Biology Commons^™

Genome-Wide Discovery Of Natural Variation In Pre-Mrna Splicing And Prioritising Causal Alternative Splicing To Salt Stress Response In Rice, Huihui Yu, Qian Du, Malachy Campbell, Bin Yu, Harkamal Walia, Chi Zhang

School of Biological Sciences: Faculty Publications

• Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VASP).
• VASP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions.
• In total, 764 significant GSS events …

Complete Genome Sequence Of Geobacter Sp. Strain Feam09, A Moderately Acidophilic Soil Bacterium, Pooja Yadav, Sanjay Antony-Babu, Erin Hayes, Olivia M. Healy, Donald Pan, Wendy H. Yang, Whendee L. Silver, Christopher L. Anderson, Adam Voshall, Samodha C. Fernando, Etsuko N. Moriyama, Joshua R. Herr, Karrie A. Weber

School of Biological Sciences: Faculty Publications

A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

The Crazy Critter Club - Lesson Plans, Caitlin Flynn Copenhaver, Audrey Anderson

Honors Program: Expanded Learning Clubs

This curriculum covers the lesson plans for the 2021 "Cool Critter Club". It is focused on teaching students about animals and the environment, especially at a local level. This club engages students through the use of games, art, and spending time outside.

Visual Control Of Refuge Recognition In The Whip Spider Phrynus Marginemaculatus, Kaylyn A.S. Flanigan, Daniel D. Wiegmann, Patrick Casto, Vincent J. Coppola, Natasha R. Flesher, Eileen Hebets, Verner Peter Bingman

Eileen Hebets Publications

Amblypygids, or whip spiders, are nocturnally active arachnids which live in structurally complex environments. Whip spiders are excellent navigators that can re-locate a home refuge without relying on visual input. Therefore, an open question is whether visual input can control any aspect of whip spider spatial behavior. In the current study, Phrynus marginemaculatus were trained to locate an escape refuge by discriminating between differently oriented black and white stripes placed either on the walls of a testing arena (frontal discrimination) or on the ceiling of the same testing arena (overhead discrimination). Regardless of the placement of the visual stimuli, the …

Identification And Quantification Of 11 Airborne Biochemicals Emitted By The Brown Recluse And Another Primitive Hunting Spider Using Headspace Solid-Phase Microextraction-Gc/Ms, Zachary Foulks, Jennifer Parks, William Stoecker, Charles Kristensen, Eileen A. Hebets, Honglan Shi

Eileen Hebets Publications

Loxosceles reclusa, or brown recluse spider, is a harmful household spider whose habitat extends throughout the Midwest in the USA and other regions in the world. The pheromones and other biomolecules that facilitate signaling for brown recluses and other spider species are poorly understood. A rapid and sensitive method is needed to analyze airborne spider signaling biomolecules to better understand the structure and function of these biochemicals in order to control the population of the spiders. In this study, we developed a novel headspace solid-phase microextraction (HS-SPME)-GC/MS method to analyze potential pheromones and biomolecules emitted by the brown recluse …

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 …

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 …

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 …

Opposing Community Assembly Patterns For Dominant And Nondominant Plant Species In Herbaceous Ecosystems Globally, Carlos Alberto Arnillas, Elizabeth T. Borer, Eric W. Seabloom, Juan Alberti, Selene Baez, Jonathan D. Bakker, Elizabeth H. Boughton, Yvonne M. Buckley, Miguel Nuno Bugalho, Ian Donohue, John Dwyer, Jennifer Firn, Riley Gridzak, Nicole Hagenah, Yann Hautier, Aveliina Helm, Anke Jentsch, Johannes M. H. Knops, Kimberly J. Komatsu, Lauri Laanisto, Ramesh Laungani, Rebecca Mcculley, Joslin L. Moore, John W. Morgan, Pablo Luis Peri, Sally A. Power, Jodi Price, Mahesh Sankaran, Brandon Schamp, Karina Speziale, Rachel Standish, Risto Virtanen, Marc W. Cadotte

School of Biological Sciences: Faculty Publications

Biotic and abiotic factors interact with dominant plants—the locally most frequent or with the largest coverage—and nondominant plants differently, partially because dominant plants modify the environment where nondominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing nondominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually limit nondominants. Hence, the nature of interactions among nondominant species could be modified by dominant species. Furthermore, these differences could translate into a disparity in the phylogenetic …

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 …

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 …

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 …

Interactions With Soil Fungi Alter Density Dependence And Neighborhood Effects In A Locally Abundant Dipterocarp Species, R. Max Segnitz, Sabrina E. Russo, Kabir G. Peay

School of Biological Sciences: Faculty Publications

Seedling recruitment can be strongly affected by the composition of nearby plant species. At the neighborhood scale (on the order of tens of meters), adult conspecifics can modify soil chemistry and the presence of host microbes (pathogens and mutualists) across their combined canopy area or rooting zones. At local or small spatial scales (on the order of one to few meters), conspecific seed or seedling density can influence the strength of intraspecific light and resource competition and also modify the density-dependent spread of natural enemies such as pathogens or invertebrate predators. Intrinsic correlation between proximity to adult conspecifics (i.e., recruitment …

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 …

Multisensory Integration Supports Configural Learning Of A Home Refuge In The Whip Spider Phrynus Marginemaculatus, Kaylyn A.S. Flanigan, Daniel D. Wiegmann, Eileen Hebets, Verner Peter Bingman

Eileen Hebets Publications

Predator diets represent a potential interaction between local prey availability, prey antipredator defenses, and predator foraging behavior. Female spider-specialist muddauber wasps (Hymenoptera: Sphecidae) collect spiders and provision them intact, but paralyzed, to their developing larvae, providing a unique means of quantifying the diversity and abundance of prey that they capture. Mud-dauber wasps are hypothesized to be a major source of selection on antipredator defenses in web-building spiders, and the spiny and thickened abdomens of female spiny orb-weaving spiders (Araneae: Araneidae) are hypothesized to function as antiwasp defenses. We inventoried spider prey from nests of the mud-dauber wasps Sceliphron caementarium (Drury) …

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 …

Solifuge (Camel Spider) Reproductive Biology: An Untapped Taxon For Exploring Sexual Selection, Alfredo V. Peretti, David E. Vrech, Eileen Hebets

Eileen Hebets Publications

The exploration of new and diverse animal groups in the study of sexual selection is both necessary and important to help better understand broad patterns and test sexual selection hypotheses regarding the evolutionary origins and maintenance of reproductive tactics and associated traits. Solifuges are, in this matter, an exceptional group and very little explored from the sexual selection point of view. At first glance, mating is apparently quite simple and conserved within this arachnid order, but solifuge reproductive behavior is unique among arachnids and more diverse than previously thought. In particular, these voracious animals appear to exhibit high sexual conflict, …

Spiders (Araneae) Collected As Prey By The Mud-Dauber Wasps Sceliphron Caementarium And Chalybion Californicum (Hymenoptera: Sphecidae) In Southeastern Nebraska1, Tyler B. Corey, Earl Agpawa, Eileen Hebets

Eileen Hebets Publications

Predator diets represent a potential interaction between local prey availability, prey antipredator defenses, and predator foraging behavior. Female spider-specialist muddauber wasps (Hymenoptera: Sphecidae) collect spiders and provision them intact, but paralyzed, to their developing larvae, providing a unique means of quantifying the diversity and abundance of prey that they capture. Mud-dauber wasps are hypothesized to be a major source of selection on antipredator defenses in web-building spiders, and the spiny and thickened abdomens of female spiny orb-weaving spiders (Araneae: Araneidae) are hypothesized to function as antiwasp defenses. We inventoried spider prey from nests of the mud-dauber wasps Sceliphron caementarium (Drury) …

Sister Species Diverge In Modality-Specific Courtship Signal Form And Function, Eileen Hebets, Mitch Bern, Rowan H. Mcginley, Andy Roberts, Arik Kershenbaum, James Starrett, Jason E. Bond

School of Biological Sciences: Faculty Publications

Understanding the relative importance of different sources of selection (e.g., the environment, social/sexual selection) on the divergence or convergence of reproductive communication can shed light on the origin, maintenance, or even disappearance of species boundaries. Using a multistep approach, we tested the hypothesis that two presumed sister species of wolf spider with overlapping ranges and microhabitat use, yet differing degrees of sexual dimorphism, have diverged in their reliance on modality- specific courtship signaling. We predicted that male Schizocosa crassipalpata (no ornamentation) rely predominantly on diet-dependent vibratory signaling for mating success. In contrast, we predicted that male S. bilineata (black foreleg …

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. …

Sterol Biosynthesis In Four Green Algae: A Bioinformatic Analysis Of The Ergosterol Versus Phytosterol Decision Point, Adam Voshall, Nakeirah T.M. Christie, Suzanne L. Rose, Maya Khasin, James L. Van Etten, Jennifer E. Markham, Wayne R. Riekhof, Kenneth Nickerson

School of Biological Sciences: Faculty Publications

Animals and fungi produce cholesterol and ergosterol, respectively, while plants produce the phytosterols stigmasterol, campesterol, and bsitosterol in various combinations. The recent sequencing of many algal genomes allows the detailed reconstruction of the sterol metabolic pathways. Here, we characterized sterol synthesis in two sequenced Chlorella spp., the free-living C. sorokiniana, and symbiotic C. variabilis NC64A. Chlamydomonas reinhardtii was included as an internal control and Coccomyxa subellipsoidea as a plant-like outlier. We found that ergosterol was the major sterol produced by Chlorella spp. and C. reinhardtii, while C. subellipsoidea produced the three phytosterols found in plants. In silico analysis …

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. …

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 …

Bringing Disciplines And People Together To Characterize The Plastic And Genetic Responses Of Molluscs To Environmental Change, Omera B. Matoo, Maurine Neiman

School of Biological Sciences: Faculty Publications

Molluscs are remarkably diverse and are found across nearly all ecosystems, meaning that members of this ancient animal phylum provide a powerful means to study genomic-phenotype connections in a climate change framework. Recent advances in genomic sequencing technologies and genome assembly approaches finally allow the relatively cheap and tractable assembly of high-quality mollusc genome resources. After a brief review of these issues and advances, we use a case-study approach to provide some concrete examples of phenotypic plasticity and genomic adaptation in molluscs in response to environmental factors expected to be influenced by climate change. Our goal is to use molluscs …

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 …

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 …

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 …

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 …