Biology Commons^™

Gis-Based Analysis Of Ice-Breeding Seal Strandings In The Gulf Of Maine, David Harris Ph.D., Sat Gupta

Faculty Publications

Phoca groenlandica (harp seals) and Cystophora cristata (hooded seals), two species of ice-breeding seals, are being sighted more frequently onshore in the Gulf of Maine since 1990, but little is known about their behavior in this ecosystem. We obtained records of 904 ice-breeding seal stranding locations in the Gulf of Maine between 1996 and 2002 from NOAA Fisheries and used a geographic information system (GIS) to conduct group-wise comparisons by species (using non-parametric techniques), and to determine the predictors of high seal-stranding density (using ordinal logistic regression analysis). Compared to harp seals, hooded seals stranded closer to deep water, farther …

Nomenclatural Innovations In Neotropical Salicaeeae, Mac H. Alford

Faculty Publications

Macrothumia M. H. Alford is described as a new genus of Salicaceae based on Neosprucea kuhlmannii Steamer from Brazil. The deciduous perianth, papillate leaf teeth, presence of receptacular disk glands, and analyses of plastid DNA data Suggest that the new genus is more closely related to Ahernia Merrill and Pleuranthodendron. L. O. Williams than to Banara Aublet or Neosprucea Sleuruer. The monotypic genus Aphaerema Miers of Brazil and Argentina is transferred to Abatia Ruiz & Pavon, based on analyses of plastid DNA sequences and on the lack of morphological discontinuities between the genera. Because the name Abatia spicata (Turczaninow) …

Response Of Plethodon Cinereus To Chemical Cues From Different Numbers Of Conspecifics, Loren M. Hurst, Geoffrey R. Smith

Faculty Publications

No abstract provided.

Patterns Of Habitat Use By Bats Along A Riparian Corridor In Northern Utah, Duke S. Rogers, Mark C. Belk, Malinda W. González, Brent L. Coleman

Faculty Publications

We examined patterns of habitat use within a community of bats along the Provo River in Heber Valley, Utah. The landscape was divided into 5 habitat categories: riparian forest, wetland, agricultural field, edge, and a habitat restoration site. We used Anabat II bat detectors to record the number of echolocation calls per night within each habitat type as an index of bat activity. Echolocation calls were classified into foraging guilds based on acoustic traits, and we analyzed activity by entire community and by the 4 guilds related to habitat type and environmental variables. Activity was not significantly related to moon …

Avian Hosts For West Nile Virus In St. Tammany Parish, Louisiana, 2002, Nicholas Komar, Nicholas A. Panella, Stanley A. Langevin, Aaron C. Brault, Manuel Amador, Eric Edwards, Jennifer C. Owen

Faculty Publications

West Nile virus (WNV) infections in free-ranging birds were studied in Slidell, St. Tammany Parish, Louisiana, after a human encephalitis outbreak peaked there in July 2002. Seroprevalence in resident, free-ranging wild birds in one suburban site was 25% and 24% in August and October, respectively, indicating that most transmission had ceased by early August. Mortality rates, seroprevalence rates, host competence, and crude population estimates were used in mathematical models to predict actual infection rates, population impacts, and importance as amplifying hosts for several common passerine birds. Northern cardinal (Cardinalis cardinalis) and house sparrow (Passer domesticus) were the principal amplifying hosts, …

Applications Of Phylogenetics To Issues In Freshwater Crayfish Biology, Keith A. Crandall

Faculty Publications

Freshwater crayfish have served as model organisms for over 125 years in scientific research, from areas such as neurobiology and vision research to conservation biology and evolution. Recently, evolutionary histories in the form of phylogenies have served as a critical foundation for testing hypotheses in such diverse research areas as well. In this article, I review the amazing diversity of freshwater crayfish, especially in a phylogenetic context and explore how these evolutionary histories have informed crayfish biology and can be used powerfully in the future to guide research in a diversity of areas. Throughout the article, I draw on examples …

Structure Of Human Thymidylate Synthase Under Low-Salt Conditions, Leslie L. Lovelace, Wladek Minor, Lukasz Lebioda

Faculty Publications

Human thymidylate synthase, a target in cancer chemotherapy, was crystallized from PEG 3350 with 30 mM ammonium sulfate (AS) in the crystallization medium. The crystals are isomorphous with the high-salt crystals (~2.0 M AS) and the structure has been solved and refined (R = 22.6%, Rfree = 24.3%) at 1.8 Å resolution. The high- and low-AS-concentration structures are quite similar, with loop 181-197 is in the inactive conformation. Also, residues 95-106 and 129-135 (eukaryotic inserts region) show high mobility as assessed by poor electron density and high values of crystallographic temperature factors (residues 1-25 and 108-129 are disordered in both …

Soy Isoflavone Glycitein Protects Against Beta Amyloid-Induced Toxicity And Oxidative Stress In Transgenic Caenorhabditis Elegans, Astrid Gutierrez-Zepeda, Ross Santell, Zhixin Wu, Marishka Brown, Yanjue Wu, Ikhlas Khan, Christopher D. Link, Baolu Zhao, Yuan Luo

Faculty Publications

Background

Epidemiological studies have associated estrogen replacement therapy with a lower risk of developing Alzheimer's disease, but a higher risk of developing breast cancer and certain cardiovascular disorders. The neuroprotective effect of estrogen prompted us to determine potential therapeutic impact of soy-derived estrogenic compounds. Transgenic C. elegans, that express human beta amyloid (Aβ), were fed with soy derived isoflavones genistein, daidzein and glycitein (100 μg/ml) and then examined for Aβ-induced paralysis and the levels of reactive oxygen species.

Results

Among the three compounds tested, only glycitein alleviated Aβ expression-induced paralysis in the transgenic C. elegans. This activity of …

Toward Sequencing The Sorghum Genome: A U.S. National Science Foundation-Sponsored Workshop Report, Stephen Kresovich, Brad Barbazuk, Joseph A. Bedell, Andrew Borrell, C. Robin Buell, John Burke, Sandra Clifton, Marie-Michéle Cordonnier-Ptratt, Stan Cox, Jeff Dahlberg, John Erpelding, Theresa M. Fulton, Bob Fulton, Lucinda Fulton, Alan R. Gingle, C. Tom Hash, Yinghua Huang, David Jordan, Patricia E. Klein, Robert R. Klein, Jurandir Magalhaes, Richard Mccombie, Paul Moore, John E. Mullet, Peggy Ozias-Akins, Andrew H. Paterson, Kay Porter, Lee Pratt, Bruce Roe, William Rooney, Patrick S. Schnable, David M. Stelly, Mitchell Tuinstra, Doreen Ware, Ujwala Warek

Faculty Publications

Members of the worldwide sorghum (Sorghum spp.) community, including private sector and international scientists as well as community representatives from closely related crops such as sugarcane (Saccharum spp.) and maize (Zea mays), met in St. Louis, Missouri, on November 9, 2004, to lay the groundwork for future advances in sorghum genomics and, in particular, to coordinate plans for sequencing of the sorghum genome. Key developments that made this workshop timely included advances in knowledge of the sorghum genome that provide for the development of a genetically anchored physical map to guide sequence assembly and annotation, the …

Photochemical Transformations Of Riverine Dissolved Organic Matter: Effects On Estuarine Bacterial Metabolism And Nutrient Demand, Erik M. Smith, Ronald Benner

Faculty Publications

By experimentally simulating the exposure of terrigenous dissolved organic matter (DOM) to sunlight during the mixing of river water and seawater in an estuary (St. Helena Sound, South Carolina), this study examined how photochemical alterations may affect both the magnitude and fate of DOM utilization by estuarine bacteria. In a series of experiments performed with water samples collected from 3 blackwater rivers draining into an estuary of the South Atlantic Bight (USA), exposure to light resulted in significant decreases in dissolved organic carbon (DOC) concentration and DOM absorption at 350 nm relative to dark controls. When these water samples were …

Ecotypic Variation In Phosphorus Acquisition Mechanisms Within Marine Picocyanobacteria, Lisa Moore Phd, M. Ostrowski, D. J. Scanlan, K. Feren, T. Sweetsir

Faculty Publications

Prochlorococcus and Synechococcus are major prokaryotic primary producers in the oligotrophic oceans that may be affected by the climate-related increases in nitrogen fixation and subsequent phosphorus (P) limitation in some parts of the oceans. Evidence that Prochlorococcus populations in the North Pacific subtropical gyre (NPSG) have increased over the past decades, possibly due to having a competitive advantage under conditions of P limitation, suggests aspects of their Pphysiology that are important for dictating their in situ success. Here, we compared the physiology of P acquisition and response to P stress (indicated by alkaline phosphatase activity, APA) among isolates of Prochlorococcus …

Effects Of Density On Timing Of Emergence And Its Consequences For Survival And Growth In Two Communities Of Annual Plants, Roy Turkington, Deborah E. Goldberg, Linda Olsvig-Whittaker, Andrew R. Dyer

Faculty Publications

We tested whether increasing seed density results in a change in the timing of emergence in two communities of sand dune annual plants in Israel. Specifically we tested (i) if emergence is accelerated or delayed due to high seed density. We also tested two predictions about the consequences of changes in the timing of emergence; (ii) seedlings emerging earlier will have higher survival and growth; (iii) the advantage of earlier emergence increases as seed density increases. We examined these predictions for both monocots and dicots growing under different irrigation regimes and using species from a desert and a semi-arid community …

Consequences Of The Historical Demography On The Global Population Structure Of Two Highly Migratory Cosmopolitan Marine Fishes: The Yellowfin Tuna (Thunnus Albacares) And The Skipjack Tuna (Katsuwonus Pelamis), Bert Ely, Jordi Viñas, Jaime R. Alvarado Bremer, Donna Black, Luciano Lucas, Kelly Covello, Alexis V. Labrie, Eric Thelen

Faculty Publications

Background

Yellowfin and skipjack tuna are globally distributed in the world's tropical and sub-tropical oceans. Since little, if any, migration of these fishes occurs between the Atlantic and Indo-Pacific Oceans, one might expect to see genetic differences between sub-populations in these ocean basins. However, yellowfin and skipjack tuna have extremely large population sizes. Thus, the rate of genetic drift should be slower than that observed for other tunas.

Results

Low levels of genetic differentiation were observed between Atlantic and Pacific samples of yellowfin tuna. In contrast, no genetic differentiation was observed between Atlantic and Pacific samples of skipjack tuna.

Conclusion …

Abejas Altoandinas De Colombia: Guía De Campo, Victor H. Gonzalez, Monica Ospina, Daniel J. Bennett

Faculty Publications

This guide is a contribution to the knowledge and conservation of bees, a group of very interesting and unknown to Colombia insects. Alrededor de 70 especies, agrupadas en 25 géneros habitan los Andes colombianos por encima de los 2.500 msnm. About 70 species, grouped in 25 genera inhabit the Colombian Andes above 2,500 meters. De éstas, por lo menos 15, son especies nuevas para la ciencia o están en proceso de descripción. Of these, at least 15 are new to science or are in the process of describing species. Igualmente, la guía busca incrementar la conciencia sobre la importancia de …

Antifungal Activity Of Camptothecin, Trifolin, And Hyperoside Isolated From Camptotheca Acuminata, Shiyou Li, Zhizhen Zhang, Abigail Cain, Bo Wang, Melissa Long, Josephine Taylor

Faculty Publications

Leaf spots and root rots are major fungal diseases in Camptotheca acuminata that limit cultivation of the plant for camptothecin (CPT), a promising anticancer and antiviral alkaloid. Bioassays showed that pure CPT and flavonoids (trifolin and hyperoside) isolated from Camptotheca effectively control fungal pathogens in vitro, including Alternaria alternata, Epicoccum nigrum, Pestalotia guepinii, Drechslera sp., and Fusarium avenaceum, although antifungal activity of these compounds in the plant is limited. CPT inhibited mycelial growth by approximately 50% (EC₅₀) at 10−30 μg/mL and fully inhibited growth at 75−125 μg/mL. The flavonoids were less effective than CPT …

A Survey Of Anuran Breeding Activity In Illinois, 1986-1989, Justin Florey, Stephen J. Mullin

Faculty Publications

tAmphibian populations have been declining worldwide, with several documented specie extinctions in the past two decades. Although monitoring population health can presen challenges, surveys of breeding choruses are relatively effective methods for assessing populations and population trends of many frog and toad species. We analyzed data from breeding chorus surveys conducted throughout Illinois from 1986 to 1989. Of the 20 species native to Illinois, 9 were stable or increasing during the survey period whereas the trends for other species were either inconsistent or indicated a decline in population size. To better assess population trends for Illinois frogs, we advocate re …

Evaluation Of A New Method For Measuring Salamanders, Leroy J. Walston, Stephen J. Mullin

Faculty Publications

Collection of morphometric data is essential to many field studies of amphibian populations. One of the most common measurements obtained from salamanders is snout-to-vent length (SVL), a parameter useful in studies of sexual dimorphism (Bovero et al. 2003), demography (Semlitsch 1985), and systematics (Carlin 1997). Measuring salamander lengths in the field is challenging because of their small size, slimy texture, and propensity to maintain a nonlinear body position. Time expenditure is another concern, especially when researchers process large numbers of salamanders. Different measurement techniques vary in accuracy and precision, limiting the reliability of the data so that comparisons cannot be …

Allometry, Sexual Size Dimorphism, And Niche Partitioning In The Mediterranean Gecko (Hemidactylus Turcicus), James B. Johnson, Lance D. Mcbrayer, Daniel Saenz

Faculty Publications

Hemidactylus tucrius is a small gekkonid lizard native to the Middle East and Asia that is known to exhibit sexual dimorphism in head size. Several potential explanations exist for the evolution and maintenance of sexual dimorphism in lizards. We tested 2 of these competing hypotheses concerning diet partitioning and differential growth. We found no differences in Average meal size (volume) or in any single dimension of prey size for similarly sized males and females. allometric patterns of increases in head size also were measured in males and females. We found that males exhibited a mixture of isometric and positively allometric …

The Malagasy Endemic Dendroportulaca (Portulacaceae) Is Referable To Deeringia (Amaranthaceae): Molecular And Morphological Evidence [Abstract], Wendy L. Applequist, Donald B. Pratt

Faculty Publications

No abstract provided.

Arrival Timing And Seasonal Reproductive Performance In A Long-Distance Migratory Landbird, Robert J. Smith, Frank R. Moore

Faculty Publications

The date when a landbird migrant arrives on its breeding grounds may have reproductive consequences. Generally, early arriving individuals begin breeding earlier and consequently experience greater seasonal reproductive performance. Here, we describe relationships between arrival timing and seasonal reproductive performance in the American redstart (Setophaga ruticilla), a long-distance passerine migrant, arriving at northerly breeding grounds in Michigan’s eastern Upper Peninsula. Evidence suggests that both males and females benefited from early arrival at the breeding grounds. Early males appeared to settle on higher quality territories and hatched nestlings sooner than later arrivals. Early females began their clutches early, produced …

Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, D. Kihara

Faculty Publications

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy …

An Experimental Study Of Substrate Selection In American Toad (Bufo Americanus) Metamorphs, Geoffrey R. Smith

Faculty Publications

No abstract provided.

Survivorship Of Xenosaurus Newmanorum (Sauria: Xenosauridae) From A Seasonal Tropical Environment In Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith, R. E. Ballinger

Faculty Publications

No abstract provided.

Neglected Taxonomy Of Rare Desert Fishes: Congruent Evidence For Two Species Of Leatherside Chub, Jerald B. Johnson, Thomas E. Dowling, Mark C. Belk

Faculty Publications

Conservation biologists rely heavily on taxonomy to set the scope for biological monitoring and recovery planning of rare or threatened species. Yet, taxonomic boundaries are seldom evaluated as falsifiable hypotheses that can be statistically tested. Here, we examine species boundaries in leatherside chub (Teleostei, Cyprinidae), an imperiled desert fish native to the Bonneville Basin and upper Snake River drainages of western North America. Recent molecular data hint that this fish could be composed of two distinct taxa that are geographically separated into northern and southern species. To formally test this hypothesis, we evaluated leatherside chub using several different categories of …

Testing Species Boundaries In An Ancient Species Complex With Deep Phylogeographic History: Genus Xantusia (Squamata: Xantusiidae), Keith A. Crandall, Elizabeth A. Sinclair, Robert L. Bezy, Kathryn Bolles, Jose L. Camarillo, Jack W. Sites

Faculty Publications

Identification of species in natural populations has recently received increased attention with a number of investigators proposing rigorous methods for species delimitation. Morphologically conservative species (or species complexes) with deep phylogenetic histories (and limited gene flow) are likely to pose particular problems when attempting to delimit species, yet this is crucial to comparative studies of the geography of speciation. We apply two methods of species delimitation to an ancient group of lizards (genus Xantusia) that occur throughout southwestern North America. Mitochondrial cytochrome b and nicotinamide adenine dinucleotide dehydrogenase subunit 4 gene sequences were generated from samples taken throughout the geographic …

Genetic Diversity Of Peanut (Arachis Hypogaea L.) And Its Wild Relatives Based On The Analysis Of Hypervariable Regions Of The Genome, Marcio De Carvalho Moretzsohn, Mark S. Hopkins, Sharon E. Mitchell, Stephen Kresovich, Jose Francisco Montenegro Valls, Marcio Elias Ferreira

Faculty Publications

Background: The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors …

Zapus Princeps, E. Blake Hart, Mark C. Belk, Eralee Jordan, Malinda W. Gonzalez

Faculty Publications

Zapus princeps Allen, 1893:71. Type locality “Florida, La Plata Co., Colorado.”
Zapus pacificus Merriam, 1897:104. Type locality “Prospect, Rogue River Valley, Jackson Co., Oregon.”
Zapus saltator Allen, 1899:3. Type locality “Telegraph Creek, British Columbia.”

Constraints On Adaptive Evolution: The Functional Trade-Off Between Reproduction And Fast-Start Swimming Performance In The Trinidadian Guppy (Poecilia Reticulata), Cameron K. Ghalambor, David N. Reznick, Jeffrey A. Walker Phd

Faculty Publications

The empirical study of natural selection reveals that adaptations often involve trade-offs between competing functions. Because natural selection acts on whole organisms rather than isolated traits, adaptive evolution may be constrained by the interaction between traits that are functionally integrated. Yet, few attempts have been made to characterize how and when such constraints are manifested or whether they limit the adaptive divergence of populations. Here we examine the consequences of adaptive life-history evolution on locomotor performance in the live-bearing guppy. In response to increased predation from piscivorous fish, Trinidadian guppies evolve an increased allocation of resources toward reproduction. These populations …

A Patch Hath Smaller Patches: Delineating Ecological Neighborhoods For Parasites, Derek Zelmer, John R. Seed

Faculty Publications

Use of the host individual as a boundary for parasite populations and communities provides an unambiguous spatial unit that is useful for pattern description, but this framework precludes consideration of the host landscape and within-host population dynamics. Recognizing host individuals as spatially and temporally complex landscapes requires modified concepts of parasite populations and communities. An outline of the currently accepted hierarchies of parasite populations and communities is provided on the basis of ecological neighborhoods that are delineated by discrete habitat patches or functional dynamics (or both), as opposed to host individuals. This parasite-based framework accommodates consideration of both within- and …

The Impact Of Species Concept On Biodiversity Studies, Keith A. Crandall, Paul-Michael Agapow, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, Jonathon C. Marshall, Andy Purvis

Faculty Publications

Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the …