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Trophic Cascades Alter Eco-Evolutionary Dynamics And Body Size Evolution, Thomas M. Luhring, John Delong

School of Biological Sciences: Faculty Publications

Trait evolution in predator–prey systems can feed back to the dynamics of interacting species as well as cascade to impact the dynamics of indirectly linked species (eco-evolutionary trophic cascades; EETCs). A key mediator of trophic cascades is body mass, as it both strongly influences and evolves in response to predator–prey interactions. Here, we use Gillespie ecoevolutionary models to explore EETCs resulting from top predator loss and mediated by body mass evolution. Our four-trophic-level food chain model uses allometric scaling to link body mass to different functions (ecological pleiotropy) and is realistically parameterized from the FORAGE database to mimic the parameter …

Making A First Impression: Exploring What Instructors Do And Say On The First Day Of Introductory Stem Courses, A Kelly Lane, Clara L. Meaders, J Kenny Shuman, Mackenzie R. Stetzer, Erin L. Vinson, Brian A. Couch, Michelle K. Smith, Marilyne Stains

School of Biological Sciences: Faculty Publications

Student impressions formed during the first day of class can impact course satisfaction and performance. Despite its potential importance, little is known about how instructors format the first day of class. Here, we report on observations of the first day of class in 23 introductory science, technology, engineering, and math (STEM) courses. We first described how introductory STEM instructors structure their class time by characterizing topics covered on the first day through inductive coding of class videos. We found that all instructors discussed policies and basic information. However, a cluster analysis revealed two groups of instructors who differed primarily in …

Pollinator Assemblage And Pollen Load Differences On Sympatric Diploid And Tetraploid Cytotypes Of The Desert-Dominant Larrea Tridentata, Robert G. Laport, Robert L. Minckley, Diana Pilson

School of Biological Sciences: Faculty Publications

PREMISE: Whole-genome duplication (polyploidy) is an important force shaping flowering plant evolution. Ploidy-specific plant–pollinator interactions represent important community-level biotic interactions that can lead to nonrandom mating and the persistence of mixed-ploidy populations. METHODS: At a naturally occurring diploid–tetraploid contact zone of the autopolyploid desert shrub Larrea tridentata, we combined flower phenology analyses, collections of bees on plants of known cytotype, and flow cytometry analyses of bee-collected pollen loads to investigate whether (1) diploid and tetraploid plants have unique bee pollinator assemblages, (2) bee taxa exhibit ploidy-specific visitation and pollen collection biases, and (3) specialist and generalist bee taxa have ploidy-specific …

Resources For Teaching And Assessing The Vision And Change Biology Core Concepts, Janet L. Branchaw, Pamela A. Pape-Lindstrom, Kimberly D. Tanner, Sarah A. Bissonnette, Tawnya L. Cary, Brian A. Couch, Alison J. Crowe, Jenny K. Knight, Katharine Semsar, Julia I. Smith, Michelle K. Smith, Mindi M. Summers, Caroline J. Wienhold, Christian D. Wright, Sara E. Brownell

School of Biological Sciences: Faculty Publications

The Vision and Change report called for the biology community to mobilize around teaching the core concepts of biology. This essay describes a collection of resources developed by several different groups that can be used to respond to the report’s call to transform undergraduate education at both the individual course and departmental levels. First, we present two frameworks that help articulate the Vision and Change core concepts, the BioCore Guide and the Conceptual Elements (CE) Framework, which can be used in mapping the core concepts onto existing curricula and designing new curricula that teach the biology core concepts. Second, we …

Book Review: Nature’S Giants: The Biology And Evolution Of The World’S Largest Lifeforms., William Gearty

School of Biological Sciences: Faculty Publications

We as humans have always been in awe of big things, whether they are in space, the oceans, or the fossil record. Ruxton uses this inspiration as the entry point to explore the biology (and even physics) and evolu- tion of large animals in Nature’s Giants, covering nu- merous great lifeforms spanning from giant whales to enormous sauropods. Although readers may ini- tially be drawn in by the size of these creatures, as the author writes in the introduction, “size matters,” and the weight of these animals brings with it many other fascinating implications that he goes into with moderate …

Origin Of Complexity In Hemoglobin Evolution, Arvind S. Pillai, Shane A. Chandler, Yang Liu, Anthony V. Signore, Carlos R. Cortez-Romero, Justin L. P. Benesch, Arthur Laganowsky, Jay F. Storz, Georg K. A. Hochberg, Joseph W. Thornton

School of Biological Sciences: Faculty Publications

Most proteins associate into multimeric complexes with specific architectures, which often have functional properties such as cooperative ligand binding or allosteric regulation. No detailed knowledge is available about how any multimer and its functions arose during evolution. Here we use ancestral protein reconstruction and biophysical assays to elucidate the origins of vertebrate hemoglobin, a heterotetramer of paralogous α- and β-subunits that mediates respiratory oxygen transport and exchange by cooperatively binding oxygen with moderate affinity. We show that modern hemoglobin evolved from an ancient monomer and characterize the historical “missing link” through which the modern tetramer evolved—a noncooperative homodimer with high …

Post‐Dispersal Factors Influence Recruitment Patterns But Do Not Override The Importance Of Seed Limitation In Populations Of A Native Thistle, Tatyana A. Rand, Natalie M. West, F. Leland Russell, Svata M. Louda

School of Biological Sciences: Faculty Publications

Whether plant populations are limited by seed or microsite availability is a long-standing debate. However, since both can be important, increasing emphasis is placed on disentangling their relative importance and how they vary through space and time. Although uncommon, seed addition studies that include multiple levels of seed augmentation, and follow plants through to the adult stage, are critical to achieving this goal. Such data are also vital to understanding when biotic pressures, such as herbivory, influence plant abundance. In this study, we experimentally added seeds of a native thistle, Cirsium canescens, at four augmentation densities to plots at two …

The Role Of Nestling Acoustic Experience In Song Discrimination In A Sparrow, Emily J. Hudson, Nicole Creanza, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Oscine songbirds are an ideal system for investigating how early experience affects vocal behavior. Young songbirds face a challenging task: how to recognize and selectively learn only their own species’ song, often during a time-limited window. Because birds are capable of hearing birdsong very early in life, early exposure to song could plausibly affect recognition of appropriate models; however, this idea conflicts with the traditional view that song learning occurs only after a bird leaves the nest. Thus, it remains unknown whether natural variation in acoustic exposure prior to song learning affects the template for recognition. In a population where …

Sex And Suicide: The Curious Case Of Toll-Like Receptors, Paulo A. Navarro-Costa, Antoine Molaro, Chandra S. Misra, Colin D. Meiklejohn, Peter J. Ellis

School of Biological Sciences: Faculty Publications

During in vitro fertilisation (IVF), pharmacological activation of the murine X chromosome–encoded receptor proteins Toll-like receptor (TLR) 7 and TLR8 reportedly results in male- biased litters by selectively disrupting the motility of X-bearing sperm cells. Thus—in the context of agonist treatment during IVF—these receptors act as ‘suicidal’ segregation distorters that impair their own transmission to the next generation. Such behaviour would, from an evolutionary perspective, be strongly selected against if present during natural fertilisation. Consequently, TLR7/8 biology in vivo must differ significantly from this in vitro situation to allow these genes to persist in the genome. Here, we use our …

Tolerance Of Novel Toxins Through Generalized Mechanisms: Simulating Gradual Host Shifts Of Butterflieskristin, Kristin L. Sikkink, Reilly Hostager, Megan E. Kobiela, Nathan Fremling, Katherine Johnston, Amod Zambre, Emilie C. Snell-Rood

School of Biological Sciences: Faculty Publications

Organisms encounter a wide range of toxic compounds in their environments, from chemicals that serve anticonsumption or anticompetition functions to pollutants and pesticides. Although we understand many detoxification mechanisms that allow organisms to consume toxins typical of their diet, we know little about why organisms vary in their ability to tolerate entirely novel toxins. We tested whether variation in generalized stress responses, such as antioxidant pathways, may underlie variation in reactions to novel toxins and, if so, their associated costs. We used an artificial diet to present cabbage white butterfly caterpillars (Pieris rapae) with plant material containing toxins not experienced …

Juvenile Rank Acquisition Is Associated With Fitness Independent Of Adult Rank, Eli D. Strauss, Daizaburo Shizuka, Kay E. Holekamp

School of Biological Sciences: Faculty Publications

Social rank is a significant determinant of fitness in a variety of species. The importance of social rank suggests that the process by which juveniles come to establish their position in the social hierarchy is a critical component of development. Here, we use the highly predictable process of rank acquisition in spotted hyenas to study the consequences of variation in rank acquisition in early life. In spotted hyenas, rank is ‘inherited’ through a learning process called ‘maternal rank inheritance.’ This pattern is very consistent: approximately 80% of juveniles acquire the exact rank expected under the rules of maternal rank inheritance. …

The Natural Selection Game: Incorporating Active Learning In Evolution Curricula For General Biology, Shabnam Mohammadi, Nicholas M. Kiriazis, Lorin A. Neuman-Lee

School of Biological Sciences: Faculty Publications

Teaching evolution in high school and in entry-level college courses can be challenging due to the inherent misinformation, misunderstanding, and biases with which students approach the topic. In this setting, it is critical to both teach the basic concepts and address common student misconceptions about evolution. We present two paired activities that allow students to (1) explore the processes of natural selection in a direct and experiential way and (2) address common misconceptions in evolutionary theory. The first activity, the “Natural Selection Game,” has students simulate a bird population and experience shifts in phenotype frequency as a result of selective …

Mitochondrial Localization Of Dictyostelium Discoideum Dutpase Mediated By Its N‑Terminus, Catherine P. Chia, Noriko Inoguchi, Kyle C. Varon, Bradley M. Barholomai, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

Objective: The nuclear and mitochondrial genomes of Dictyostelium discoideum, a unicellular eukaryote, have relatively high A+T-contents of 77.5% and 72.65%, respectively. To begin to investigate how the pyrimidine biosynthetic pathway fulfills the demand for dTTP, we determined the catalytic properties and structure of the key enzyme deoxyuridine triphosphate nucleotidohydrolase (dUTPase) that hydrolyzes dUTP to dUMP, the precursor of dTTP. Results: The annotated genome of D. discoideum identifies a gene encoding a polypeptide containing the five conserved motifs of homotrimeric dUTPases. Recombinant proteins, comprised of either full-length or core polypeptides with all conserved motifs but lacking residues 1-37 of the …

An Ortholog Of The Vasa Intronic Gene Is Required For Small Rna-Mediated Translation Repression In Chlamydomonas Reinhardtii, Xinrong Ma, Fadia Ibrahim, Eun-Jeong Kim, Scott Shaver, James Becker, Fareha Razvi, Ronald L. Cerny, Heriberto D. Cerutti

School of Biological Sciences: Faculty Publications

Small RNAs (sRNAs) associate with Argonaute (AGO) proteins in effector complexes, termed RNA-induced silencing complexes (RISCs), which regulate complementary transcripts by translation inhibition and/or RNA degradation. In the unicellular alga Chlamydomonas, several metazoans, and land plants, emerging evidence indicates that polyribosome-associated transcripts can be translationally repressed by RISCs without substantial messenger RNA (mRNA) destabilization. However, the mechanism of translation inhibition in a polyribosomal context is not understood. Here we show that Chlamydomonas VIG1, an ortholog of the Drosophila melanogaster Vasa intronic gene (VIG), is required for this process. VIG1 localizes predominantly in the cytosol and comigrates with monoribosomes and …

Mammal Community Structure Through The Paleocene-Eocene Thermal Maximum, Danielle Fraser, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

Human-mediated species invasion and climate change are leading to global extinctions and are predicted to result in the loss of important axes of phylogenetic and functional diversity. However, the long-term robustness of modern communities to invasion is unknown, given the limited timescales over which they can be studied. Using the fossil record of the Paleocene- Eocene Thermal Maximum (PETM; ~ 56 Ma) in North America, we evaluate mammalian community-level response to a rapid global warming event (5° to 8°C) and invasion by three Eurasian mammalian orders and by species undergoing northward range shifts. We assembled a database of 144 species …

Local Control Of Resource Allocation Is Sufficient To Model Optimal Dynamics In Syntrophic Systems, Glenn Ledder, Sabrina E. Russo, Erik B. Muller, Angela Peace, Roger M. Nisbet

School of Biological Sciences: Faculty Publications

Syntrophic systems are common in nature and include forms of obligate mutualisms in which each participating organism or component of an organism obtains from the other an essential nutrient or metabolic product that it cannot provide for itself. Models of how these complementary resources are allocated between partners often assume optimal behavior, but whether mechanisms enabling global control exist in syntrophic systems, and what form they might take, is unknown. Recognizing that growth of plant organs that supply complementary resources, like roots and shoots, can occur autonomously, we present a theory of plant growth in which rootshoot allocation is determined …

The Globin Gene Family In Arthropods: Evolution And Functional Diversity, Andreas Prothmann, Federico G. Hoffmann, Juan C. Opazo, Peter Herbener, Jay F. Storz, Thorsten Burmester, Thomas Hankeln

School of Biological Sciences: Faculty Publications

Globins are small heme-proteins that reversibly bind oxygen. Their most prominent roles in vertebrates are the transport and storage of O2 for oxidative energy metabolism, but recent research has suggested alternative, non-respiratory globin functions. In the species-rich and ecologically highly diverse taxon of arthropods, the coppercontaining hemocyanin is considered the main respiratory protein. However, recent studies have suggested the presence of globin genes and their proteins in arthropod taxa, including model species like Drosophila. To systematically assess the taxonomic distribution, evolution and diversity of globins in arthropods, we systematically searched transcriptome and genome sequence data and found a conserved, widespread …

How Demographic Processes Shape Animal Social Networks, Daizaburo Shizuka, Allison E. Johnson

School of Biological Sciences: Faculty Publications

Invited review

Demographic processes play a key role in shaping the patterns of social relations among individuals in a population. Social network analysis is a powerful quantitative tool for assessing the social structure formed by associations between individuals. However, demographic processes are rarely accounted for in such analyses. Here, we summarize how the structure of animal social networks is shaped by the joint effects of social behavior and turnover of individuals and suggest how a deeper understanding of these processes can open new, exciting avenues for research. Death or dispersal can have the direct effect of removing an individual and …

Divergent Density Feedback Control Of Migratory Predator Recovery Following Sex-Biased Perturbations, Daisuke Goto, Martin J. Hamel, Mark A. Pegg, Jeremy J. Hammen, Matthew L. Rugg, Valery E. Forbes

School of Biological Sciences: Faculty Publications

Uncertainty in risks posed by emerging stressors such as synthetic hormones im-pedes conservation efforts for threatened vertebrate populations. Synthetic hor-mones often induce sex-biased perturbations in exposed animals by disrupting gonad development and early life-history stage transitions, potentially diminishing per capita reproductive output of depleted populations and, in turn, being manifest as Allee effects. We use a spatially explicit biophysical model to evaluate how sex-biased perturbation in life-history traits of individuals (maternal investment in egg production and male-skewed sex allocation in offspring) modulates density feedback control of year-class strength and recovery trajectories of a long-lived, migratory fish—shovelnose sturgeon (Scaphirhynchus platorynchus)—under spatially …

Phenotypic Divergence In Two Sibling Species Of Shorebird: Common Snipe And Wilson’S Snipe (Charadriiformes: Scolopacidae), Tiago M. Rodrigues, Edward H. Miller, Sergei V. Drovetski, Robert M. Zink, Jon Fjeldså, David Gonçalves

School of Biological Sciences: Faculty Publications

Natural and social selection are among the main shapers of biological diversity but their relative importance in divergence remains understudied. Additionally, although neutral evolutionary processes may promote phenotypic divergence, their potential contribution in speciation is often overlooked in studies of comparative morphology. In this study, we investigated phenotypic differentiation in two allopatric shorebirds: the Palaearctic Common Snipe Gallinago gallinago and the Nearctic Wilson’s Snipe Gallinago delicata. Specimens of Common Snipe (n = 355 skins, n = 163 skeletons) and Wilson’s Snipe (n = 403 skins, n = 141 skeletons) in natural history collections were examined to quantify differences in skeletal …

Evolutionary Origin And Genetic Diversity Of Ring‐Necked Pheasants In The Upper Midwest United States, Hernán Vázquez-Miranda, Magdalena Jean Olson, Robert M. Zink

School of Biological Sciences: Faculty Publications

We compared mitochondrial cytochrome b sequences of ring‐necked pheasants (Phasianus colchicus) from Midwestern United States (SD and NE, USA) to a molecular phylogeographic hypothesis of pheasants in the native Eurasian range to understand which subspecies are represented by wild and captive released birds. We found that these birds represent 2 Eurasian lineages, which we refer to generally as northern Eurasian (Colchicus group) and eastern China (Torquatus group). These mitochondrial DNA lineages occur in different frequencies in the wild, with the latter being 3 times more common. This suggests that 1) the eastern China lineage is either …

Innovative Teaching Knowledge Stays With Users, A. Kelly Lane, Jacob D. Mcalpin, Brittnee Earl, Stephanie Feola, Jennifer E. Lewis, Karl Mertens, Susan E. Shadle, John Svoretz, John P. Ziker, Brian A. Couch, Luanna B. Prevost, Marilyne Stains

School of Biological Sciences: Faculty Publications

Programs seeking to transform undergraduate science, technology, engineering, and mathematics courses often strive for participating faculty to share their knowledge of innovative teaching practices with other faculty in their home departments. Here, we provide interview, survey, and social network analyses revealing that faculty who use innovative teaching practices preferentially talk to each other, suggesting that greater steps are needed for information about innovative practices to reach faculty more broadly.

A High-Throughput Method To Quantify Feeding Rates In Aquatic Organisms: A Case Study With Daphnia, Jessica L. Hite, Alaina C. Pfenning-Butterworth, Rachel E. Vetter, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

1. Food ingestion is one of the most basic features of all organisms. However, obtaining precise—and high-throughput—estimates of feeding rates remains challenging, particularly for small, aquatic herbivores such as zooplankton, snails, and tadpoles. These animals typically consume low volumes of food that are time-consuming to accurately measure.

2. We extend a standard high-throughput fluorometry technique, which uses a microplate reader and 96-well plates, as a practical tool for studies in ecology, evolution, and disease biology. We outline technical and methodological details to optimize quantification of individual feeding rates, improve accuracy, and minimize sampling error.

3. This high-throughput assay offers several …

Lithological Constraints On Resource Economies Shape The Mycorrhizal Composition Of A Bornean Rain Forest, Monique Weemstra, Kabir G. Peay, Stuart J. Davies, Mohizah Mohamad, Akira Itoh, Sylvester Tan, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

• Arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) produce contrasting plant–soil feedbacks, but how these feedbacks are constrained by lithology is poorly understood.

• We investigated the hypothesis that lithological drivers of soil fertility filter plant resource economic strategies in ways that influence the relative fitness of trees with AMF or EMF symbioses in a Bornean rain forest containing species with both mycorrhizal strategies.

• Using forest inventory data on 1245 tree species, we found that although AMF-hosting trees had greater relative dominance on all soil types, with declining lithological soil fertility EMF-hosting trees became more dominant. Data on …

Predator-Dependent Functional Responses Alter The Coexistence And Indirect Effects Among Prey That Share A Predator, Kyle E. Coblentz, John P. Delong

School of Biological Sciences: Faculty Publications

Predator functional responses describe predator feeding rates as a function of prey abundance and are central to pred-ator–prey theory. Despite ample evidence that functional responses also depend on predator abundance, theory incor-porating predator-dependent functional responses has focused almost exclusively on specialist predator–prey pairs or linear food chains. This leaves a large gap in our knowledge as many predators feed on multiple prey, and in so doing, generate indirect effects among prey that can alter their coexistence. Here we investigate how predator-dependent functional responses in a one predator–two prey model alter the coexistence among prey and their net effects on one …

Extreme Offspring Ornamentation In American Coots Is Favored By Selection Within Families, Not Benefits To Conspecific Brood Parasites, Bruce E. Lyon, Daizaburo Shizuka

School of Biological Sciences: Faculty Publications

Offspring ornamentation typically occurs in taxa with parental care, suggesting that selection arising from social interactions between parents and offspring may underlie signal evolution. American coot babies are among the most ornamented offspring found in nature, sporting vividly orange-red natal plumage, a bright red beak, and other red parts around the face and pate. Previous plumage manipulation experiments showed that ornamented plumage is favored by strong parental choice for chicks with more extreme ornamentation but left unresolved the question as to why parents show the preference. Here we explore natural patterns of variation in coot chick plumage color, both within …

Mitochondrial Dna Repair In An Arabidopsis Thaliana Uracil N-Glycosylase Mutant, Emily L. Wynn, Emma Purfeerst, Alan Christensen

School of Biological Sciences: Faculty Publications

Substitution rates in plant mitochondrial genes are extremely low, indicating strong selective pressure as well as efficient repair. Plant mitochondria possess base excision repair pathways; however, many repair pathways such as nucleotide excision repair and mismatch repair appear to be absent. In the absence of these pathways, many DNA lesions must be repaired by a different mechanism. To test the hypothesis that double-strand break repair (DSBR) is that mechanism, we maintained independent self-crossing lineages of plants deficient in uracil-N-glycosylase (UNG) for 11 generations to determine the repair outcomes when that pathway is missing. Surprisingly, no single nucleotide polymorphisms (SNPs) were …

A Role For Triglyceride Lipase Brummer In The Regulation Of Sex Differences In Drosophila Fat Storage And Breakdown, Lianna W. Wat, Chien Chao, Rachael Bartlett, Justin L. Buchanan, Jason W. Millington, Hui Ju Chih, Zahid S. Chowdhury, Puja Biswas, Vivian Huang, Leah J. Shin, Lin Chuan Wang, Marie-Pierre L. Gauthier, Maria C. Barone, Kristi L. Montooth, Michael A. Welte, Elizabeth J. Rideout

School of Biological Sciences: Faculty Publications

Triglycerides are the major form of stored fat in all animals. One important determinant of whole-body fat storage is whether an animal is male or female. Here, we use Drosophila, an established model for studies on triglyceride metabolism, to gain insight into the genes and physiological mechanisms that contribute to sex differences in fat storage. Our analysis of triglyceride storage and breakdown in both sexes identified a role for triglyceride lipase brummer (bmm) in the regulation of sex differences in triglyceride homeostasis. Normally, male flies have higher levels of bmm mRNA both under normal culture conditions and …

Trade-Offs Between Morphology And Thermal Niches Mediate Adaptation In Response To Competing Selective Pressures, Stella F. Uiterwaal, Ian T. Lagerstrom, Thomas M. Luhring, Miranda E. Salsbery, John P. Delong

School of Biological Sciences: Faculty Publications

The effects of climate change—such as increased temperature variability and novel predators—rarely happen in isolation, but it is unclear how organisms cope with mul- tiple stressors simultaneously. To explore this, we grew replicate Paramecium caudatum populations in either constant or variable temperatures and exposed half to predation. We then fit thermal performance curves (TPCs) of intrinsic growth rate (r_max) for each replicate population (N = 12) across seven temperatures (10°C–38°C). TPCs of P. caudatum exposed to both temperature variability and predation re- sponded only to one or the other (but not both), resulting in unpredictable outcomes. …

Radiomics-Based Outcome Prediction For Pancreatic Cancer Following Stereotactic Body Radiotherapy, Elsa Parr, Qian Du, Chi Zhang, Chi Lin, Ahsan Kamal, Josiah Mcalister, Xiaoying Liang, Kyle Bavitz, Gerard Rux, Michael Hollingsworth, Michael Baine, Dandan Zheng

School of Biological Sciences: Faculty Publications

(1) Background: Radiomics use high-throughput mining of medical imaging data to extract unique information and predict tumor behavior. Currently available clinical prediction models poorly predict treatment outcomes in pancreatic adenocarcinoma. Therefore, we used radiomic features of primary pancreatic tumors to develop outcome prediction models and compared them to traditional clinical models. (2) Methods: We extracted and analyzed radiomic data from pre-radiation contrast-enhanced CTs of 74 pancreatic cancer patients undergoing stereotactic body radiotherapy. A panel of over 800 radiomic features was screened to create overall survival and local-regional recurrence prediction models, which were compared to clinical prediction models and models combining …