Digital Commons Network^™

Maptogenome: A Comparative Genomic Tool That Aligns Transcript Maps To Sequenced Genomes, Srikrishna Putta, Jeramiah J. Smith, Chuck Staben, S. Randal Voss

Biology Faculty Publications

Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome …

Winter 2007, Nsu Oceanographic Center

Currents

No abstract provided.

Pathways Of Anaerobic Carbon Cycling Across An Ombrotrophic–Minerotrophic Peatland Gradient, Jason K. Keller, Scott D. Bridgham

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatland soils represent globally significant stores of carbon, and understanding carbon cycling pathways in these ecosystems has important implications for global climate change. We measured aceticlastic and autotrophic methanogenesis, sulfate reduction, denitrification, and iron reduction in a bog, an intermediate fen, and a rich fen in the Upper Peninsula of Michigan for one growing season. In 3-d anaerobic incubations of slurried peat, denitrification and iron reduction were minor components of anaerobic carbon mineralization. Experiments using 14C-labeled methanogenic substrates showed that methanogenesis in these peatlands was primarily through the aceticlastic pathway, except early in the growing season in more ombrotrophic peatlands, …

Does Increasing Biology Teacher Knowledge Of Evolution And The Nature Of Science Lead To Greater Advocacy For The Teaching Of Evolution In Schools?, Ross Nehm, Irvin Sam Schonfeld

Publications and Research

This study investigated whether or not an increase in secondary science teacher knowledge about evolution and the nature of science gained from completing a graduate-level evolution course was associated with greater preference for the teaching of evolution in schools. Forty-four precertified secondary biology teachers participated in a 14-week intervention designed to address documented misconceptions identified by a precourse instrument. The course produced statistically significant gains in teacher knowledge of evolution and the nature of science and a significant decrease in misconceptions about evolution and natural selection. Nevertheless, teachers' postcourse preference positions remained unchanged; the majority of science teachers still preferred …

Ocpat: An Online Codon-Preserved Alignment Tool For Evolutionary Genomic Analysis Of Protein Coding Sequences, Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I. Grossman, Roberto Romero, Derek E. Wildman

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.

Results

Here we report an online codon-preserved alignment tool (OCPAT) that generates …

Bottom-Up Forcing And The Decline Of Steller Sea Lions (Eumetopias Jubatus) In Alaska: Assessing The Ocean Climate Hypothesis, Andrew W. Trites, Arthur J. Miller, Michael A. Alexander, Steven J. Bograd, John A. Calder, Antonietta Capotondi, Kenneth O. Coyle, Emanuele Di Lorenzo, Bruce P. Finney, Edward J. Gregr, Chester E. Grosch, Thomas C. Royer

CCPO Publications

Declines of Steller sea lion ( Eumetopias jubatus) populations in the Aleutian Islands and Gulf of Alaska could be a consequence of physical oceanographic changes associated with the 1976–77 climate regime shift. Changes in ocean climate are hypothesized to have affected the quantity, quality, and accessibility of prey, which in turn may have affected the rates of birth and death of sea lions. Recent studies of the spatial and temporal variations in the ocean climate system of the North Pacific support this hypothesis. Ocean climate changes appear to have created adaptive opportunities for various species that are preyed upon …

Stormwater Influence On Phytoplankton Composition And Dynamics In Lake Joyce, Virginia, Lewis F. Affronti Jr., B. Thomas Duquette

Virginia Journal of Science

A three year study of Lake Joyce, Virginia revealed relationships between the timing, duration, and amount of stormwater runoff and phytoplankton abundance and composition. Major phytoplankton taxa were identified and cyanophytes dominanted during periods of decreased rainwater input and increased lake water retention times. Increased freshwater input was associated with the growth of a diverse assemblage of both chlorophytes and diatoms. Phytoplankton dynamics as a result of significant rain events (i.e., hurricanes Floyd and Irene, 1999) were documented and specific taxa involved in nuisance algal blooms were identified.

Biogeochemical Consequences Of Rapid Microbial Turnover And Seasonal Succession In Soil, S. K. Schmidt, E. K. Costello, D. R. Nemergut, Cory C. Cleveland, S. C. Reed, M. N. Weintraub, A. F. Meyer, A. M. Martin

Ecosystem and Conservation Sciences Faculty Publications

Soil microbial communities have the metabolic and genetic capability to adapt to changing environmental conditions on very short time scales. In this paper we combine biogeochemical and molecular approaches to reveal this potential, showing that microbial biomass can turn over on time scales of days to months in soil, resulting in a succession of microbial communities over the course of a year. This new understanding of the year-round turnover and succession of microbial communities allows us for the first time to propose a temporally explicit N cycle that provides mechanistic hypotheses to explain both the loss and retention of dissolved …

Controls Over Foliar N:P Ratios In Tropical Rain Forests, Alan R. Townsend, Cory C. Cleveland, Gregory P. Asner, Mercedes M. C. Bustamante

Ecosystem and Conservation Sciences Faculty Publications

Correlations between foliar nutrient concentrations and soil nutrient availability have been found in multiple ecosystems. These relationships have led to the use of foliar nutrients as an index of nutrient status and to the prediction of broadscale patterns in ecosystem processes. More recently, a growing interest in ecological stoichiometry has fueled multiple analyses of foliar nitrogen : phosphorus (N:P) ratios within and across ecosystems. These studies have observed that N:P values are generally elevated in tropical forests when compared to higher latitude ecosystems, adding weight to a common belief that tropical forests are generally N rich and P poor. However, …

Sensory Genes And Mate Choice: Evidence That Duplications, Mutations, And Adaptive Evolution Alter Variation In Mating Cue Genes And Their Receptors, Lisa Horth

Biological Sciences Faculty Publications

Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity—behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes’ products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and …

Administering The Clean Water Act: Do Regulators Have "Bigger Fish To Fry" When It Comes To Addressing The Practice Of Chumming On The Chesapeake Bay?, Hope M. Babcock

Georgetown Law Faculty Publications and Other Works

The Chesapeake Bay is one of the country's most productive estuaries. However, for decades the health of the Bay has been declining due in large part to nutrification. Excessive nutrients encourage algal blooms, which lower dissolved oxygen and increase turbidity in the Bay's waters. More than 40% of the Bay's main stern is now dead largely as a result of this problem. The practice of chumming, the discarding of baitfish, usually menhaden, over the sides of fishing boats to attract game fish like striped bass, is contributing to the Bay's nutrification problem because the decomposing chum raises the waters biological …

Current Status And Long-Term Trends In Water Quality And Living Resources In The Virginia Tributaries And Chesapeake Bay Mainstem From 1985 Through 2005, Daniel M. Dauer, Harold G. Marshall, John R. Donat, Michael F. Lane, Suzanne C. Doughten, Frederick A. Hoffman

Status and Trends for Virginia Chesapeake Bay

A marked decline in the water quality of the Chesapeake Bay has occurred over the past several decades. The disappearance of submerged aquatic vegetation in certain regions of the Bay, declines in the abundance of some commercially and recreationally important species, increases in the incidence of low dissolved oxygen events, changes in the Bay's food web, and other ecological problems have been related to the deteriorating water quality. The results of concentrated research efforts in the late 1970s and early 1980s stimulated the establishment of Federal and state directives to better manage the Chesapeake Bay watershed. By way of the …

Phytoplankton Productivity In The Tidal Regions Of Four Chesapeake Bay (U.S.A.) Tributaries, Kneeland K. Nesius, Harold G. Marshall, Todd A. Egerton

Virginia Journal of Science

Monthly and annual phytoplankton productivity rates of four Virginia tidal rivers were determined based on a 12-year monitoring study that included sampling stations from tidal freshwater, oligohaline, and mesohaline regions in these rivers. The mean monthly rates and range at these locations were 5.52 (Dec.) to 175.12 (Aug.) mg C m^-3 h^-1 for tidal freshwater, 12.21 (Jan.) to 149.90 (May) mg C m^-3 h^-1 in oligohaline regions, and 16.20 (Jan.) to 151.33 (May) mg C m^-3 h^-1 for the mesohaline. The estimated mean annual 12 year productivity for the different Virginia river sites in …

Grotius, Ocean Fish Ranching, And The Public Trust Doctrine: Ride 'Em Charlie Tuna, Hope M. Babcock

Georgetown Law Faculty Publications and Other Works

Seventy percent of the world's fish populations are in serious decline; some have been fished to near extinction. While domestic and international efforts are underway to curb the rate at which the remaining fish are being depleted, the demand for fish appears to be outstripping these initiatives--before they can take hold, the fish may be gone. In response to this increasingly dire situation, many countries, including the United States, have turned to fish farming in hope of taking pressure off of certain wild stocks of fish while still meeting consumer demands for them. More recently, non-U.S. fish farmers have moved …

A Scent-Station Survey Of Medium-Size Mammals On The Callaway Preserve, Harris County, Georgia, Anna-Maria Giacobello

Theses and Dissertations

The objective of this project was to determine the relative abundance of medium- sized mammals on the Callaway Preserve in Harris County, Georgia, using the scent- station technique, to determine species preference in regard to habitat, to compare relative abundance of species in regard to habitat, and to compare habitats in terms of the species present. Thirty-six scent-stations were established on the property and monitored to observe the presence of coyotes, raccoons, armadillos, foxes, opossums, and skunks. Of the total number of visits to the scent-stations, 36.36 % were coyotes, 18.18% were foxes 22.73% were armadillos, and 22.73% were raccoons. …

Amazonian Exploitation Revisited: Ecological Asymmetry And The Policy Pendulum, Mark B. Bush, Miles R. Silman

Ocean Engineering and Marine Sciences Faculty Publications

The influence of pre-Columbian human populations on Amazonian ecosystems is being actively debated. The long-standing view that Amazonia was only minimally impacted by human actions has been challenged, and a new paradigm of Amazonia as a "manufactured landscape" is emerging. If such disturbance was the norm until just 500 years ago, Amazonian ecosystems could be far more ecologically resilient to disturbance than previously supposed. Alternatively, if the "manufactured landscape" label is an overstatement, then policy that assumes such resilience may cause substantial and long-lasting ecological damage. We present paleoecological data suggesting a middle path, in which some areas were heavily …

Possible Use Of Foresight, Understanding, And Planning By Wolves Hunting Muskoxen, L. David Mech

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

On Ellesmere Island in 2006, arctic wolves (Canis lupus arctos) were observed making a two-pronged approach to a herd of muskoxen (Ovibos moschatus) and, on another occasion, ambushing muskoxen. Both observations seemed to provide evidence that the wolves were using foresight, understanding, and planning. Although the possible use of insight and purposiveness has been documented in captive wolves, the present report is one of the few to document the possibility that freeranging wolves use these other three mental processes.

En 2006, sur l’île Ellesmere, des loups arctiques (Canis lupus arctos) ont été observés en …

Annual Arctic Wolf Pack Size Related To Arctic Hare Numbers, L. David Mech

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

During the summers of 2000 through 2006, I counted arctic wolf (Canis lupus arctos) pups and adults in a pack, arctic hares (Lepus arcticus) along a 9 km index route in the area, and muskoxen (Ovibos moschatus) in a 250 km² part of the area near Eureka (80° N, 86° W), Ellesmere Island, Nunavut, Canada. Adult wolf numbers did not correlate with muskox numbers, but they were positively related (r² = 0.89; p < 0.01) to an arctic hare index. This is the first report relating wolf numbers to non-ungulate prey.

Pendant les étés 2000 à 2006, j’ai compté les jeunes loups arctiques et les adultes (Canis lupus arctos …

Pigeons And People Select Efficient Routes When Solving A One-Way “Traveling Salesperson” Task, Brett M. Gibson, Edward A. Wasserman, Alan C. Kamil

Papers in Behavior in Biological Sciences

The authors presented people (Experiment 1) and pigeons (Experiments 2 and 3) with a large number of 1-way traveling salesperson problems that consisted of 3, 4, and 5 identical stimuli (nodes) on a computer monitor. The sequence of nodes that each traveler selected was recorded, and the distance of the route was subsequently determined. The routes the pigeons and people selected were reliably more efficient than those used by a Monte Carlo model given the same problems. The pigeons’ routes were significantly less efficient than a nearest neighbor model of performance, however. In Experiment 3, pigeons were required to select …

Geographic Distribution: Ramphotyphlops Braminus (Brahminy Blindsnake). Usa: Florida: Volusia Co, Louis A. Somma, Paul E. Skelley

Papers in Herpetology

RAMPHOTYPHLOPS BRAMINUS (Brahminy Blindsnake). USA: FLORIDA: VOLUSIA Co.: New Smyrna Beach. 23Septernber 2006. Collected by Stacy Simmons. Verified by Kenneth L. Krysko, Florida Museum ofN atural History, University of Florida. One individual found on floor of residence. UF 151313. First county record. Originally turned in to Division of Plant Industry (DPI) , Florida Department of Agriculture and Consumer Services, Gainesville, Florida, as a "worm for ID" on 27 September 2006; Entomology Log No. 6879. It is not clear if this single specimen indicates an established breeding colony in this county. However, this invasive, parthenogenic exotic is established in other Florida …

Eastward Ho: Phylogeographical Perspectives On Colonization Of Hosts And Parasites Across The Beringian Nexus [Guest Editorial], Eric Waltari, Eric P. Hoberg, Enrique P. Lessa, Joseph A. Cook

Harold W. Manter Laboratory of Parasitology: Faculty Publications

The response of Arctic organisms and their parasites to dramatic fluctuations in climate during the Pleistocene has direct implications for predicting the impact of current climate change in the North. An increasing number of phylogeographical studies in the Arctic have laid a framework for testing hypotheses concerning the impact of shifting environmental conditions on transcontinental movement. We review 35 phylogeographical studies of trans-Beringian terrestrial and freshwater taxa, both hosts and parasites, to identify generalized patterns regarding the number, direction and timing of trans-continental colonizations. We found that colonization across Beringia was primarily from Asia to North America, with many events …

Chlorophacinone Baiting For Belding’S Ground Squirrels, Craig A. Ramey, George H. Matschke, Richard M. Engeman

United States Department of Agriculture Wildlife Services: Staff Publications

The efficacy of using 0.01% chlorophacinone on steam-rolled oat (SRO) groats applied in CA alfalfa by spot-baiting/hand baiting around burrow entrances (~11.5 g) to control free-ranging Belding's ground squirrels (Spermophilus beldingi) were compared in 6 randomly assigned square treatment units (TUs). Four TUs were given the rodenticide and 2 treated with placebo bait. Each TU was a 0.4 ha square surrounded by a similarly treated 5.5 ha square buffer zone. Baits were applied on May 13 and re-applied, on May 20 and May 22, after 7 days of un-forecasted cool wet weather greatly reduced their above ground activity. Pesticide (EPA …

Parasites, Proteomics And Performance: Effects Of Gregarine Gut Parasites On Dragonfly Flight Muscle Composition And Function, Rudolf J. Schilder, James H. Marden

School of Biological Sciences: Faculty Publications

In previous work, we found that dragonflies infected with gregarine gut parasites have reduced muscle power output, loss of lipid oxidation in their flight muscles, and a suite of symptoms similar to mammalian metabolic syndrome. Here, we test the hypothesis that changes in muscle protein composition underlie the observed changes in contractile performance. We found that gregarine infection was associated with a 10-fold average reduction in abundance of a ~155·kDa fragment of muscle myosin heavy chain (MHC; ~206·kDa intact size). Insect MHC gene sequences contain evolutionarily conserved amino acid motifs predicted for calpain cleavage, and we found that calpain digestion …

Microarray Challenges In Ecology, Jan E. Kammenga, Michael A. Herman, N. Joop Ouborg, Loretta Johnson, Rainer Bretling

School of Biological Sciences: Faculty Publications

Microarrays are used to measure simultaneously the amount of mRNAs transcribed from many genes. They were originally designed for gene expression profiling in relatively simple biological systems, such as cell lines and model systems under constant laboratory conditions. This poses a challenge to ecologists who increasingly want to use microarrays to unravel the genetic mechanisms underlying complex interactions among organisms and between organisms and their environment. Here, we discuss typical experimental and statistical problems that arise when analyzing genome-wide expression profiles in an ecological context. We show that experimental design and environmental confounders greatly influence the identification of candidate genes …

Grânulos De Amido E Fitólitos Em Cálculos Dentários Humanos: Contribuição Ao Estudo Do Modo De Vida E Subsistência De Grupos Sambaquianos Do Litoral Sul Do Brasil, Verônica Wesolowski, Sheila Maria Ferraz Mendonça De Souza, Karl Reinhard, Gregório Ceccantini

Karl Reinhard Publications

Este artigo tem por objetivo apresentar os resultados da recuperação e análise de micro-vestígios vegetais retidos em cálculos dentários de grupos de pescadores-coletores do litoral sul do Brasil. Apresenta também os resultados das relações mantidas entre grânulos de amido e cárie, e entre fitólitos e desgaste dentário.

Através da dissolução química de cálculos dentários foram recuperados microvestígios vegetais em todos os indivíduos estudados. Foi evidenciado o consumo de alimentos amiláceos em todas as séries esqueléticas estudadas, demonstrando independência entre dieta com aporte de produtos vegetais e utilização de cerâmica. Foram encontrados resultados sugestivos de padrões de escolha de alimentos diferenciados …

Mist Netting Bias, Species Accumulation Curves, And The Rediscovery Of Two Bats On Montserrat (Lesser Antilles), Roxanne Larsen, Karen A. Boegler, Hugh H. Genoways, Will P. Masefield, Ronan A. Kirsch, Scott C. Pedersen

University of Nebraska State Museum: Mammalogy Papers

Mist nets are commonly used to survey bat populations and to estimate bat biodiversity, but several studies have found that mist net capture data and methods are biased due to a number of factors, including size and placement of nets, and the frequency at which investigators check their nets. Despite the wealth of literature and anecdotal reports, few investigators have quantified the interactions of bats with mist nets directly. We employed night vision camcorders to monitor bat behavior when bats encountered a mist net and then utilized these data to reevaluate years of survey data collected on Montserrat, Lesser Antilles. …

Hydrologic Connectivity And The Contribution Of Stream Headwaters To Ecological Integrity At Regional Scales, Mary C. Freeman, Catherine M. Pringle, C. Rhett Jackson

United States Geological Survey: Staff Publications

Cumulatively, headwater streams contribute to maintaining hydrologic connectivity and ecosystem integrity at regional scales. Hydrologic connectivity is the water-mediated transport of matter, energy and organisms within or between elements of the hydrologic cycle. Headwater streams compose over two-thirds of total stream length in a typical river drainage and directly connect the upland and riparian landscape to the rest of the stream ecosystem. Altering headwater streams, e.g., by channelization, diversion through pipes, impoundment and burial, modifies fluxes between uplands and downstream river segments and eliminates distinctive habitats. The large-scale ecological effects of altering headwaters are amplified by land uses that alter …

Vegetation Re-Establishment Of Mojave Desert Plant Communities After 2005-2006 Wildland Fires, E. Cayenne Engel, Scott R. Abella

Fire Science Presentations

Examine biotic and abiotic patterns that determine vegetative regrowth after wildfires to better inform land managers about what to expect after fires and how to manage restoration efforts.

Seeding Effectiveness For Eight Mojave Desert Perennials After A 2005 Wildfire, E. Cayenne Engel, Scott R. Abella, Christina L. Lund

Fire Science Presentations

To assess BLM seeding effectiveness in a mid-elevation burn where pre-burn plant communities were dominated by blackbrush, Joshua trees, and creosote.

Past, Present, And Future Old Growth In Frequent-Fire Conifer Forests Of The Western United States, Scott R. Abella, W. Wallace Covington, Peter Z. Fule, Leigh B. Lentile, Andrew J. Sanchez Meador, Penelope Morgan

Public Policy and Leadership Faculty Research

Old growth in the frequent-fire conifer forests of the western United States, such as those containing ponderosa pine (Pinus ponderosa), Jeffrey pine (P. jeffreyi), giant sequoia (Sequioa giganteum) and other species, has undergone major changes since Euro-American settlement. Understanding past changes and anticipating future changes under different potential management scenarios are fundamental to developing ecologically based fuel reduction or ecological restoration treatments. Some of the many changes that have occurred in these forests include shifts from historically frequent surface fire to no fire or to stand-replacing fire regimes, increases in tree density, increased abundance of fire-intolerant trees, decreases in understory …