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Vertebrate Body Size Jumps The Wright Way, Peter J. Wagner

School of Biological Sciences: Faculty Publications

Fossil data provide copious evidence that anatomical (morphological) change within individual lineages is not constant: short bursts of great change commonly separate long durations of little change (1, 2). Despite this, most models of morphological change assume that probabilities of morphological character change are the same from one generation to the next: even if rates change over time—such as in “Cambrian explosion” or “early burst” models, where high disparity among anatomies evolves early—then it is still assumed that fast rates of continuous character change gave way to slow rates of continuous change (3). In statistical parlance, early bursts usually are …

Nitrogen Addition And Ecosystem Functioning: Both Species Abundances And Traits Alter Community Structure And Function, Anna R. Tatarko, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

Increased nutrient inputs can cause shifts in plant community composition and plant functional traits, both of which affect ecosystem function. We studied community- and species-level leaf functional trait changes in a full factorial nitrogen (N), phosphorus (P), and potassium (K) fertilization experiment in a semi-arid grassland. Nitrogen was the only nutrient addition to significantly affect leaf functional traits, and N addition increased community-weighted specific leaf area (SLA) by 19%, leaf chlorophyll content by 34%, height by 26%, and leaf dry matter content (LDMC) decreased by 11% while leaf thickness and toughness did not change significantly. At the species level, most …

Multiple Hypotheses Explain Variation In Extra-Pair Paternity At Different Levels In A Single Bird Family, Lyanne Brouwer, Martijn Van De Pol, Nataly Hidalgo Aranzamendi, Glen Bain, Daniel T. Baldassarre, Lesley C. Brooker, Michael G. Brooker, Diane Diane Colombelli-Négrel, Erik Enbody, Kurt Gielow, Michelle L. Hall, Allison E. Johnson, Jordan Karubian, Sjouke A. Kingma, Sonia Kleindorfer, Marina Louter, Raoul A. Mulder, Anne Peters, Stephen Pruett-Jones, Keith A. Tarvin, Derrick J. Thrasher, Claire W. Varian-Ramos, Michael S. Webster, Andrew Cockburn

School of Biological Sciences: Faculty Publications

Extra-pair paternity (EPP), where offspring are sired by a male other than the social male, varies enormously both within and among species. Trying to explain this variation has proved difficult because the majority of the interspecific variation is phylogenetically based. Ideally, variation in EPP should be investigated in closely related species, but clades with sufficient variation are rare. We present a comprehensive multifactorial test to explain variation in EPP among individuals in 20 populations of nine species over 89 years from a single bird family (Maluridae). Females had higher EPP in the presence of more helpers, more neighbors or …

Phosphate Starvation Induces Replacement Of Phospholipids With The Betaine Lipid Diacylglycerol-N,N,N-Trimethylhomoserine In The Human Fungal Pathogen Candida Albicans, Surabhi Naik, Rebecca E. Cahoon, Bridget Tripp, Christian Elowsky, Sophie Alvarez, Kan Liu, Chi Zhang, Wayne R. Riekhof

School of Biological Sciences: Faculty Publications

We have previously demonstrated that phosphate starvation induces replacement of phosphatidylcholine with the betaine lipid diacylglyceryl-N,N,N-trimethylhomoserine (DGTS) in fungi. In Neurospora crassa, the BTA1 gene encodes the betaine lipid synthase, which is necessary and sufficient for DGTS synthesis. BTA1 expression and DGTS accumulation are part of the fungal phosphorus (P_i) deprivation (PHO) regulon, mediated by the NUC-1/Pho4p transcription factor. We now demonstrate that the human pathogen Candida albicans encodes a BTA1 ortholog (CaBTA1), which is activated during P_i scarcity. The CaBTA1 gene is also induced under certain biofilm-promoting conditions independent of P …

Multiple Streptomyces Species With Distinct Secondary Metabolomes Have Identical 16s Rrna Gene Sequences, Sanjay Antony-Babu, Didier Stien, Véronique Eparvier, Delphine Parrot, Sophie Tomasi, Marcelino Suzuki

School of Biological Sciences: Faculty Publications

Microbial diversity studies using small subunit (SSU) rRNA gene sequences continue to advance our understanding of biological and ecological systems. Although a good predictor of overall diversity, using this gene to infer the presence of a species in a sample is more controversial. Here, we present a detailed polyphasic analysis of 10 bacterial strains isolated from three coastal lichens Lichina confinis, Lichina pygmaea and Roccella fuciformis with SSU rRNA gene sequences identical to the type strain of Streptomyces cyaneofuscatus. This analysis included phenotypic, microscopic, genetic and genomic comparisons and showed that despite their identical SSU rRNA sequences the …

Assessing The Influence Of Temporal Autocorrelations On The Population Dynamics Of A Disturbance Specialist Plant Population In A Random Environment, Eric A. Eager, Diana Pilson, Helen M. Alexander, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Biological populations are strongly influenced by random variations in their environment, which are often autocorrelated in time. For disturbance specialist plant populations, the frequency and intensity of environmental stochasticity (via disturbances) can drive the qualitative nature of their population dynamics. In this article, we extended our earlier model to explore the effect of temporally autocorrelated disturbances on population persistence. In our earlier work, we only assumed disturbances were independent and identically distributed in time. We proved that the plant seed bank population converges in distribution, and we showed that the mean and variance in seed bank population size were both …

Geographical Variation In Community Divergence: Insights From Tropical Forest Monodominance By Ectomycorrhizal Trees*, Tadashi Fukami, Mifuyu Nakajima, Claire Fortunel, Paul V. Fine, Christopher Baraloto, Sabrina E. Russo, Kabir G. Peay

School of Biological Sciences: Faculty Publications

Convergence occurs in both species traits and community structure, but how convergence at the two scales influences each other remains unclear. To address this question, we focus on tropical forest monodominance, in which a single, often ectomycorrhizal (EM) tree species occasionally dominates forest stands within a landscape otherwise characterized by diverse communities of arbuscular mycorrhizal (AM) trees. Such monodominance is a striking potential example of community divergence resulting in alternative stable states. However, it is observed only in some tropical regions. A diverse suite of AM and EM trees locally codominate forest stands elsewhere. We develop a hypothesis to explain …

Abundance And Distribution Of Microbial Cells And Viruses In An Alluvial Aquifer, Donald Pan, Jason Nolan, Kenneth H. Williams, Karrie A. Weber

School of Biological Sciences: Faculty Publications

Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Colorado …

How Question Types Reveal Student Thinking: An Experimental Comparison Of Multiple-True-False And Free-Response Formats, Joanna K. Hubbard, Macy A. Potts, Brian Couch

School of Biological Sciences: Faculty Publications

Assessments represent an important component of undergraduate courses because they affect how students interact with course content and gauge student achievement of course objectives. To make decisions on assessment design, instructors must understand the affordances and limitations of available question formats. Here, we use a crossover experimental design to identify differences in how multiple-true-false (MTF) and free-response (FR) exam questions reveal student thinking regarding specific conceptions. We report that correct response rates correlate across the two formats but that a higher percentage of students provide correct responses for MTF questions. We find that MTF questions reveal a high prevalence of …

Identification Of The Atpase Subunit Of The Primary Maltose Transporter In The Hyperthermophilic Anaerobe Thermotoga Maritima, Raghuveer Singh, Derrick White, Paul H. Blum

School of Biological Sciences: Faculty Publications

Thermotoga maritima is a hyperthermophilic anaerobic bacterium that produces molecular hydrogen (H₂) by fermentation. It catabolizes a broad range of carbohydrates through the action of diverse ABC transporters. However, in T. maritima and related species, highly similar genes with ambiguous annotation obscure a precise understanding of genome function. In T. maritima, three putative malK genes, all annotated as ATPase subunits, exhibited high identity to each other. To distinguish between these genes, malK disruption mutants were constructed by gene replacement, and the resulting mutant cell lines were characterized. Only a disruption of malK3 produced a defect in maltose …

Nutrient Addition Shifts Plant Community Composition Towards Earlier Flowering Species In Some Prairie Ecoregions In The U.S. Central Plains, Lori A. Biederman, Brent Mortensen, Philip Fay, Nicole Hagenah, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Eric Lind, Rebecca Mcculley, Sally Power, Eric W. Seabloom, Pedro Tognetti

School of Biological Sciences: Faculty Publications

The distribution of flowering across the growing season is governed by each species' evolutionary history and climatic variability. However, global change factors, such as eutrophication and invasion, can alter plant community composition and thus change the distribution of flowering across the growing season. We examined three ecoregions (tall-, mixed, and short-grass prairie) across the U.S. Central Plains to determine how nutrient (nitrogen (N), phosphorus, and potassium (+micronutrient)) addition alters the temporal patterns of plant flowering traits. We calculated total community flowering potential (FP) by distributing peakseason plant cover values across the growing season, allocating each species' cover to only those …

Unexpected Nongenetic Individual Heterogeneity And Trait Covariance In Daphnia And Its Consequences For Ecological And Evolutionary Dynamics, Clayton E. Cressler, Stefan Bengtson, William A. Nelson

School of Biological Sciences: Faculty Publications

Individual differences in genetics, age, or environment can cause tremendous differences in individual life-history traits. This individual heterogeneity generates demographic heterogeneity at the population level, which is predicted to have a strong impact on both ecological and evolutionary dynamics. However, we know surprisingly little about the sources of individual heterogeneity for particular taxa or how different sources scale up to impact ecological and evolutionary dynamics. Here we experimentally study the individual heterogeneity that emerges from both genetic and nongenetic sources in a species of freshwater zooplankton across a large gradient of food quality. Despite the tight control of environment, we …

The Combined Effects Of Reactant Kinetics And Enzyme Stability Explain The Temperature Dependence Of Metabolic Rates, John Delong, J. P. Gibert, Thomas M. Luhring, Gwendolyn C. Bachman, B. Reed, A. Neyer, Kristi Montooth

School of Biological Sciences: Faculty Publications

A mechanistic understanding of the response of metabolic rate to temperature is essential for understanding thermal ecology and metabolic adaptation. Although the Arrhenius equation has been used to describe the effects of temperature on reaction rates and metabolic traits, it does not adequately describe two aspects of the thermal performance curve (TPC) for metabolic rate—that metabolic rate is a unimodal function of temperature often with maximal values in the biologically relevant temperature range and that activation energies are temperature dependent. We show that the temperature dependence of metabolic rate in ectotherms is well described by an enzyme-assisted Arrhenius (EAAR) model …

Testing The Terminal Investment Hypothesis In California Oaks, Walter D. Koenig, Johannes M.H. Knops, William J. Carmen, Mario B. Pesendorfer

School of Biological Sciences: Faculty Publications

The terminal investment hypothesis—which proposes that reproductive investment should increase with age-related declines in reproductive value—has garnered support in a range of animal species but has not been previously examined in long-lived plants, such as trees. We tested this hypothesis by comparing relative acorn production and radial growth among 1,0001 mature individuals of eight species of California oaks (genus Quercus) followed for up to 37 years, during which time 70 trees died apparently natural deaths. We found no significant differences in the radial growth, acorn production, or index of reproductive effort, taking into consideration both growth and reproduction among dying …

Microbial Strains And Methods Of Making And Using, Nicole Roswitha Buan Murphy, Jennifer Catlett

School of Biological Sciences: Faculty Publications

Microbial strains are provided, as are methods of making and using such microbial strains.

Methane is an increasingly important global energy Source, both as the primary component of natural gas and as a biologically produced fuel. Currently, Sweden uses 100% renewable methane (biogas) in place of compressed natural gas (CNG) for transportation fuel, and several European countries are implementing policies to increase their pro portion of biogas transportation fuel. In addition, methane is a valuable chemical for conversion into other higher-order carbon compounds (e.g., methanol, formate, alkanes, ter penes). More than 50% of the world's methane is produced biologically by …

Ecological Pleiotropy Suppresses The Dynamic Feedback Generated By A Rapidly Changing Trait, John Delong

School of Biological Sciences: Faculty Publications

Population dynamics may carry a signature of an ecology- evolution-ecology feedback, known as eco-evolutionary dynamics, when functionally important traits change. Given current theory, the absence of a feedback from a trait with strong links to species interactions should not occur. In a previous study with the Didinium-Paramecium predator-prey system, however, rapid and large-magnitude changes in predator cell volume occurred without any noticeable effect on the population dynamics. Here I resolve this theory-data conflict by showing that ecological pleiotropy—when a trait has more than one functional effect on an ecological process—suppresses shifts in dynamics that would arise, given the links between …

Contribution Of Pentose Catabolism To Molecular Hydrogen Formation By Targeted Disruption Of Arabinose Isomerase (Araa) In The Hyperthermophilic Bacterium Thermotoga Maritima, Derrick White, Raghuveer Singh, Deepak Rudrappa, Jackie Mateo, Levi Kramer, Laura Freese, Paul H. Blum

School of Biological Sciences: Faculty Publications

Thermotoga maritima ferments a broad range of sugars to form acetate, carbon dioxide, traces of lactate, and near theoretic yields of molecular hydrogen (H₂). In this organism, the catabolism of pentose sugars such as arabinose depends on the interaction of the pentose phosphate pathway with the Embden-Myerhoff and Entner-Doudoroff pathways. Although the values for H₂ yield have been determined using pentose-supplemented complex medium and predicted by metabolic pathway reconstruction, the actual effect of pathway elimination on hydrogen production has not been reported due to the lack of a genetic method for the creation of targeted mutations. Here, …

First-Year And Non-First-Year Student Expectations Regarding In-Class And Out-Of-Class Learning Activities In Introductory Biology, Tanya L. Brown, Brian A. Couch

School of Biological Sciences: Faculty Publications

National calls for teaching transformation build on a constructivist learning theory and propose that students learn by actively engaging in course activities and interacting with other students. While interactive pedagogies can improve learning, they also have the potential to challenge traditional norms regarding class participation and learning strategies. To better understand the potential openness of students to interactive teaching practices, we administered a survey during the first week of two sections of an introductory biology course to characterize how students envisioned spending time during class as well as what activities they expected to complete outside of class during non-exam weeks …

Sensory System Plasticity In A Visually Specialized, Nocturnal Spider, Jay A. Stafstrom, Peter Michalik, Eileen Hebets

School of Biological Sciences: Faculty Publications

The interplay between an animal’s environmental niche and its behavior can influence the evolutionary form and function of its sensory systems. While intraspecific variation in sensory systems has been documented across distant taxa, fewer studies have investigated how changes in behavior might relate to plasticity in sensory systems across developmental time. To investigate the relationships among behavior, peripheral sensory structures, and central processing regions in the brain, we take advantage of a dramatic within-species shift of behavior in a nocturnal, net-casting spider (Deinopis spinosa), where males cease visually-mediated foraging upon maturation. We compared eye diameters and brain region volumes across …

Biotic Interchange Has Structured Western Hemisphere Mammal Communities, Danielle Fraser, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

Aim.— Many hypotheses posit that species-rich tropical communities are dominated by speciesspecies interactions, apparent as competitive exclusion or character displacement, whereas species-poor temperate communities are dominated by species-environment interactions. Recent studies demonstrate a strong influence of macroevolutionary and biogeographic factors. We simultaneously test for the effects of species interactions, climate, and biotic interchange on Western Hemisphere mammal communities using a phylogenetic and functional diversity approach.

Location.— Western Hemisphere.

Time period.— Modern

Major taxa studied.— Mammalia

Methods.— Using Western Hemisphere mammal distributional and body mass data, we calculate body mass dispersion, phylogenetic diversity (Net Relatedness Index), and assemblage-averaged rates of co-occurrence …

Phytophagous Insect Oviposition Shifts In Response To Probability Of Flower Abortion Owing To The Presence Of Basal Fruits, Shivani Jadeja, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Phytophagous insects use a wide range of indicators or associated cues to avoid laying eggs in sites where offspring survival is low. For insects that lay eggs in flowers, these unsuitable sites may be created by the host plant’s resource allocation to flowers. In the sequentially flowering host plant, Yucca glauca, late-opening distal flowers are more likely to be aborted in the presence of already-initiated basal fruits because they are strong resource sinks. If flowers are aborted, all eggs of the phytophagous insect, Tegeticula yuccasella, within the flower die. We used the phytophagous insect T. yuccasella that lays …

Student Buy-In Toward Formative Assessments: The Influence Of Student Factors And Importance For Course Success, Kathleen R. Brazeal, Brian A. Couch

School of Biological Sciences: Faculty Publications

Formative assessment (FA) techniques, such as pre-class assignments, in-class activities, and post-class homework, have been shown to improve student learning. While many students find these techniques beneficial, some students may not understand how they support learning or may resist their implementation. Improving our understanding of FA buy-in has important implications, since buy-in can potentially affect whether students fully engage with and learn from FAs. We investigated FAs in 12 undergraduate biology courses to understand which student characteristics influenced buy-in toward FAs and whether FA buy-in predicted course success. We administered a mid-semester survey that probed student perceptions toward several different …

Cumulative Herbivory Outpaces Compensation For Early Floral Damage On A Monocarpic Perennial Thistle, Natalie M. West, Svata M. Louda

School of Biological Sciences: Faculty Publications

Floral herbivory represents a major threat to plant reproductive success, driving the importance of plant tolerance mechanisms that minimize fitness costs. However, the cumulative insect herbivory plants experience under natural conditions complicates predictions about tolerance contributions to net fitness. Apical damage can lead to compensatory seed production from late season flowering that ameliorates early season fitness losses. Yet, the compensation realized depends on successful development and herbivore escape by later season flowers. Using monocarpic perennial Cirsium canescens, we quantified seed-reproductive fitness of plants with vs. without experimental damage to the early-developing large apical flower head, with and without a …

Cooperative Processing Of Primary Mirnas By Dus16 And Dcl3 In The Unicellular Green Alga Chlamydomonas Reinhardtii, Tomohito Yamasaki, Heriberto D. Cerutti

School of Biological Sciences: Faculty Publications

We have previously reported that the RNA-binding protein Dull slicer 16 (DUS16) plays a key role in the processing of primary miRNAs (pri-miRNAs) in the unicellular green alga Chlamydomonas reinhardtii. In the present report, we elaborate on the interaction of DUS16 with Dicer-like 3 (DCL3) during pri-miRNA processing. Comprehensive analyses of small RNA libraries derived from mutant and wild-type algal strains allowed the de novo prediction of 35 pri-miRNA genes, including 9 previously unknown ones. The pri-miRNAs dependent on DUS16 for processing largely overlapped with those dependent on DCL3. Our findings suggest that DUS16 and DCL3 work cooperatively, presumably …

Host Allometry Influences The Evolution Of Parasite Host-Generalism: Theory And Meta-Analysis, Josephine G. Walker, Amy Hurford, Jo Cable, Amy R. Ellison, Stephen J. Price, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists—infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy …

Large But Uneven Reduction In Fish Size Across Species In Relation To Changing Sea Temperatures, Itai Van Rijn, Yehezkel Buba, John Delong, Moshe Kiflawi, Jonathan Belmaker

School of Biological Sciences: Faculty Publications

Ectotherms often attain smaller body sizes when they develop at higher temperatures. This phenomenon, known as the temperature size rule, has important consequences for global fisheries, whereby ocean warming is predicted to result in smaller fish and reduced biomass. However, the generality of this phenomenon and the mechanisms that drive it in natural populations remain unresolved. In this study we document the maximal size of 74 fish species along a steep temperature gradient in the Mediterranean Sea and find strong support for the temperature size rule. Importantly, we additionally find that size reduction in active fish species is dramatically larger …

Host Allometry Influences The Evolution Of Parasite Host-Generalism: Theory And Meta-Analysis, Josephine G. Walker, Amy Hurford, Jo Cable, Amy R. Ellison, Stephen J. Price, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists—infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy …

Distinct Transcriptome Profiles Of Gag-Specific Cd8+ T Cells Temporally Correlated With The Protection Elicited By Sivδnef Live Attenuated Vaccine, Wuxun Lu, Yanmin Wan, Fangrui Ma, R. Paul Johnson, Qingsheng Li

School of Biological Sciences: Faculty Publications

The live attenuated vaccine (LAV) SIVmac239Δnef (SIVΔnef) confers the best protection among all the vaccine modalities tested in rhesus macaque model of HIV-1 infection. This vaccine has a unique feature of time-dependent protection: macaques are not protected at 3±5 weeks post vaccination (WPV), whereas immune protection emerges between 15 and 20 WPV. Although the exact mechanisms of the time-dependent protection remain incompletely understood, studies suggested that both cellular and humoral immunities contribute to this time-dependent protection. To further elucidate the mechanisms of protection induced by SIVΔnef, we longitudinally compared the global gene expression profiles of SIV Gag-CM9+ CD8+ (Gag-specific CD8+) …

The Economic Value Of Grassland Species For Carbon Storage, Bruce A. Hungate, Edward B. Barbier, Amy W. Ando, Samuel P. Marks, Peter B. Reich, Natasja Van Gestel, David Tilman, Johannes M. H. Knops, David U. Hooper, Bradley J. Butterfield, Bradley J. Cardinale

School of Biological Sciences: Faculty Publications

Carbon storage by ecosystems is valuable for climate protection. Biodiversity conservation may help increase carbon storage, but the value of this influence has been difficult to assess. We use plant, soil, and ecosystem carbon storage data from two grassland biodiversity experiments to show that greater species richness increases economic value: Increasing species richness from 1 to 10 had twice the economic value of increasing species richness from 1 to 2. The marginal value of each additional species declined as species accumulated, reflecting the nonlinear relationship between species richness and plant biomass production. Our demonstration of the economic value of biodiversity …

Increased Productivity In Wet Years Drives A Decline In Ecosystem Stability With Nitrogen Additions In Arid Grasslands, Junfeng Wang, Johannes M.H. Knops, Chad E. Brassil, Chunsheng Mu

School of Biological Sciences: Faculty Publications

Adding nutrients to nutrient-limited ecosystems typically lowers plant diversity and decreases species asynchrony. Both, in turn, decrease the stability of productivity in the response to negative climate fluctuations such as droughts. However, most classic studies examining stability have been done in relatively wet grasslands dominated by perennial grasses. We examined how nutrient additions influence the stability of productivity to rainfall variability in an arid grassland with a mix of perennial and annual species. Of the nutrients, only nitrogen increased productivity, and only in wet years. In addition, only nitrogen decreased the stability of productivity. Thus, nutrient addition makes ecosystem productivity …