Life Sciences Commons^™

Climate Change Alters Seedling Emergence And Establishment In An Old-Field Ecosystem, Aimée T. Classen, Richard J. Norby, Courtney E. Campany, Katherine E. Sides, Jake F. Weltzin

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Ecological succession drives large-scale changes in ecosystem composition over time, but the mechanisms whereby climatic change might alter succession remain unresolved. Here, we asked if the effects of atmospheric and climatic change would alter tree seedling emergence and establishment in an old-field ecosystem, recognizing that small shifts in rates of seedling emergence and establishment of different species may have long-term repercussions on the transition of fields to forests in the future.

Methodology/Principal Findings

We introduced seeds from three early successional tree species into constructed old-field plant communities that had been subjected for 4 years to altered temperature, precipitation, and …

Temporal Diversification Of Central American Cichlids, C Darrin Hulsey, Phillip R. Hollingsworth, James A. Fordyce

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Cichlid fishes are classic examples of adaptive radiation because of their putative tendency to explosively diversify after invading novel environments. To examine whether ecological opportunity increased diversification (speciation minus extinction) early in a species-rich cichlid radiation, we determined if Heroine cichlids experienced a burst of diversification following their invasion of Central America.

Results

We first reconstructed the Heroine phylogeny and determined the basal node to use as the root of Central American Heroine diversification. We then examined the influence of incomplete taxon sampling on this group's diversification patterns. First, we added missing species randomly to the phylogeny and assessed …

Effect Of Correlated Tran Abundances On Translation Errors And Evolution Of Codon Usage Bias, Premal Shah, Michael A. Gilchrist

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find …

Interpreting The Γ Statistic In Phylogenetic Diversification Rate Studies: A Rate Decrease Does Not Necessarily Indicate An Early Burst, James A. Fordyce

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Phylogenetic hypotheses are increasingly being used to elucidate historical patterns of diversification rate-variation. Hypothesis testing is often conducted by comparing the observed vector of branching times to a null, pure-birth expectation. A popular method for inferring a decrease in speciation rate, which might suggest an early burst of diversification followed by a decrease in diversification rate is the γ statistic.

Methodology

Using simulations under varying conditions, I examine the sensitivity of γ to the distribution of the most recent branching times. Using an exploratory data analysis tool for lineages through time plots, tree deviation, I identified trees with a …

Is Thermosensing Property Of Rna Thermometers Unique?, Premal Shah, Michael A. Gilchrist

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

A large number of studies have been dedicated to identify the structural and sequence based features of RNA thermometers, mRNAs that regulate their translation initiation rate with temperature. It has been shown that the melting of the ribosome-binding site (RBS) plays a prominent role in this thermosensing process. However, little is known as to how widespread this melting phenomenon is as earlier studies on the subject have worked with a small sample of known RNA thermometers. We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at …

Retention Of Low-Fitness Genotypes Over Six Decades Of Admixture Between Native And Introduced Tiger Salamanders, Jarrett R. Johnson, Benjamin M. Fitzpatrick, Bradley H. Shaffer

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Background

Introductions of non-native tiger salamanders into the range of California tiger salamanders have provided a rare opportunity to study the early stages of secondary contact and hybridization. We produced first- and second-generation hybrid salamanders in the lab and measured viability among these early-generation hybrid crosses to determine the strength of the initial barrier to gene exchange. We also created contemporary-generation hybrids in the lab and evaluated the extent to which selection has affected fitness over approximately 20 generations of admixture. Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary …

Bias Correction And Bayesian Analysis Of Aggregate Counts In Sage Libraries, Russell L. Zaretzki, Michael A. Gilchrist, William M. Briggs, Artin Armagan

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Background

Tag-based techniques, such as SAGE, are commonly used to sample the mRNA pool of an organism's transcriptome. Incomplete digestion during the tag formation process may allow for multiple tags to be generated from a given mRNA transcript. The probability of forming a tag varies with its relative location. As a result, the observed tag counts represent a biased sample of the actual transcript pool. In SAGE this bias can be avoided by ignoring all but the 3' most tag but will discard a large fraction of the observed data. Taking this bias into account should allow more of …

Non-Additive Effects Of Genotypic Diversity Increase Floral Abundance And Abundance Of Floral Visitors, Mark A. Genung, Jean-Philippe Lessard, Claire B. Brown, Windy A. Bunn, Melissa A. Cregger, Wm. Nicholas Reynolds, Emmi Felker-Quinn, Mary L. Stevenson, Amanda S. Hartley, Gregory M. Crutsinger, Jennifer A. Schweitzer, Joseph K. Bailey

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

In the emerging field of community and ecosystem genetics, genetic variation and diversity in dominant plant species have been shown to play fundamental roles in maintaining biodiversity and ecosystem function. However, the importance of intraspecific genetic variation and diversity to floral abundance and pollinator visitation has received little attention.

Methodology/Principal Findings

Using an experimental common garden that manipulated genotypic diversity (the number of distinct genotypes per plot) of Solidago altissima, we document that genotypic diversity of a dominant plant can indirectly influence flower visitor abundance. Across two years, we found that 1) plant genotype explained 45% and 92% …

The Biology Of Reality Testing - Implications For Cognitive Education, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

• This report explores the proposition that teaching effectiveness can be enhanced by accommodating the key differences between two complementary and deeply engrained modes of reality testing, each predominantly centered in different hemispheres of the brain. • (1) Correspondence involves “reality-testing” of a percept, the cerebral representation of an experience in the world. • (2) Coherence involves “textualizing”, that is, reality-testing of a percept by how easily it relates to previous and ongoing parallel and collateral experiences. • Confidence in the validity of any percept throughout development is related to the interplay of these key processes. • As organisms develop, …

The Delimitation Of Flammulina Fennae, Soňa Ripková, Karen Hughes, Slavomír Adamčík, Viktor Kučera, Katarína Adamčíková

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Multivariate morphometric analyses of micromorphological characters measured on 35 specimens of Flammulina fennae and related species show that only a combination of spore dimensions and ixohyphidia characters are suitable for delimitation of this species. In order to confirm species identifications based on micromorphology, ribosomal ITS DNA sequences were obtained and compared with those previously deposited in GenBank, and phylogenetic analyses were performed using an ITS dataset of all known Flammulina species. All six specimens morphologically determined as F. fennae were identified by molecular data. Two of twelve specimens morphologically assigned to F. velutipes had F. elastica sequences. One ITS sequence …

A New Genus To Accommodate Gymnopus Acervatus (Agaricales), Karen Hughes, David A. Mather, Ronald H. Peterson

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Phylogenies based on ITS and LSU nrDNA sequences show Agaricus (Gymnopus) acervatus as unique within the Gymnopus/Rhodocollybia complex. These phylogenies imply that a separate genus is necessary, and Connopus is proposed. Infraspecific morphological and DNA-based variation within C. acervatus suggests that a western North American clade might be reproductively isolated from the eastern North American/Scandinavian clade and that in this species complex the European and eastern North American clade might be conspecific. A Scandinavian exemplar is selected for bar-coding. Two GenBank sequences with name-phylogenetic placement inconsistencies are identified.

Rapid Fixation Of Non-Native Alleles Revealed By Genome-Wide Snp Analysis Of Hybrid Tiger Salamanders, Benjamin M Fitzpatrick, Jarrett R. Johnson, Kevin D. Kump, Bradley H. Shaffer, Jeremiah J. Smith, Randal S. Voss

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into …

Rapid Fixation Of Non-Native Alleles Revealed By Genome-Wide Snp Analysis Of Hybrid Tiger Salamanders, Benjamin M. Fitzpatrick, Jarrett R. Johnson, D Kevin Kump, H Bradley Shaffer, Jeramiah J. Smith, S Randal Voss

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into …

The Relative Ages Of Ectomycorrhizal Mushrooms And Their Plant Hosts Estimated Using Bayesian Relaxed Molecular Clock Analyses, David S. Hibbett, P. Brandon Matheny

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Ectomycorrhizae (ECM) are symbioses formed by polyphyletic assemblages of fungi (mostly Agaricomycetes) and plants (mostly Pinaceae and angiosperms in the rosid clade). Efforts to reconstruct the evolution of the ECM habit in Agaricomycetes have yielded vastly different results, ranging from scenarios with many relatively recent origins of the symbiosis and no reversals to the free-living condition; a single ancient origin of ECM and many subsequent transitions to the free-living condition; or multiple gains and losses of the association. To test the plausibility of these scenarios, we performed Bayesian relaxed molecular clock analyses including fungi, plants, and other eukaryotes, based …

Frequency-Dependent Selection By Wild Birds Promotes Polymorphism In Model Salamanders, Benjamin M. Fitzpatrick, Kim Shook, Reuben Izally

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Co-occurrence of distinct colour forms is a classic paradox in evolutionary ecology because both selection and drift tend to remove variation from populations. Apostatic selection, the primary hypothesis for maintenance of colour polymorphism in cryptic animals, proposes that visual predators focus on common forms of prey, resulting in higher survival of rare forms. Empirical tests of this frequency-dependent foraging hypothesis are rare, and the link between predator behaviour and maintenance of variation in prey has been difficult to confirm. Here, we show that predatory birds can act as agents of frequency-dependent selection on terrestrial salamanders. Polymorphism for presence/absence of …

"The Natural History Of Truth: The Neurobiology Of Belief", Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

The pursuit of truth is woven into the fabric of every organism*. Any estimate of how best to survive and thrive in the reality in which we are immersed requires a sense of self, of the world, and of their relationship to each other. I wish to explore the idea that this pursuit has at its heart two complementary modes of reality testing utilizing separate cerebral systems which deal, respectively with the correspondence of experience with the world and the coherence of the experience with previous experiences: “is it real” and “does it fit?” At multiple levels of the nervous …

The Beasts In Our Brain, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

In the neuropsychology of art, we must remember that the Brain of Man has not abandoned its ancient animal foundations, it has built upon them . . . . But it has also reconstructed them as the shifting earth beneath dictates . . . . We have done the best possible in the landscape in which we have found ourselves with the raw materials we have inherited." --(Greenberg, Prolegomena to a Study of Mind, 1973, ch. 42)

Mutrack: A Genome Analysis System For Large-Scale Mutagenesis In The Mouse, Erich J. Baker, Leslie Galloway, Barbara Jackson, Denise Schmoyer, Jay Snoddy

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Background

Modern biological research makes possible the comprehensive study and development of heritable mutations in the mouse model at high-throughput. Using techniques spanning genetics, molecular biology, histology, and behavioral science, researchers may examine, with varying degrees of granularity, numerous phenotypic aspects of mutant mouse strains directly pertinent to human disease states. Success of these and other genome-wide endeavors relies on a well-structured bioinformatics core that brings together investigators from widely dispersed institutions and enables them to seamlessly integrate data, observations and discussions.

Description

MuTrack was developed as the bioinformatics core for a large mouse phenotype screening effort. It is …

Adaptive Functions Of The Corpus Striatum: The Past And Future Of The R-Complex, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

The basal ganglia is emerging from the shadow cast by the most conspicuous clinical expression of its dysfunction: motor disorders.What is revealed is the nexus of a widely distributed system which functions in integrating action with cognition, motivation, and affect. Prominent among non-motor functions are striatal involvement in building up of sequences of behavior into meaningful, goal-directed patterns and repertoires and the selection of appropriate learned or innate sequences in concert with their possible predictive control. Further, striatum seems involved in declarative and strategic memory (involving intentional recollection and the management of retrieved memories, respectively). Findings from reptile experiments indicate …

Ethological Aspects Of Stress In A Model Lizard, Anolis Carolinensis, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Research on the stress response in reptiles can provide a useful comparative perspective for understanding how the constituent elements of the response can be put into service of diverse behavioral adaptations. A summary of the neural and endocrine causes and consequences of specific behavioral patterns seen in the small diurnal lizard, Anolis carolinensis, has provided a model for the exploration of the dynamics of autonomic and neurohormonal contributions to adaptive behavior.

In this species, changes in body color provide indices of the flux of circulating stress relevant hormones, and are seen in situations from spontaneous exploration through agonistic behavior. Furthermore, …

Ethological Causes And Consequences Of The Stress Response, Neil Greenberg, James A. Carr, Cliff H. Summers

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Stress involves real or perceived changes within an organism or in the environment that activate an organism’s attempts to cope by means of evolutionarily ancient neural and endocrine mechanisms. Responses to acute stressors involve catecholamines released in varying proportion at different sites in the sympathetic and central nervous systems. These responses may interact with and be complemented by intrinsic rhythms and responses to chronic or intermittent stressors involving the hypothalamic-pituitary-adrenal axis. Varying patterns of responses to stressors are also affected by an animal=s assessment of their prospects for successful coping. Subsequent central and systemic consequences of the stress response include …

The Saurian Psyche Revisted: Lizards In Research, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

This essay is intended to guide researchers interested in lizards as prospective experimental models to identify an appropriate species for their research needs and to care for lizards in a manner that will not compromise their utility. Coupled with these is a concern for critical thinking about the ethical dimension of lizard research, one guide for which is to consider the intersection of human needs and lizard needs.

Before proceeding further, several arbitrary premises must be made clear:

1. While wholly deserving of study because of their intrinsic interest, I will assume that the lizard research to be undertaken is …

Art, Science, Areté, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

No abstract provided.

Ethological Considerations In The Experimental Study Of Lizard Behavior, Neil Greenberg

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

The importance of an ethological approach to the experimental study of an unfamiliar species is described and several of its problems discussed. The selection of units of behavior is a crucial first step in the development of a behavior inventory. The correlation of a behavioral unit with a particular context is necessary to ascribe function to that to that unit and to develop an ethogram. Methods of studying lizards under controlled conditions are described and discussed. Constraints on behavior that must be considered in an experimental study include the microclimate and its thermal qualities, food and water, shelter utilization, and …