Life Sciences Commons^™

Reintroducing Environmental Change Drivers In Biodiversity-Ecosystem Functioning Research., Frederik De Laender, Jason R. Rohr, Roman Ashauer, Donald J Baird, Uta Berger, Nico Eisenhauer, Volker Grimm, Udo Hommen, Lorraine Maltby, Carlos J Meliàn

Integrative Biology Faculty and Staff Publications

For the past 20 years, research on biodiversity and ecosystem functioning (B-EF) has only implicitly considered the underlying role of environmental change. We illustrate that explicitly reintroducing environmental change drivers in B-EF research is needed to predict the functioning of ecosystems facing changes in biodiversity. Next we show how this reintroduction improves experimental control over community composition and structure, which helps to provide mechanistic insight on how multiple aspects of biodiversity relate to function and how biodiversity and function relate in food webs. We also highlight challenges for the proposed reintroduction and suggest analyses and experiments to better understand how …

Step By Step: Biology Undergraduates' Problem-Solving Procedures During Multiple-Choice Assessment, Luanna B Prevost, Paula P Lemons

Integrative Biology Faculty and Staff Publications

This study uses the theoretical framework of domain-specific problem solving to explore the procedures students use to solve multiple-choice problems about biology concepts. We designed several multiple-choice problems and administered them on four exams. We trained students to produce written descriptions of how they solved the problem, and this allowed us to systematically investigate their problem-solving procedures. We identified a range of procedures and organized them as domain general, domain specific, or hybrid. We also identified domain-general and domain-specific errors made by students during problem solving. We found that students use domain-general and hybrid procedures more frequently when solving lower-order …

Mathematical Models Are A Powerful Method To Understand And Control The Spread Of Huanglongbing, Rachel A Taylor, Erin A Mordecai, Christopher A Gilligan, Jason R. Rohr, Leah R Johnson

Integrative Biology Faculty and Staff Publications

Huanglongbing (HLB), or citrus greening, is a global citrus disease occurring in almost all citrus growing regions. It causes substantial economic burdens to individual growers, citrus industries and governments. Successful management strategies to reduce disease burden are desperately needed but with so many possible interventions and combinations thereof it is difficult to know which are worthwhile or cost-effective. We review how mathematical models have yielded useful insights into controlling disease spread for other vector-borne plant diseases, and the small number of mathematical models of HLB. We adapt a malaria model to HLB, by including temperature-dependent psyllid traits, "flushing" of trees, …

Human-Associated Bacteroides Spp. And Human Polyomaviruses As Microbial Source Tracking Markers In Hawaii, Marek Kirs, Roberto A Caffaro-Filho, Mayee Wong, Valerie J. Harwood, Philip Moravcik, Roger S Fujioka

Integrative Biology Faculty and Staff Publications

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although …

Home-Field Advantage? Evidence Of Local Adaptation Among Plants, Soil, And Arbuscular Mycorrhizal Fungi Through Meta-Analysis, Megan A. Rúa, Anita Antoninka, Pedro M. Antunes, V Bala Chaudhary, Catherine Gehring, Louis J. Lamit, Bridget J. Piculell, James D. Bever, Cathy Zabinski, James F. Meadow, Marc J. Lajeunesse, Brook G. Milligan, Justine Karst, Jason D. Hoeksema

Integrative Biology Faculty and Staff Publications

BACKGROUND: Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the importance of concurrent abiotic and biotic factors as drivers of local adaptation has only recently been investigated. Local adaptation to biotic interactions may be particularly important for plants, as they associate with microbial symbionts that can significantly affect their fitness and may enable rapid evolution. The arbuscular mycorrhizal (AM) symbiosis is ideal for investigations of local adaptation because it is globally widespread among most plant taxa and can significantly affect plant growth and fitness. Using meta-analysis on 1170 studies …

Current Status Of Marker Genes Of Bacteroides And Related Taxa For Identifying Sewage Pollution In Environmental Waters, Warish Ahmed, Bridie Hughes, Valerie J. Harwood

Integrative Biology Faculty and Staff Publications

Microbial source tracking (MST) endeavors to determine sources of fecal pollution in environmental waters by capitalizing on the association of certain microorganisms with the gastrointestinal tract and feces of specific animal groups. Several decades of research have shown that bacteria belonging to the gut-associated order Bacteroidales, and particularly the genus Bacteroides, tend to co-evolve with the host, and are, therefore, particularly suitable candidates for MST applications. This review summarizes the current research on MST methods that employ genes belonging to Bacteroidales/Bacteroides as tracers or “markers” of sewage pollution, including known advantages and deficiencies of the many polymerase chain …

Transforming Ecosystems: When, Where, And How To Restore Contaminated Sites, Jason R. Rohr, Aïda M. Farag, Marc W. Cadotte, William H. Clements, James R. Smith, Cheryl P. Ulrich, Richard Woods

Integrative Biology Faculty and Staff Publications

Chemical contamination has impaired ecosystems, reducing biodiversity and the provisioning of functions and services. This has spurred a movement to restore contaminated ecosystems and develop and implement national and international regulations that require it. Nevertheless, ecological restoration remains a young and rapidly growing discipline and its intersection with toxicology is even more nascent and underdeveloped. Consequently, we provide guidance to scientists and practitioners on when, where, and how to restore contaminated ecosystems. Although restoration has many benefits, it also can be expensive, and in many cases systems can recover without human intervention. Hence, the first question we address is: "When …

Hunting, Food Subsidies, And Mesopredator Release: The Dynamics Of Crop-Raiding Baboons In A Managed Landscape, Rachel A. Taylor, Sadie J. Ryan, Justin S. Brashares, Leah R. Johnson

Integrative Biology Faculty and Staff Publications

The establishment of protected areas or parks has become an important tool for wildlife conservation. However, frequent occurrences of human-wildlife conflict at the edges of these parks can undermine their conservation goals. Many African protected areas have experienced concurrent declines of apex predators alongside increases in both baboon abundance and the density of humans living near the park boundary. Baboons then take excursions outside of the park to raid crops for food, conflicting with the human population. We model the interactions of mesopredators (baboons), apex predators, and shared prey in the park to analyze how four components affect the proportion …

Combined Effects Of Pesticides And Trematode Infections On Hourglass Tree Frog Polypedates Cruciger., Uthpala A. Jayawardena, Jason R. Rohr, Ayanthi N. Navaratne, Priyanie H. Amerasinghe, Rupika S. Rajakaruna

Integrative Biology Faculty and Staff Publications

The impact of widespread and common environmental factors, such as chemical contaminants, on infectious disease risk in amphibians is particularly important because both chemical contaminants and infectious disease have been implicated in worldwide amphibian declines. Here we report on the lone and combined effects of exposure to parasitic cercariae (larval stage) of the digenetic trematode, Acanthostomum burminis, and four commonly used pesticides (insecticides: chlorpyrifos, dimethoate; herbicides: glyphosate, propanil) at ecologically relevant concentrations on the survival, growth, and development of the common hourglass tree frog, Polypedates cruciger Blyth 1852. There was no evidence of any pesticide-induced mortality on cercariae because all …

Darwinian Sex Roles Confirmed Across The Animal Kingdom, Tim Janicke, Ines K. Häderer, Marc J. Lajeunesse, Nils Anthes

Integrative Biology Faculty and Staff Publications

Since Darwin's conception of sexual selection theory, scientists have struggled to identify the evolutionary forces underlying the pervasive differences between male and female behavior, morphology, and physiology. The Darwin-Bateman paradigm predicts that anisogamy imposes stronger sexual selection on males, which, in turn, drives the evolution of conventional sex roles in terms of female-biased parental care and male-biased sexual dimorphism. Although this paradigm forms the cornerstone of modern sexual selection theory, it still remains untested across the animal tree of life. This lack of evidence has promoted the rise of alternative hypotheses arguing that sex differences are entirely driven by environmental …

Dynamics And Thermal Sensitivity Of Ballistic And Non-Ballistic Feeding In Salamanders, Stephen M, Deban, Jeffrey A. Scales

Integrative Biology Faculty and Staff Publications

Low temperature reduces the performance of muscle-powered movements, but in movements powered by elastic recoil mechanisms, this effect can be mitigated and performance can be increased. To better understand the morphological basis of high performance and thermal robustness of elastically powered movements, we compared feeding dynamics at a range of temperatures (5-25°C) in two species of terrestrial plethodontid salamanders, Plethodon metcalfi and Ensatina eschscholtzii, which differ in tongue muscle architecture and the mechanism of tongue projection. We found that Ensatina is capable of ballistic projection with a mean muscle mass-specific power of 2100 W kg(-1), revealing an elastic mechanism. Plethodon, …

Predator Diet And Trophic Position Modified With Altered Habitat Morphology, Alexander Tewfik, Susan S. Bell, Kevin S. Mccann, Kristina Morrow

Integrative Biology Faculty and Staff Publications

Empirical patterns that emerge from an examination of food webs over gradients of environmental variation can help to predict the implications of anthropogenic disturbance on ecosystems. This “dynamic food web approach” is rarely applied at the coastal margin where aquatic and terrestrial systems are coupled and human development activities are often concentrated. We propose a simple model of ghost crab (Ocypode quadrata) feeding that predicts changing dominant prey (Emerita talpoida, Talorchestia sp., Donax variablis) along a gradient of beach morphology and test this model using a suite of 16 beaches along the Florida, USA coast. …

Ultrafiltration And Microarray For Detection Of Microbial Source Tracking Marker And Pathogen Genes In Riverine And Marine Systems, Xiang Li, Valerie J. Harwood, Bina Nayak, Jennifer L Weidhaas

Integrative Biology Faculty and Staff Publications

Pathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of > 95% for Escherichia coli and human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. …

The Pros And Cons Of Ecological Risk Assessment Based On Data From Different Levels Of Biological Organization, Jason R. Rohr, Christopher J. Salice, Roger M. Nisbet

Integrative Biology Faculty and Staff Publications

Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Here we review the pros and cons of ERA across levels of biological organization, including suborganismal (e.g., biomarkers), individual, population, community, ecosystem and landscapes levels. Our review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) …

Spatial Spread Of The West Africa Ebola Epidemic, Andrew M. Kramer, J. Tomlin Pulliam, Laura W. Alexander, Andrew W. Park, Pejman Rohani, John M. Drake

Integrative Biology Faculty and Staff Publications

Controlling Ebola outbreaks and planning an effective response to future emerging diseases are enhanced by understanding the role of geography in transmission. Here we show how epidemic expansion may be predicted by evaluating the relative probability of alternative epidemic paths. We compared multiple candidate models to characterize the spatial network over which the 2013–2015 West Africa epidemic of Ebola virus spread and estimate the effects of geographical covariates on transmission during peak spread. The best model was a generalized gravity model where the probability of transmission between locations depended on distance, population density and international border closures between Guinea, Liberia …

Ordination Obscures The Influence Of Environment On Plankton Metacommunity Structure, Tad A. Dallas, Andrew M. Kramer, Marcus Zokan, John M. Drake

Integrative Biology Faculty and Staff Publications

The composition of plankton communities in individual habitats is often influenced by environmental conditions like pH or hydroperiod. At larger scales, environmental gradients can influence community structure across interconnected local communities. Detecting the role of environmental and spatial factors on metacommunity structure depends on the ordering of sites and species prior to analysis. We investigated this ordination in two wetland metacommunities; a well-sampled, hyper-diverse zooplankton metacommunity, and a Central American phytoplankton metacommunity. We calculated coherence, turnover, and boundary clumping to classify the structure of the metacommunity, and we propose a statistic that responds to variation in both coherence and turnover. …

The Contribution Of Marine Aggregate-Associated Bacteria To The Accumulation Of Pathogenic Bacteria In Oysters: An Agent-Based Model, Andrew M. Kramer, J. Evan Ward, Fred C. Dobbs, Melissa L. Pierce, John M. Drake

Integrative Biology Faculty and Staff Publications

Bivalves process large volumes of water, leading to their accumulation of bacteria, including potential human pathogens (e.g., vibrios). These bacteria are captured at low efficiencies when freely suspended in the water column, but they also attach to marine aggregates, which are captured with near 100% efficiency. For this reason, and because they are often enriched with heterotrophic bacteria, marine aggregates have been hypothesized to function as important transporters of bacteria into bivalves. The relative contribution of aggregates and unattached bacteria to the accumulation of these cells, however, is unknown. We developed an agent-based model to simulate accumulation of vibrio-type bacteria …

Mathematical Models Are A Powerful Method To Understand And Control The Spread Of Huanglongbing, Rachel A. Taylor, Erin Mordecai, Christopher A. Gilligan, Jason R. Rohr, Leah R. Johnson

Integrative Biology Faculty and Staff Publications

Huanglongbing, or citrus greening, is a global citrus disease occurring in almost all citrus growing regions and causing substantial economic burdens to individual growers, citrus industries and governments. Successful management strategies to reduce disease burden are desperately needed but with so many possible interventions and combinations thereof, it is difficult to know which are worthwhile or cost-effective. We review how mathematical models have yielded useful insights into controlling disease spread for other vector-borne plant diseases, and the small number of mathematical models of Huanglongbing. We adapt a malaria model to Huanglongbing, by including temperature-dependent psyllid traits and economic costs, to …

Synthetic Biology Open Language (Sbol) Version 2.1.0, Zhen Zhang

Integrative Biology Faculty and Staff Publications

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 …

Effects Of Nutrient Supplementation On Host-Pathogen Dynamics Of The Amphibian Chytrid Fungus: A Community Approach, Julia C. Buck, Jason R. Rohr, Andrew R. Blaustein

Integrative Biology Faculty and Staff Publications

1. Anthropogenic stressors may influence hosts and their pathogens directly or may alter host–pathogen dynamics indirectly through interactions with other species. For example, in aquatic ecosystems, eutrophication may be associated with increased or decreased disease risk. Conversely, pathogens can influence community structure and function and are increasingly recognised as important members of the ecological communities in which they exist.
2. In outdoor mesocosms, we experimentally manipulated nutrients (nitrogen and phosphorus) and the presence of a fungal pathogen, Batrachochytrium dendrobatidis (Bd), and examined the effects on Bd abundance on larval amphibian hosts (Pseudacris regilla: Hylidae), amphibian traits and community dynamics. We …

An Experiment In Graduate Education: A Marine Science Adventure Across The Indian Ocean, Vicki Buchsbaum Pearse, John C. Ogden, Sharon J. Proctor

Integrative Biology Faculty and Staff Publications

In the fall of 1964, Stanford University’s R/V Te Vega Cruise 5 crossed the equatorial Indian Ocean from Mombasa to Singapore, one of many ships participating in the International Indian Ocean Expedition. The cruise achieved two goals: (1) it provided hands-on oceanography training for graduate students in marine sciences, and (2) it documented the deep scattering layers of the Indian Ocean, only poorly known at the time. Taking place on the other side of the globe from the United States, the cruise also exposed students to cultural and personal experiences that shaped their lives and professions. It demonstrated the importance …