Life Sciences Commons^™

Identifying Landscape Scale Patterns From Individual Scale Processes, Andrew J. Tyre, Brigitte Tenhumberg, C. Michael Bull

School of Biological Sciences: Faculty Publications

Extrapolating across scales is a critical problem in ecology. Explicit mechanistic models of ecological systems provide a bridge from measurements of processes at small and short scales to larger scales; spatial patterns at large scales can be used to test the outcomes of these models. However, it is necessary to identify patterns that are not dependent on initial conditions, because small scale initial conditions will not normally be measured at large scales. We examined one possible pattern that could meet these conditions, the relationship between mean and variance in abundance of a parasitic tick in an individual based model of …

Plant Reproductive Allocation Predicts Herbivore Dynamics Across Spatial And Temporal Scales, Tom E. X. Miller, Andrew J. Tyre, Svata M. Louda

School of Biological Sciences: Faculty Publications

Life-history theory suggests that iteroparous plants should be flexible in their allocation of resources toward growth and reproduction. Such plasticity could have consequences for herbivores that prefer or specialize on vegetative versus reproductive structures. To test this prediction, we studied the response of the cactus bug (Narnia pallidicornis) to meristem allocation by tree cholla cactus (Opuntia imbricata). We evaluated the explanatory power of demographic models that incorporated variation in cactus relative reproductive effort (RRE; the proportion of meristems allocated toward reproduction). Field data provided strong support for a single model that defined herbivore fecundity as a …

Mining The Arabidopsis Thaliana Genome For Highly-Divergent Seven Transmembrane Receptors, Etsuko N. Moriyama, Pooja K. Strope, Stephen O. Opiyo, Zhongying Chen, Alan M. Jones

School of Biological Sciences: Faculty Publications

To identify divergent seven-transmembrane receptor (7TMR) candidates from the Arabidopsis thaliana genome, multiple protein classification methods were combined, including both alignmentbased and alignment-free classifiers. This resolved problems in optimally training individual classifiers using limited and divergent samples, and increased stringency for candidate proteins. We identified 394 proteins as 7TMR candidates and highlighted 54 with corresponding expression patterns for further investigation.

Mig-5/Dsh Controls Cell Fate Determination And Cell Migration In C. Elegans, Timothy Walston, Chaobo Guo, Rui Proenca, Mingfu Wu, Michael Herman, Jeff Hardin, Edward Hedgecock

School of Biological Sciences: Faculty Publications

Cell fate determination and cell migration are two essential events in the development of an organism. We identify mig-5, a Dishevelled family member, as a gene that regulates several cell fate decisions and cell migrations that are important during C. elegans embryonic and larval development. In offspring from mig-5 mutants, cell migrations are defective during hypodermal morphogenesis, QL neuroblast migration, and the gonad arm migration led by the distal tip cells (DTCs). In addition to abnormal migration, DTC fate is affected, resulting in either an absent or an extra DTC. The cell fates of the anchor cell in hermaphrodites …

The Importance Of Demographic Niches To Tree Diversity, Richard Condit, Peter Ashton, Sarayudh Bunyavejchewin, H. S. Dattaraja, Stuart J. Davies, Shameema Esufali, Corneille Ewango, Robin Foster, I. A.U.N. Gunatilleke, C. V.S. Gunatilleke, Pamela Hall, Kyle E. Harms, Terese Hart, Consuelo Hernandez, Stephen Hubbell, Akira Ito, Somboon Kiratiprayoon, James Lafrankie, Suzanne Loo De Lao, Jean-Remy Makana, Md. Nur Supardi Noor, Abdul Rahman Kassim, Sabrina E. Russo, Raman Sukumar, Cristián Samper, Hebbalulu S. Suresh, Sylvester Tan, Sean Thomas, Renato Valencia, Martha Vallejo, Gorky Villa, Tommaso Zillio

School of Biological Sciences: Faculty Publications

Most ecological hypotheses about species coexistence hinge on species differences, but quantifying trait differences across species in diverse communities is often unfeasible. We examined the variation of demographic traits using a global tropical forest data set covering 4,500 species in 10 large-scale tree inventories. With a hierarchical Bayesian approach, we quantified the distribution of mortality and growth rates of all tree species at each site. This allowed us to test the prediction that demographic differences facilitate species richness, as suggested by the theory that a tradeoff between high growth and high survival allows species to coexist. Contrary to the prediction, …

Abundance Of And Floral Herbivory On Exotic Bull Thistle Versus Native Tall Thistle In Western Tallgrass Prairie, Chad P. Andersen, Svata M. Louda

School of Biological Sciences: Faculty Publications

An important, yet poorly quantified mechanism to explain the failure of some exotic species to increase and spread is that indigenous natural enemies provide ecosystem resistance to invasiveness. To evaluate this idea, we hypothesized that spillover of native thistle-feeding floral insect herbivores onto Eurasian bull thistle (Cirsium vulgare) from the prairie native tall thistle (C. altissimum) helps limit bull thistle population growth and spread throughout the western tallgrass prairie region in Nebraska. To test this hypothesis, we quantified both the occurrence of bull thistle, a known invasive species worldwide, and the floral herbivory on it by …

Anaerobic Nitrate-Dependent Iron(Ii) Bio-Oxidation By A Novel Lithoautotrophic Betaproteobacterium, Strain 2002, Karrie A. Weber, Jarrod Pollock, Kimberly A. Cole, Susan M. O'Connor, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

Microbial nitrate-dependent Fe(II) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. In an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent Fe(II)-oxidizing microbial community and subsequent isolation of a nitrate-dependent Fe(II)-oxidizing microorganism. Throughout the sediment core, ambient concentrations of Fe(II) and nitrate were observed to coexist. Concomitant most probable number enumeration revealed the presence of an abundant nitrate-dependent Fe(II)- oxidizing microbial community (2.4 × 10^{3 …}

The Pea Aphid, Acyrthosiphon Pisum: An Emerging Genomic Model System For Ecological, Developmental, And Evolutionary Studies, Jennifer A. Brisson, David L. Stern

School of Biological Sciences: Faculty Publications

Aphids display an abundance of adaptations that are not easily studied in existing model systems. Here we review the biology of a new genomic model system, the pea aphid, Acyrthosiphon pisum. We then discuss several phenomena that are particularly accessible to study in the pea aphid: the developmental genetic basis of polyphenisms, aphid–bacterial symbioses, the genetics of adaptation and mechanisms of virus transmission. The pea aphid can be maintained in the laboratory and natural populations can be studied in the field. These properties allow controlled experiments to be performed on problems of direct relevance to natural aphid populations. Combined …

Invasive Insect Abundance Varies Across The Biogeographic Distribution Of A Native Host Plant, Tatyana A. Rand, Svata M. Louda

School of Biological Sciences: Faculty Publications

Studies of biogeographic variation in species abundances are fundamental to understanding and predicting the impacts of invasive exotic species. We quantified the abundance of the introduced and now invasive biocontrol weevil, Rhinocyllus conicus, on a newly adopted native host plant, Cirsium canescens (Platte thistle), across the plant’s distributional range. We used regression and structural equation analyses to examine variation in weevil abundance at 92–108 sites over three years in relation to variation in abiotic and biotic parameters hypothesized to be important in insect or plant dynamics and distribution. We found that R. conicus now occurs throughout the majority of …

Can Environmental Variation Generate Positive Indirect Effects In A Model Of Shared Predation?, Chad Brassil

School of Biological Sciences: Faculty Publications

Classic models of apparent competition predict negative indirect effects between prey with a shared enemy. If predator per capita growth rates are nonlinear, then endogenously generated periodic cycles are predicted to generate less negative or even positive indirect effects between prey. Here I determine how exogenous mechanisms such as environmental variation could modify indirect effects. I find that exogenous variation can have a broader range of effects on indirect interactions than endogenously generated cycles. Indirect effects are altered by environmental variation even in simple models for which the per capita growth rate of the predator species is a linear function …

Regulation Of Mercury Resistance In The Crenarchaeote Sulfolobus Solfataricus, James Schelert, Melissa Drozda, Vidula Dixit, Amanda Dillman, Paul H. Blum

School of Biological Sciences: Faculty Publications

Mercuric ion, Hg(II), inactivates generalized transcription in the crenarchaeote Sulfolobus solfataricus. Metal

challenge simultaneously derepresses transcription of mercuric reductase (merA) by interacting with the

archaeal transcription factor aMerR. Northern blot and primer extension analyses identified two additional

Hg(II)-inducible S. solfataricus genes, merH and merI (SSO2690), located on either side of merA. Transcription

initiating upstream of merH at promoter merHp was metal inducible and extended through merA and merI,

producing a merHAI transcript. Northern analysis of a merRA double mutant produced by linear DNA

recombination demonstrated merHp promoter activity was dependent on aMerR to overcome Hg(II) …

Phylogenetic Analysis Of The Cardini Group Of Drosophila With Respect To Changes In Pigmentation, Jennifer A. Brisson, Jason Wilder, Hope Hollocher

School of Biological Sciences: Faculty Publications

Phenotypic variability is the engine that drives future diversification with the expectation that polymorphic ancestors give rise to descendants harboring a subset of the ancestral variation. Here we examine evolutionary transitions from polymorphism to monomorphism in a visually striking New World radiation of fruit flies, the Drosophila cardini group. This group is distributed across the Americas and the Caribbean islands and exhibits a wide spectrum of abdominal pigmentation variation. Specifically, the D. dunni subgroup consists of Caribbean island endemics, each of which is monomorphic for its pigmentation pattern, with an interspecific cline of pigmentation across the islands. The D. cardini …

Nonparametric Estimation Of Natural Selection On A Quantitative Trait Using Mark-Recapture Data, Olivier Gimenez, Rita Covas, Charles R. Brown, Mark D. Anderson, Mary Bomberger Brown, Thomas Lenormand

School of Biological Sciences: Faculty Publications

Assessing natural selection on a phenotypic trait in wild populations is of primary importance for evolutionary ecologists. To cope with the imperfect detection of individuals inherent to monitoring in the wild, we develop a nonparametric method for evaluating the form of natural selection on a quantitative trait using mark-recapture data. Our approach uses penalized splines to achieve flexibility in exploring the form of natural selection by avoiding the need to specify an a priori parametric function. If needed, it can help in suggesting a new parametric model. We employ Markov chain Monte Carlo sampling in a Bayesian framework to estimate …

Glucocorticoid Hormone Levels Increase With Group Size And Parasite Load In Cliff Swallows, Samrrah A. Raouf, Linda C. Smith, Mary Bomberger Brown, John C. Wingfield, Charles R. Brown

School of Biological Sciences: Faculty Publications

Animals often cope with adverse events by releasing glucocorticoid hormones, which in turn promote increased energy assimilation. In captive animals, crowding also leads to increased glucocorticoid activity, probably because of increased levels of social competition. We investigated how group size and ectoparasite infestations affected endogenous levels of the glucocorticoid hormone, corticosterone, in colonial cliff swallows, Petrochelidon pyrrhonota, in southwestern Nebraska, USA. Parasites were removed from some colonies by fumigating nests. Baseline levels of corticosterone in breeding adults varied significantly with whether parasites were present, colony size (measured by total number of active nests at a site), and nesting stage. …

Feather Mites Are Positively Associated With Daily Survival In Cliff Swallows, Charles R. Brown, Kathleen R. Brazeal, Stephanie A. Strickler, Mary Bomberger Brown

School of Biological Sciences: Faculty Publications

Feather mites (Acari: Astigmata) have been reported to be parasitic, commensal, and even mutualis-tic on the birds that serve as their hosts. We investigated whether there was a relationship between number of feather mites (Pteronyssoides obscurus (Berlese, 1885)) on the wing and daily survival of cliff swallows (Petrochelidon pyrrhonota (Vieillot, 1817)) during the breeding season at 12 nesting colonies in Nebraska in 2005. Survival of birds with known mite loads was monitored by mark–recapture, and survival models with and without a linear effect of mites were compared with the program MARK. For adult swallows, mites were positively associated …

Fire Does Not Alter Vegetation In Infertile Prairie, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

The paradigm in prairie ecology is that fire is one of the key factors deter-mining vegetation composition. fire can impact grassland ecosystems in various ways, including changing plant species composition and inducing nitro-gen loss. I found that 17 years of different burning frequencies in infertile grassland had only a minor impact on the vegetation composition and diversity. The only major impact from increasing the frequency of fires was a decrease of Poa pratensis abundance. However, other plant species did not r-spond to the change in Poa abundance. This result contrasts with previous studies in savannas and more productive grasslands, where …

Optimal Time Allocation In Parasitic Wasps Searching For Hosts And Food, Brigitte Tenhumberg, Gitta Siekmann, Michael A. Keller

School of Biological Sciences: Faculty Publications

Many species of parasitic wasp feed on sugar sources such as nectar and honeydew in order to replenish their energy reserves and so extend their life expectancy, which is often correlated with higher reproductive success. Recent research suggests that carbohydrates are also a key component in flight fuel in such insects. The importance of sugar in fuelling locomotion suggests location of sugar-rich food may be more important in parasitoid foraging behavior than has previously been assumed. If sugar sources and hosts are separated in space, parasitoids have to allocate their time between sugar-searching and host-searching. Using a stochastic dynamic programming …

Sex-Specific Expression Of Alternative Transcripts In Drosophila, Lauren Mcintyre, Lisa Bono, Anne Genissel, Rick Westerman, Damion Junk, Marina Telonis-Scott, Lawrence G. Harshman, Marta Wayne, Artyom Kopp, Sergey V. Nuzhdin

School of Biological Sciences: Faculty Publications

Background: Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster.

Results: We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us …

Wing Dimorphism In Aphids, Christian Braendle, Gregory K. Davis, Jennifer A. Brisson, David L. Stern

School of Biological Sciences: Faculty Publications

Many species of insects display dispersing and nondispersing morphs. Among these, aphids are one of the best examples of taxa that have evolved specialized morphs for dispersal versus reproduction. The dispersing morphs typically possess a full set of wings as well as a sensory and reproductive physiology that is adapted to flight and reproducing in a new location. In contrast, the nondispersing morphs are wingless and show adaptations to maximize fecundity. In this review, we provide an overview of the major features of the aphid wing dimorphism. We first provide a description of the dimorphism and an overview of its …

Spillover Of Agriculturally Subsidized Predators As A Potential Threat To Native Insect Herbivores In Fragmented Landscapes, Tatyana A. Rand, Svata M. Louda

School of Biological Sciences: Faculty Publications

Habitat loss and fragmentation can have strong negative impacts on populations of some native species. Spillover of generalist natural enemies from the surrounding landscape matrix is one mechanism potentially generating such effects, yet this has been rarely studied in insects. We examined the influence of habitat conversion to agriculture on the abundance and potential effects of predatory coccinellid beetles on native insect herbivores within 12 grassland remnants in central Nebraska (U.S.A.). Results of sweep sampling revealed that coccinellids were three to six times more abundant at native grassland sites embedded within cropland- dominated landscapes compared with control sites in grassland-dominated …

Assembly Of The Eastern North American Herpetofauna: New Evidence From Lizards And Frogs, J. Robert Macy, James A. Schulte Ii, Jared L. Strasburg, Jennifer A. Brisson, Allan Larson, Natalia B. Ananjeva, Yuezhao Wang, James F. Parham, Theodore J. Papenfuss

School of Biological Sciences: Faculty Publications

Darwin first recognized the importance of episodic intercontinental dispersal in the establishment of worldwide biotic diversity. Faunal exchange across the Bering Land Bridge is a major example of such dispersal. Here, we demonstrate with mitochondrial DNA evidence that three independent dispersal events from Asia to North America are the source for almost all lizard taxa found in continental eastern North America. Two other dispersal events across Beringia account for observed diversity among North American ranid frogs, one of the most species-rich groups of frogs in eastern North America. The contribution of faunal elements from Asia via dispersal across Beringia is …

The Developmental And Molecular Basis Of Allometry In Drosophila, Alexander W. Shingleton, Jennifer A. Brisson, David L. Stern

School of Biological Sciences: Faculty Publications

Allometry is the scaling relationship between the size of an organism and the size of its constituent parts. Despite its obvious developmental and evolutionary importance, very little is known of the mechanisms that regulate allometries. Here, we look at one particular type of allometry—that created by rearing Drosophila under different nutritional conditions. Drosophila larvae that are fed increasingly suboptimal diets eclose into increasingly small adults with increasingly small body parts. Surprisingly, however, the male genitals remain approximately the same size under a range of nutritional conditions. The genitals therefore maintain a different allometric relationship with the body than other structures. …

Phylogenetics Of The Florally Diverse Andean Clade Iochrominae (Solanaceae), Stacey Dewitt Smith, David A. Baum

School of Biological Sciences: Faculty Publications

Recent molecular phylogenetic studies of Solanaceae have identified many well-supported clades within the family and have permitted the creation of a phylogenetic system of classification. Here we estimate the phylogeny for Iochrominae, a clade of Physaleae sensu Olmstead et al. (1999), which contains 34 Andean species encompassing an immense diversity of floral forms and colors. Using three nuclear regions, ITS, the second intron of LEAFY, and exons 2 to 9 of the granule-bound starch synthase gene (waxy), we evaluated the monophyly of the traditional genera comprising Iochrominae and assessed the extent of interspecific hybridization within the clade. …

Microorganisms Pumping Iron: Anaerobic Microbial Iron Oxidation And Reduction, Karrie A. Weber, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

Iron (Fe) has long been a recognized physiological requirement for life, yet for many microorganisms that persist in water, soils and sediments, its role extends well beyond that of a nutritional necessity. Fe(II) can function as an electron source for iron-oxidizing microorganisms under both oxic and anoxic conditions and Fe(III) can function as a terminal electron acceptor under anoxic conditions for iron-reducing microorganisms. Given that iron is the fourth most abundant element in the Earth’s crust, iron redox reactions have the potential to support substantial microbial populations in soil and sedimentary environments. As such, biological iron apportionment has been described …

Anaerobic Redox Cycling Of Iron By Freshwater Sediment Microorganisms, Karrie A. Weber, Matilde M. Urrutia, Perry F. Churchill, Ravi K. Kukkadapu, Eric E. Roden

School of Biological Sciences: Faculty Publications

The potential for microbially mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. Most probable number enumerations revealed the presence of significant populations of Fe(III)-reducing (approximately 10⁸ cells ml^-1 ) and Fe(II)-oxidizing, nitrate-reducing organisms (approximately 10⁵ cells ml^-1 ) in the freshwater sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (approximately 1 mM) medium with a small quantity (1% v/v) of wetland sediment, and resulted in the transient accumulation of NO₂^– and production of a mixture of …

Protein Binding Site Prediction Using An Empirical Scoring Function, Shide Liang, Chi Zhang, Song Liu, Yaoqi Zhou

School of Biological Sciences: Faculty Publications

Most biological processes are mediated by interactions between proteins and their interacting partners including proteins, nucleic acids and small molecules. This work establishes a method called PINUP for binding site prediction of monomeric proteins. With only two weight parameters to optimize, PINUP produces not only 42.2% coverage of actual interfaces (percentage of correctly predicted interface residues in actual interface residues) but also 44.5% accuracy in predicted interfaces (percentage of correctly predicted interface residues in the predicted interface residues) in a cross validation using a 57-protein dataset. By comparison, the expected accuracy via random prediction (percentage of actual interface residues in …