Digital Commons Network^™

Displaying To Females May Lower Male Foraging Time And Vigilance In A Lekking Bird, Sarah A. Cowles, Robert M. Gibson

School of Biological Sciences: Faculty Publications

Males of many species use courtship behavior to attract mates. However, by doing so males may face the associated costs of increased energetic expenditure, reduced foraging time, and elevated predation risk. We investigated the costs of display in lekking male Sharp-tailed Grouse (Tympanuchus phasianellus). We used lek-wide scan sampling to study how males allocated time among courtship display (‘‘dancing’’), agonism, foraging, and inactivity in relation to female numbers both within and across days. We also addressed the limited attention hypothesis and estimated visual attentiveness by videotaping 13 males and scoring head turns during these different activities. We found that the …

Exploring The Influence Of Ancient And Historic Megaherbivore Extirpations On The Global Methane Budget, Felisa A. Smith, John I. Hammond, Meghan A. Balk, Scott M. Elliott, S. Kathleen Lyons, Melissa I. Pardi, Catalina P. Tomé, Peter J. Wagner, Marie L. Westover, Christopher E. Doughty

School of Biological Sciences: Faculty Publications

Globally, large-bodied wild mammals are in peril. Because “megamammals” have a disproportionate influence on vegetation, trophic interactions, and ecosystem function, declining populations are of considerable conservation concern. However, this is not new; trophic downgrading occurred in the past, including the African rinderpest epizootic of the 1890s, the massive Great Plains bison kill-off in the 1860s, and the terminal Pleistocene extinction of megafauna. Examining the consequences of these earlier events yields insights into contemporary ecosystem function. Here, we focus on changes inmethane emissions, produced as a byproduct of enteric fermentation by herbivores. Although methane is ∼200 times less abundant than carbon …

Socio-Economic Instability And The Scaling Of Energy Use With Population Size, John P. Delong, Oskar Burger

School of Biological Sciences: Faculty Publications

The size of the human population is relevant to the development of a sustainable world, yet the forces setting growth or declines in the human population are poorly understood. Generally, population growth rates depend on whether new individuals compete for the same energy (leading to Malthusian or density-dependent growth) or help to generate new energy (leading to exponential and super-exponential growth). It has been hypothesized that exponential and super-exponential growth in humans has resulted from carrying capacity, which is in part determined by energy availability, keeping pace with or exceeding the rate of population growth. We evaluated the relationship between …

Interspecific Egg Rejection As Ecological Collateral Damage From Selection Driven By Conspecific Brood Parasitism, Bruce E. Lyon, Daizaburo Shizuka, John M. Eadie

School of Biological Sciences: Faculty Publications

Distinguishing between interspecific and intraspecific coevolution as the selective driver of traits can be difficult in some taxa. A previous study of an avian obligate brood parasite, the black-headed duck, Heteronetta atricapilla, suggested that egg rejection by its two main hosts (two species of coot) is an incidental by-product of selection from conspecific brood parasitism within the hosts, not selection imposed by the interspecific parasite. However, although both species of coot can recognize and reject eggs of conspecific brood parasites, which closely resemble their own, they paradoxically also accept a moderate fraction of duck eggs (40–60%), which differ strikingly …

Composite Random Search Strategies Based On Non-Directional Sensory Cues, Ben C. Nolting, Travis M. Hinkelman, Chad Brassil, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Many foraging animals find food using composite random search strategies, which consist of intensive and extensive search modes. Models of composite search can generate predictions about how optimal foragers should behave in each search mode, and how they should determine when to switch between search modes. Most of these models assume that foragers use resource encounters to decide when to switch between search modes. Empirical observations indicate that a variety of organisms use nondirectional sensory cues to identify areas that warrant intensive search. These cues are not precise enough to allow a forager to directly orient itself to a resource, …

The Network Motif Architecture Of Dominance Hierarchies, Daizaburo Shizuka, David B. Mcdonald

School of Biological Sciences: Faculty Publications

The widespread existence of dominance hierarchies has been a central puzzle in social evolution, yet we lack a framework for synthesizing the vast empirical data on hierarchy structure in animal groups. We applied network motif analysis to compare the structures of dominance networks from data published over the past 80 years. Overall patterns of dominance relations, including some aspects of non-interactions, were strikingly similar across disparate group types. For example, nearly all groups exhibited high frequencies of transitive triads, whereas cycles were very rare. Moreover, pass-along triads were rare, and double-dominant triads were common in most groups. These patterns did …

The Molecular Biology Capstone Assessment: A Concept Assessment For Upper-Division Molecular Biology Students, Brian A. Couch, William B. Wood, Jennifer K. Knight

School of Biological Sciences: Faculty Publications

Measuring students’ conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty …

Scientific Teaching: Defining A Taxonomy Of Observable Practices, Brian Couch, Tanya L. Brown, Tyler J. Schelpat, Mark J. Graham, Jennifer K. Knight

School of Biological Sciences: Faculty Publications

Over the past several decades, numerous reports have been published advocating for changes to undergraduate science education. These national calls inspired the formation of the National Academies Summer Institutes on Undergraduate Education in Biology (SI), a group of regional workshops to help faculty members learn and implement interactive teaching methods. The SI curriculum promotes a pedagogical framework called Scientific Teaching (ST), which aims to bring the vitality of modern research into the classroom by engaging students in the scientific discovery process and using student data to inform the ongoing development of teaching methods. With the spread of ST, the need …

The Body Size Dependence Of Trophic Cascades, John Delong, Benjamin Gilbert, Jonathan B. Shurin, Van M. Savage, Brandon T. Barton, Christopher F. Clements, Anthony I. Dell, Hamish S. Greig, Christopher D.G. Harley, Pavel Kratina, Kevin S. Mccann, Tyler D. Tunney, David A. Vasseur, Mary I. O’Connor

School of Biological Sciences: Faculty Publications

Trophic cascades are indirect positive effects of predators on resources via control of intermediate consumers. Larger-bodied predators appear to induce stronger trophic cascades (a greater rebound of resource density toward carrying capacity), but how this happens is unknown because we lack a clear depiction of how the strength of trophic cascades is determined. Using consumer-resource models, we first show that the strength of a trophic cascade has an upper limit set by the interaction strength between the basal trophic group and its consumer and that this limit is approached as the interaction strength between the consumer and its predator increases. …

Variation In The Local Population Dynamics Of The Short-Lived Opuntia Macrorhiza (Cactaceae), C. V. Haridas, Kathleen H. Keeler, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Spatiotemporal variation in demographic rates can have profound effects for population persistence, especially for dispersal-limited species living in fragmented landscapes. Long-term studies of plants in such habitats help with understanding the impacts of fragmentation on population persistence but such studies are rare. In this work, we reanalyzed demographic data from seven years of the short-lived cactus Opuntia macrorhiza var. macrorhiza at five plots in Boulder, Colorado. Previous work combining data from all years and all plots predicted a stable population (deterministic log λ=0). This approach assumed that all five plots were part of a single population. Since the plots were …

Pollen Limitation And Flower Abortion In A Wind-Pollinated, Masting Tree, Ian S. Pearse, Walter D. Koenig, Kyle A. Funk, Mario B. Pesendorfer

School of Biological Sciences: Faculty Publications

Pollen limitation is a key assumption of theories that explain mast seeding, which is common among wind-pollinated and woody plants. In particular, the pollen coupling hypothesis and pollination Moran effect hypothesis assume pollen limitation as a factor that synchronizes seed crops across individuals. The existence of pollen limitation has not, however, been unambiguously demonstrated in wind-pollinated, masting trees. We conducted a two-year pollen supplementation experiment on a masting oak species, Quercus lobata. Supplemental pollen increased acorn set in one year but not in the other, supporting the importance of pollen coupling and pollination Moran effect models of mast seeding. …

Convergent Evolution Of Hemoglobin Function In High-Altitude Andean Waterfowl Involves Limited Parallelism At The Molecular Sequence Level, Chandrasekhar Natarajan, Joana Projecto-Garcia, Hideaki Moriyama, Roy E. Weber, Violeta Muñoz-Fuentes, Andy J. Green, Cecilia Kopuchian, Pablo L. Tubaro, Luis Alza, Mariana Bulgarella, Matthew M. Smith, Robert E. Wilson, Angela Fago, Kevin G. Mccracken, Jay F. Storz

School of Biological Sciences: Faculty Publications

A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on sitedirected mutagenesis revealed the phenotypic effects of specific amino acid replacements that were …

Structural Insights Into The Mechanism Defining Substrate Affinity In Arabidopsis Thaliana Dutpase: The Role Of Tryptophan 93 In Ligand Orientation, Noriko Inoguchi, Kittichai Chaiseeda, Mamoru Yamanishi, Moon Ki Kim, Yunho Jang, Mamta Bajaj, Catherine P. Chia, Donald F. Becker, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

Background: Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) hydrolyzes dUTP to dUMP and pyrophosphate to maintain the cellular thymine-uracil ratio. dUTPase is also a target for cancer chemotherapy. However, the mechanism defining its substrate affinity remains unclear. Sequence comparisons of various dUTPases revealed that Arabidopsis thaliana dUTPase has a unique tryptophan at position 93, which potentially contributes to its degree of substrate affinity. To better understand the roles of tryptophan 93, A. thaliana dUTPase was studied.

Results: Enzyme assays showed that A. thaliana dUTPase belongs to a high-affinity group of isozymes, which also includes the enzymes from Escherichia coli and Mycobacterium tuberculosis. Enzymes …

Transgenic Virus Resistance In Crop-Wild Cucurbita Pepo Does Not Prevent Vertical Transmission Of Zucchini Yellow Mosaic Virus, H. E. Simmons, H. R. Prendeville, J. P. Dunham, M. J. Ferrari, J. D. Earnest, Diana Pilson, G. P. Munkvold, E. C. Holmes, A. G. Stephenson

School of Biological Sciences: Faculty Publications

Zucchini yellow mosaic virus (ZYMV) is an economically important pathogen of cucurbits that is transmitted both horizontally and vertically. Although ZYMV is seed-transmitted in Cucurbita pepo, the potential for seed transmission in virus-resistant transgenic cultivars is not known. We crossed and backcrossed a transgenic squash cultivar with wild C. pepo, and determined whether seed-to-seedling transmission of ZYMV was possible in seeds harvested from transgenic backcrossed C. pepo.We then compared these transmission rates to those of non-transgenic (backcrossed and wild) C. pepo. The overall seed-to-seedling transmission rate in ZYMV was similar to those found in previous studies …

Plant Species’ Origin Predicts Dominance And Response To Nutrient Enrichment And Herbivores In Global Grasslands, Eric W. Seabloom, Elizabeth T. Borer, Yvonne Buckley, Elsa E. Cleland, Kendi F. Davies, Jennifer Firn, W. Stanley Harpole, Yann Hautier, Eric M. Lind, Andrew Macdougall, John L. Orrock, Suzanne M. Prober, Peter B. Adler, T. Michael Anderson, Jonathan D. Bakker, Lori A. Biederman, Dana M. Blumenthal, Cynthia S. Brown, Lars A. Brudvig, Marc W. Cadotte, Chengjin Chu, Kathryn L. Cottingham, Michael J. Crawley, Ellen I. Damschen, Carla M. Dantonio, Nicole M. Decrappeo, Guozhen Du, Philip A. Fay, Paul Frater, Daniel S. Gruner, Nicole Hagenah, Andy Hector, Helmut Hillebrand, Kirsten S. Hofmockel, Hope Humphries, Virginia L. Jin, Adam Kay, Kevin P. Kirkman, Julia A. Klein, Johannes M. H. Knops, Kimberly J. La Pierre, Laura M. Ladwig, John G. Lambrinos, Qi Li, Wei Li, Robin Marushia, Rebecca Mcculley, Brett Melbourne, Charles E. Mitchell, Joslin L. Moore, John Morgan, Brent Mortensen, Lydia R. O'Halloran, David A. Pyke, Anita C. Risch, Mahesh Sankaran, Martin Schuetz, Anna Simonsen, Melinda D. Smith, Carly J. Stevens, Lauren L. Sullivan, Elizabeth M. Wolkovich, Peter D. Wragg, Justin Wright, Louie Yang

School of Biological Sciences: Faculty Publications

Exotic species dominate many communities; however the functional significance of species’ biogeographic origin remains highly contentious. This debate is fuelled in part by the lack of globally replicated, systematic data assessing the relationship between species provenance, function and response to perturbations. We examined the abundance of native and exotic plant species at 64 grasslands in 13 countries, and at a subset of the sites we experimentally tested native and exotic species responses to two fundamental drivers of invasion, mineral nutrient supplies and vertebrate herbivory. Exotic species are six times more likely to dominate communities than native species. Furthermore, while experimental …

Analysis Of A Coupled N-Patch Population Model With Ceiling Density Dependence, Jason Callahan, Richard Rebarber, Eva Strawbridge, Brigitte Tenhumberg, Shenglan Yuan

School of Biological Sciences: Faculty Publications

We consider a system of difference equations with ceiling density dependence to model the dynamics of a coupled population on an arbitrary, finite number of distinct patches where migration between all patches is possible. In this model, each patch possesses a separate carrying capacity, and the dynamics of the coupled population is governed by a linear model until the population of a patch reaches its capacity, after which it remains at this maximum value. Further, we analyze the global attractors of this model and apply these results to an Arabian oryx metapopulation model with some patches protected and others unprotected …

Site-Specific Differences In T Cell Frequencies And Phenotypes In The Blood And Gut Of Hivuninfected And Art-Treated Hiv+ Adults, Steven A. Yukl, Amandeep K. Shergill, Valerie Girling, Qingsheng Li, Maudi Killian, Lorrie Epling, Peilin Li, Philipp Kaiser, Ashley Haase, Diane V. Havlir, Kenneth Mcquaid, Elizabeth Sinclair, Joseph K. Wong

School of Biological Sciences: Faculty Publications

Gastrointestinal T lymphocytes are critical for mucosal immunity and HIV pathogenesis, yet little is known about normal T cell numbers and phenotypes in different regions of the gut, or the degree to which ART can restore levels to those of HIV-uninfected individuals. To investigate these questions, we measured T cell frequencies and markers of memory, activation, anergy, and homing in the blood, ileum, and rectum of HIV- and ART-suppressed HIV+ adults. In HIV- individuals, T cell frequencies and phenotypes differed significantly between sites. Compared to HIV- adults, HIV+ adults had lower absolute CD4+T cell counts in the ileal lamina propria …

What Drives Masting? The Phenological Synchrony Hypothesis, Walter D. Koenig, Johannes M.H. Knops, William J. Carmen, Ian S. Pearse

School of Biological Sciences: Faculty Publications

Annually variable and synchronous seed production, or masting behavior, is a widespread phenomenon with dramatic effects on wildlife populations and their associated communities. Proximally, masting is often correlated with environmental factors and most likely involves differential pollination success and resource allocation, but little is known about how these factors interact or how they influence seed production. We studied masting in the valley oak (Quercus lobata Nee), a California endemic tree, and report evidence that phenological synchrony in flowering driven by microclimatic variability determines the size of the acorn crop through its effects on pollen availability and fertilization success. These …

Gene Turnover In The Avian Globin Gene Families And Evolutionary Changes In Hemoglobin Isoform Expression, Juan C. Opazo, Federico G. Hoffmann, Chandrasekhar Natarajan, Christopher C. Witt, Michael Berenbrink, Jay F. Storz

School of Biological Sciences: Faculty Publications

The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the α- and β-type subunits of hemoglobin (Hb), the tetrameric α₂β₂ protein responsible for blood-O₂ transport. A comparative genomic analysis of 52 bird species revealed that the size and membership composition of the α- and β-globin gene families have remained remarkably constant during …

Revisiting Operons: An Analysis Of The Landscape Of Transcriptional Units In E. Coli, Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang, Ying Xu

School of Biological Sciences: Faculty Publications

Background: Bacterial operons are considerably more complex than what were thought. At least their components are dynamically rather than statically defined as previously assumed. Here we present a computational study of the landscape of the transcriptional units (TUs) of E. coli K12, revealed by the available genomic and transcriptomic data, providing new understanding about the complexity of TUs as a whole encoded in the genome of E. coli K12.

Results and conclusion: Our main findings include that (i) different TUs may overlap with each other by sharing common genes, giving rise to clusters of overlapped TUs (TUCs) along the genomic …

Females Sample More Males At High Nesting Densities, But Ultimately Obtain Less Attractive Mates, Robin M. Tinghitella, Chelsea Stehle, Janette W. Boughman

School of Biological Sciences: Faculty Publications

Background: Sexual selection is largely driven by the availability of mates. Theory predicts that male competition and female choice should be density-dependent, with males competing more intensely at relatively high density, and females becoming increasingly discriminating when there are more males from whom to choose. Evidence for flexible mating decisions is growing, but we do not understand how environmental variation is incorporated into mate sampling strategies. We mimicked threespine stickleback (Gasterosteus aculeatus) breeding conditions in pools with high and low densities of nesting males and allowed females to search for mates to determine whether 1) mate search strategies change with …

Complete Genome Sequence Of Sulfolobus Solfataricus Strain 98/2 And Evolved Derivatives, Samuel Mccarthy, Julien Gradnigo, Tyler Johnson, Sophie Payne, Anna Lipzen, Joel Martin, Wendy Schackwitz, Etsuko Morlyama, Paul H. Blum

School of Biological Sciences: Faculty Publications

Sulfolobus solfataricus strain 98/2 is a thermoacidophilic chemoheterotrophic crenarcheote that grows optimally at 80°C and pH3.0 (1). The S. solfataricus 98/2 genome reported in 2009 (Gen- Bank accession no. CP001800.1, RefSeq NC_017274.1, GI: 261600703) is a deletion derivative of strain 98/2 called PBL2025 (2). It is often misconstrued as the wild-type strain 98/2, yet lacks a 50-kb region encoding numerous genes involved in sugar metabolism. A new closed and complete genome sequence for wildtype strain 98/2 referred to as SULA is presented here as GenBank accession no. CP011057 using locus tag SULA. This strain has been deposited at the Japan …

Membrane Association And Catabolite Repression Of The Sulfolobus Solfataricus Α-Amylase, Edith Soo, Deepak Rudrappa, Paul H. Blum

School of Biological Sciences: Faculty Publications

Sulfolobus solfataricus is a thermoacidophilic member of the archaea whose envelope consists of an ether-linked lipid monolayer surrounded by a protein S-layer. Protein translocation across this envelope must accommodate a steep proton gradient that is subject to temperature extremes. To better understand this process in vivo, studies were conducted on the S. solfataricus glycosyl hydrolyase family 57 α-Amylase (AmyA). Cell lines harboring site specific modifications of the amyA promoter and AmyA structural domains were created by gene replacement using markerless exchange and characterized by Western blot, enzyme assay and culture-based analysis. Fusion of amyA to the malAp promoter overcame amyAp …

Evaluation Of Stem Rot In 339 Bornean Tree Species: Implications Of Size, Taxonomy, And Soil-Related Variation For Aboveground Biomass Estimates, K. D. Heineman, S. E. Russo, I. C. Baillie, J. D. Mamit, P. P.-K. Chai, L. Chai, E. W. Hindley, B.-T. Lau, S. Tan, P. S. Ashton

School of Biological Sciences: Faculty Publications

Fungal decay of heart wood creates hollows and areas of reduced wood density within the stems of living trees known as stem rot. Although stem rot is acknowledged as a source of error in forest aboveground biomass (AGB) estimates, there are few data sets available to evaluate the controls over stem rot infection and severity in tropical forests. Using legacy and recent data from 3180 drilled, felled, and cored stems in mixed dipterocarp forests in Sarawak, Malaysian Borneo, we quantified the frequency and severity of stem rot in a total of 339 tree species, and related variation in stem rot …

Genetic Diversity In Oxytocin Ligands And Receptors In New World Monkeys, Dongren Ren, Guoqing Lu, Hideaki Moriyama, Aaryn C. Mustoe, Emily B. Harrison, Jeffery A. French

School of Biological Sciences: Faculty Publications

Oxytocin (OXT) is an important neurohypophyseal hormone that influences wide spectrum of reproductive and social processes. Eutherian mammals possess a highly conserved sequence of OXT (Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly). However, in this study, we sequenced the coding region for OXT in 22 species covering all New World monkeys (NWM) genera and clades, and characterize five OXT variants, including consensus mammalian Leu8-OXT, major variant Pro8-OXT, and three previously unreported variants: Ala8-OXT, Thr8-OXT, and Phe2-OXT. Pro8-OXT shows clear structural and physicochemical differences from Leu8-OXT. We report multiple predicted amino acid substitutions in the G protein- coupled OXT receptor (OXTR), especially in the critical N-terminus, which …

Distinct And Cooperative Activities Of Heso1 And Urt1 Nucleotidyl Transferases In Microrna Turnover In Arabidopsis, Bin Tu, Li Liu, Chi Xu, Jixinan Zhai, Shengben Li, Miguel A. Lopez, Yuanyuan Zhao, Yu Yu, Vanitharani Ramachandran, Guodong Ren, Bin Yu, Shigui Li, Blake C. Meyers, Beixin Mo, Xuemei Chen

School of Biological Sciences: Faculty Publications

3’ uridylation is increasingly recognized as a conserved RNA modification process associated with RNA turnover in eukaryotes. 2’-O-methylation on the 3’ terminal ribose protects micro(mi)RNAs from 3’ truncation and 3’ uridylation in Arabidopsis. Previously, we identified HESO1 as the nucleotidyl transferase that uridylates most unmethylated miRNAs in vivo, but substantial 3’ tailing of miRNAs still remains in heso1 loss-of-function mutants. In this study, we found that among nine other potential nucleotidyl transferases, UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) is the single most predominant nucleotidyl transferase that tails miRNAs. URT1 and HESO1 prefer substrates with different 3’ end nucleotides in vitro and act …

Terrestrial Orchids In A Tropical Forest: Best Sites For Abundance Differ From Those For Reproduction, Melissa Whitman, James D. Ackerman

School of Biological Sciences: Faculty Publications

Suitable habitat for a species is often modeled by linking its distribution patterns with landscape characteristics. However, modeling the relationship between fitness and landscape characteristics is less common. In this study we take a novel approach towards species distribution modeling (SDM) by investigating factors important not only for species occurrence, but also abundance and physical size, as well as fitness measures. We used the Neotropical terrestrial orchid Prescottia stachyodes as our focal species, and compiled geospatial information on habitat and neighboring plants for use in a two-part conditional SDM that accounted for zero inflation and reduced spatial autocorrelation bias. First, …

Contribution Of A Mutational Hot Spot To Hemoglobin Adaptation In High-Altitude Andean House Wrens, Spencer C. Galen, Chandrasekhar Natarajan, Hideaki Moriyama, Roy E. Weber, Angela Fago, Phred M. Benham, Andrea N. Chavez, Zachary A. Cheviron, Jay F. Storz, Christopher C. Witt

School of Biological Sciences: Faculty Publications

A key question in evolutionary genetics is why certain mutations or certain types of mutation make disproportionate contributions to adaptive phenotypic evolution. In principle, the preferential fixation of particular mutations could stem directly from variation in the underlying rate of mutation to function-altering alleles. However, the influence of mutation bias on the genetic architecture of phenotypic evolution is difficult to evaluate because data on rates of mutation to function-altering alleles are seldom available. Here, we report the discovery that a single point mutation at a highly mutable site in the βA-globin gene has contributed to an evolutionary change in hemoglobin …

Complete Genome Sequence Of An Evolved Thermotoga Maritima Isolate, Raghuveer Singh, Julien Gradnigo, Derrick White, Anna Lipzen, Joel Martin, Wendy Schackwitz, Estuko N. Moriyama, Paul H. Blum

School of Biological Sciences: Faculty Publications

Thermotoga maritima MSB8 genomovar DSM3109 is a hyperthermophilic

anaerobic bacterium (1) that grows at 80°C, producing

a maximum of 4 mol of H2 per mol of glucose (2). There

are a variety of duplicated genes and direct repeats in its genome,

suggesting the potential for genome instability. Genome resequencing

of T. maritima MSB8 genomovar DSM3109 in 2011 and

2013 (3, 4) indicated that the earlier sequenced T. maritima MSB8

reported by Nelson et al. (NC_000853.1) (5) was an evolved laboratory

variant with an approximately 8-kb deletion located between

TM1847 and TM1848 (annotation according to reference

5). The 8-kb deletion may …

Assessing Pesticide Risks To Threatened And Endangered Species Using Population Models: Findings And Recommendations From A Croplife America Science Forum, V. E. Forbes, R. Brain, D. Edwards, N. Galic, T. Hall, J. Honegger, C. Meyer, D.R.J. Moore, D. Nacci, R. Pastorok, T. G. Preuss, S. F. Railsback, C. Salice, R. M. Sibly, B. Tenhumberg, P. Thorbek, M. Wang

School of Biological Sciences: Faculty Publications

This brief communication reports on the main findings and recommendations from the 2014 Science Forum organized by CropLife America. The aim of the forum was to gain a better understanding of the current status of population models and how they could be used in ecological risk assessments for threatened and endangered species potentially exposed to pesticides in the United States. The forum panelists' recommendations are intended to assist the relevant government agencies with implementation of population modeling in future endangered species risk assessments for pesticides. The forum included keynote presentations that provided an overview of current practices, highlighted the findings …