily Robinson, Kathleen R. Brazeal, Brian A. Couch

School of Biological Sciences: Faculty Publications

Clicker questions are a commonly used active learning technique that stimulates student interactions to help advance understanding of key concepts. Clicker questions are often administered with an initial vote, peer discussion, and a second vote, followed by broader classroom explanation. While clickers can promote learning, some studies have questioned whether students maintain this performance on later exams, highlighting the need to further understand how student answer patterns relate to their understanding of the material and to identify ways for clickers to benefit a broader range of students. Systematic requizzing of concepts during at-home assignments represents a promising mechanism to improve …

Reconstructed Evolutionary Patterns For Crocodile-Line Archosaurs Demonstrate Impact Of Failure To Log-Transform Body Size Data, Roger B. J. Benson, Pedro Godoy, Mario Bronzati, Richard J. Butler, William Gearty

School of Biological Sciences: Faculty Publications

No abstract provided.

Pea Aphid Winged And Wingless Males Exhibit Reproductive, Gene Expression, And Lipid Metabolism Differences, Omid Saleh Ziabari, Qingyi Zhong, Swapna R. Purandare, Joel Reiter, Anthony J. Zera, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

Alternative, intraspecific phenotypes offer an opportunity to identify the mechanistic basis of differences asso- ciated with distinctive life history strategies. Wing dimorphic insects, in which both flight-capable and flight- incapable individuals occur in the same population, are particularly well-studied in terms of why and how the morphs trade offflight for reproduction. Yet despite a wealth of studies examining the differences between fe- male morphs, little is known about male differences, which could arise from different causes than those acting on females. Here we examined reproductive, gene expression, and biochemical differences between pea aphid ( Acyrthosiphon pisum ) winged and wingless …