Life Sciences Commons^™

Testing The Strength And Direction Of Selection On Vocal Frequency Using Metabolic Scaling Theory, Clinton D. Francis, Matthew R. Wilkins

School of Biological Sciences: Faculty Publications

A major challenge for studies assessing drivers of phenotypic divergence is the statistical comparison of taxa with unique, often unknown, evolutionary histories, and for which there are no clear expected trait values. Because many traits are fundamentally constrained by energy availability, we suggest that trait values predicted by scaling theories such as the metabolic theory of ecology (MTE) can provide baseline expectations. Here, we introduce a metabolic scaling-based approach to test theory involving the direction and magnitude of ecological and sexual selection, using vocal frequency as an example target of selection. First, we demonstrate that MTE predicts the relationship between …

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 Iii, Kelsey M. Jenkins, Kristopher Mm. Kusnerik, Carmi Milagros Thompson, Ashley W. Poust, Selina V. Robson, Judith A. Sclafani, Kelsey T. Stilson, Shamindri D. Tennakoon

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 …

Testing A Global Standard For Quantifying Species Recovery And Assessing Conservation Impact, Molly K. Grace, John Carroll, 201 Other Scholars

School of Biological Sciences: Faculty Publications

Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a “Green List of Species” (now the IUCN Green Status of Species). A draft Green Status framework for assessing species’ progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species’ viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics ( …

Unique Structure And Positive Selection Promote The Rapid Divergence Of Drosophila Y Chromosomes, Ching-Ho Chang, Lauren E. Gregory, Kathleen E. Gordon, Colin D. Meiklejohn, Amanda M. Larracuente

School of Biological Sciences: Faculty Publications

Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long-read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence …

The Potential Use Of Radiomics With Pre-Radiation Therapy Mr Imaging In Predicting Risk Of Pseudoprogression In Glioblastoma Patients, Michael J. Baine, Justin Burr, Qian Du, Chi Zhang, Xiaoying Liang, Luke Krajewski, Laura Zima, Gerard Rux, Chi Zhang, Dandan Zheng

School of Biological Sciences: Faculty Publications

Glioblastoma (GBM) is the most common adult glioma. Differentiating post-treatment effects such as pseudoprogression from true progression is paramount for treatment. Radiomics has been shown to predict overall survival and MGMT (methylguanine-DNA methyltransferase) pro- moter status in those with GBM. A potential application of radiomics is predicting pseudoprogression on pre-radiotherapy (RT) scans for patients with GBM. A retrospective review was performed with radiomic data analyzed using pre-RT MRI scans. Pseudoprogression was defined as post-treatment findings on imaging that resolved with steroids or spontaneously on subsequent imaging. Of the 72 patients identified for the study, 35 were able to be assessed …

Body Mass-Related Changes In Mammal Community Assembly Patterns During The Late Quaternary Of North America, Silvia Pineda-Munoz, Advait M. Jukar, Anikó B. Toth, Danielle Fraser, Andrew Du, W. Andrew Barr, Kathryn L. Amatangelo, Meghan A. Balk, Anna K. Behrensmeyer, Jessica Blois, Matt Davis, Jussi T. Eronen, Nicholas J. Gotelli, Cindy Looy, Joshua H. Miller, Alexandria B. Shupinski, Laura C. Soul, Amelia Villaseñor, Scott Wing, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

The late Quaternary of North America was marked by prominent ecological changes, including the end-Pleistocene megafaunal extinction, the spread of human settlements and the rise of agriculture. Here we examine the mechanistic reasons for temporal changes in mammal species association and body size during this time period. Building upon the co-occurrence results from Lyons et al. (2016) – wherein each species pair was classified as spatially aggregated, segregated or random – we examined body mass differences (BMD) between each species pair for each association type and time period (Late Pleistocene: 40 000 ¹⁴C–11 700 ¹⁴C ybp, Holocene: 11 …

Associations Between Statin/Omega3 Usage And Mri-Based Radiomics Signatures In Prostate Cancer, Yu Shi, Ethan Wahle, Qian Du, Luke Krajewski, Xiaoying Liang, Sumin Zhou, Chi Zhang, Michael J. Baine, D Zheng

School of Biological Sciences: Faculty Publications

Prostate cancer is the most common noncutaneous cancer and the second leading cause of cancer deaths among American men. Statins and omega-3 are two medications recently found to correlate with prostate cancer risk and aggressiveness, but the observed associations are complex and controversial. We therefore explore the novel application of radiomics in studying statin and omega-3 usage in prostate cancer patients. On MRIs of 91 prostate cancer patients, two regions of interest (ROIs), the whole prostate and the peripheral region of the prostate, were manually segmented. From each ROI, 944 radiomic features were extracted after field bias correction and normalization. …

The Interspecific Growth–Mortality Trade-Off Is Not A General Framework For Tropical Forest Community Structure, Sabrina E. Russo, Sean M. Mcmahon, Matteo Detto, Glenn Ledder, S. Joseph Wright, Richard S. Condit, Stuart J. Davies, Peter S. Ashton, Sarayudh Bunyavejchewin, Chia-Hao Chang-Yang, Sisira Ediriweera, Corneille E.N. Ewango, Christine Fletcher, Robin B. Foster, C.V. Savi Gunatilleke, I.A.U. Nimal Gunatilleke, Terese Hart, Chang-Fu Hseih, Stephen P. Hubbell, Akira Itoh, Abdul Rahman Kassim, Yao Tze Leong, Yi Ching Lin, Jean-Remy Makana, Mohizah Bt. Mohamad, Perry Ong, Anna Sugiyama, I-Fang Sun, Sylvester Tan, Jill Thompson, Takuo Yamakura, Sandra L. Yap, Jess K. Zimmerman

School of Biological Sciences: Faculty Publications

Resource allocation within trees is a zero-sum game. Unavoidable trade-offs dictate that allocation to growth-promoting functions curtails other functions, generating a gradient of investment in growth versus survival along which tree species align, known as the interspecific growth–mortality trade-off. This paradigm is widely accepted but not well established. Using demographic data for 1,111 tree species across ten tropical forests, we tested the generality of the growth–mortality trade-off and evaluated its underlying drivers using two species-specific parameters describing resource allocation strategies: tolerance of resource limitation and responsiveness of allocation to resource access. Globally, a canonical growth–mortality trade-off emerged, but the trade-off …

Temperature But Not Ocean Acidification Affects Energy Metabolism And Enzyme Activities In The Blue Mussel, Mytilus Edulis, Omera B. Matoo, Gisela Lannig, Christian Bock, Inna M. Sokolova

School of Biological Sciences: Faculty Publications

1. In mosaic marine habitats, such as intertidal zones, ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO₂ production. The nonlinear interactions among these drivers can be context-specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation.

2. We were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of the Gulf of Maine (GOM), USA, for this study. GOM is a hot spot of global climate change (average sea surface temperature (SST) increasing by >0.2°C/year) with >60% decline in mussel population over the past 40 years. …

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 …

Co-Targeting Strategy For Precise, Scarless Gene Editing With Crispr/Cas9 And Donor Ssodns In Chlamydomonas, Soujanya Akella, Xinrong Ma, Romana Bacova, Zachary P. Harmer, Martina Kolackova, Xiaoxue Wen, David A. Wright, Martin H. Spalding, Donald P. Weeks, Heriberto Cerutti

School of Biological Sciences: Faculty Publications

Programmable site-specific nucleases, such as the clustered regularly interspaced short palindromic repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) ribonucleoproteins (RNPs), have allowed creation of valuable knockout mutations and targeted gene modifications in Chlamydomonas (Chlamydomonas reinhardtii).

However, in walled strains, present methods for editing genes lacking a selectable phenotype involve co-transfection of RNPs and exogenous doublestranded DNA (dsDNA) encoding a selectable marker gene. Repair of the dsDNA breaks induced by the RNPs is usually accompanied by genomic insertion of exogenous dsDNA fragments, hindering the recovery of precise, scarless mutations in target genes of interest. Here, we tested whether co-targeting two …

A Functional Genomic Screen In Saccharomyces Cerevisiae Reveals Divergent Mechanisms Of Resistance To Different Alkylphosphocholine Chemotherapeutic Agents, Jaquelin M. Garcia, Michael J. Schwabe, Dennis R. Voelker, Wayne R. Riekhof

School of Biological Sciences: Faculty Publications

The alkylphosphocholine (APC) class of antineoplastic and antiprotozoal drugs, such as edelfosine and miltefosine, are structural mimics of lyso-phosphatidylcholine (lyso-PC), and are inhibitory to the yeast Saccharomyces cerevisiae at low micromolar concentrations. Cytotoxic effects related to inhibition of phospholipid synthesis, induction of an unfolded protein response, inhibition of oxidative phosphorylation, and disruption of lipid rafts have been attributed to members of this drug class, however, the molecular mechanisms of action of these drugs remain incompletely understood. Cytostatic and cytotoxic effects of the APCs exhibit variability with regard to chemical structure, leading to differences in effectiveness against different organisms or cell …

Targeted Manipulation Of Abundant And Rare Taxa In The Daphnia Magna Microbiota With Antibiotics Impacts Host Fitness Differentially, Reilly O. Cooper, Janna M. Vavra, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Host-associated microbes contribute to host fitness, but it is unclear whether these contributions are from rare keystone taxa, numerically abundant taxa, or interactions among community members. Experimental perturbation of the microbiota can highlight functionally important taxa; however, this approach is primarily applied in systems with complex communities where the perturbation affects hundreds of taxa, making it difficult to pinpoint contributions of key community members. Here, we use the ecological model organism Daphnia magna to examine the importance of rare and abundant taxa by perturbing its relatively simple microbiota with targeted antibiotics. We used sublethal antibiotic doses to target either rare …

Within- And Trans-Generational Environmental Adaptation To Climate Change: Perspectives And New Challenges, Naim M. Bautista, Amélie Crespel

School of Biological Sciences: Faculty Publications

The current and projected impacts of climate change are shaped by unprecedented rates of change in environmental conditions. These changes likely mismatch the existing coping capacities of organisms within-generations and impose challenges for population resilience across generations. To better understand the impacts of projected scenarios of climate change on organismal fitness and population maintenance, it is crucial to consider and integrate the proximate sources of variability of plastic and adaptive responses to environmental change in future empirical approaches. Here we explore the implications of considering: (a) the variability in different time-scale events of climate change; (b) the variability in plastic …

A Consensus‑Based Ensemble Approach To Improve Transcriptome Assembly, Adam Voshall, Sairam Behera, Xiangjun Li, Xiao‑Hong Yu, Kushagra Kapil, Jitender S. Deogun, John Shanklin, Edgar B. Cahoon, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Background: Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the …

Genbio-Maps As A Case Study To Understand And Address The Effects Of Test-Taking Motivation In Low-Stakes Program Assessments, Crystal Uminski, Brian A. Couch

School of Biological Sciences: Faculty Publications

The General Biology–Measuring Achievement and Progression in Science (GenBio-MAPS) assessment measures student understanding of the Vision and Change core concepts at the beginning, middle, and end of undergraduate biology degree programs. Assessment coordinators typically administer this instrument as a low-stakes assignment for which students receive participation credit. While these conditions can elicit high participation rates, it remains unclear how to best measure and account for potential variation in the amount of effort students give to the assessment. To better understand student test-taking motivation, we analyzed GenBio-MAPS data from more than 8000 students at 20 institutions. While the majority of students …

Sex Role Similarity And Sexual Selection Predict Male And Female Song Elaboration And Dimorphism In Fairy-Wrens, Karan J. Odom, Kristal E. Cain, Michelle L. Hall, Naomi E. Langmore, Raoul A. Mulder, Sonia Kleindorfer, Jordan Karubian, Lyanne Brouwer, Emma I. Greig, Christine Evans, Allison E. Johnson, Kimberley K.-A. Meyers, Marcelo Araya-Salas, Michael S. Webster, Erik D. Enbody, John Anthony Jones, Jenélle L. Dowling, Ana V. Leitão

School of Biological Sciences: Faculty Publications

Historically, bird song complexity was thought to evolve primarily through sexual selection on males; yet, in many species, both sexes sing and selection pressure on both sexes may be broader. Previous research suggests competition for mates and resources during short, synchronous breeding seasons leads to more elaborate male songs at high, temperate latitudes. Furthermore, we expect male–female song structure and elaboration to be more similar at lower, tropical latitudes, where longer breeding seasons and year-round territoriality yield similar social selection pressures in both sexes. However, studies seldom take both types of selective pressures and sexes into account. We examined song …

Catalysis Of Chlorovirus Production By The Foraging Of Bursaria Truncatella On Paramecia Bursaria Containing Endosymbiotic Algae, Zeina T. Al-Ameeli, Maitham A. Al-Sammak, John Delong, David Dunigan, James L. Van Etten

School of Biological Sciences: Faculty Publications

Chloroviruses are large viruses that replicate in chlorella-like green algae and normally exist as mutualistic endosymbionts (referred to as zoochlorellae) in protists such as Paramecium bursaria. Chlorovirus populations rise and fall in indigenous waters through time; however, the factors involved in these virus fluctuations are still under investigation. Chloroviruses attach to the surface of P. bursaria but cannot infect their zoochlorellae hosts because the viruses cannot reach the zoochlorellae as long as they are in the symbiotic phase. Predators of P. bursaria, such as copepods and didinia, can bring chloroviruses into contact with zoochlorellae by disrupting the paramecia, which results …