Biology Faculty Publications and Presentations

Phytochemistry Predicts Habitat Selection by an Avian Herbivore at Multiple Spatial Scales

Graham G. Frye et al. — Wed, 15 May 2013 14:49:49 PDT

Animal habitat selection is a process that functions at multiple, hierarchically structured spatial scales. Thus multi-scale analyses should be the basis for inferences about factors driving the habitat selection process. Vertebrate herbivores forage selectively on the basis of phytochemistry, but few studies have investigated the influence of selective foraging (i.e., fine-scale habitat selection) on habitat selection at larger scales. We tested the hypothesis that phytochemistry is integral to the habitat selection process for vertebrate herbivores. We predicted that habitats selected at three spatial scales would be characterized by higher nutrient concentrations and lower concentrations of plant secondary metabolites (PSMs) than unused habitats. We used the Greater Sage-Grouse (Centrocercus urophasianus), an avian herbivore with a seasonally specialized diet of sagebrush, to test our hypothesis. Sage-Grouse selected a habitat type (black sagebrush, Artemisia nova) with lower PSM concentrations than the alternative (Wyoming big sagebrush, A. tridentata wyomingensis). Within black sagebrush habitat, Sage-Grouse selected patches and individual plants within those patches that were higher in nutrient concentrations and lower in PSM concentrations than those not used. Our results provide the first evidence for multi-scale habitat selection by an avian herbivore on the basis of phytochemistry, and they suggest that phytochemistry may be a fundamental driver of habitat selection for vertebrate herbivores.

A Pharm-Ecological Perspective of Terrestrial and Aquatic Plant-Herbivore Interactions

Jennifer Sorensen Forbey et al. — Wed, 15 May 2013 14:28:47 PDT

We describe some recent themes in the nutritional and chemical ecology of herbivores and the importance of a broad pharmacological view of plant nutrients and chemical defenses that we integrate as “Pharm-ecology”. The central role that dose, concentration, and response to plant components (nutrients and secondary metabolites) play in herbivore foraging behavior argues for broader application of approaches derived from pharmacology to both terrestrial and aquatic plant-herbivore systems. We describe how concepts of pharmacokinetics and pharmacodynamics are used to better understand the foraging phenotype of herbivores relative to nutrient and secondary metabolites in food. Implementing these concepts into the field remains a challenge, but new modeling approaches that emphasize tradeoffs and the properties of individual animals show promise. Throughout, we highlight similarities and differences between the historic and future applications of pharm-ecological concepts in understanding the ecology and evolution of terrestrial and aquatic interactions between herbivores and plants. We offer several pharm-ecology related questions and hypotheses that could strengthen our understanding of the nutritional and chemical factors that modulate foraging behavior of herbivores across terrestrial and aquatic systems.

Bromus tectorum Litter Alters Photosynthetic Characteristics of Biological Soil Crusts from a Semiarid Shrubland

Marcelo D. Serpe et al. — Tue, 30 Apr 2013 12:07:44 PDT

Invasion by the exotic annual grass Bromus tectorum has increased the cover and connectivity of fine litter in the sagebrush steppes of western North America. This litter tends to cover biological soil crusts, which could affect their metabolism and growth. To investigate this possible phenomenon, biological soil crusts dominated by either the moss Bryum argenteum or the lichen Diploschistes muscorum were covered with B.tectorum litter (litter treatment) or left uncovered (control treatment) and exposed to natural field conditions. After periods of five and ten months, we removed the litter and compared the photosynthetic performance of biological soil crusts from the two treatments. Litter induced photosynthetic changes in our samples. In bothB. argenteum and D. muscorum, biological soil crusts that had been covered with litter for ten months had lower rates of gross photosynthesis and lower chlorophyll content than control samples. Similarly in both biological soil crust types, litter reduced the rate of dark respiration. For D. muscorum, the reduction in dark respiration fully compensated for the decrease in gross photosynthesis, resulting in similar values of net photosynthesis in the two treatments. In contrast, for B. argenteum, net photosynthesis was four-times greater in the control than the litter treatment. Also under litter cover, D. muscorum showed three common adaptations to shade conditions: a decrease in the light compensation point, in the light intensity needed to achieve 95% of maximal net photosynthesis, and in the chlorophyll a/b ratio. None of these changes was apparent in B. argenteum. Overall, our results indicate that photosynthetic responses to the presence of litter varied among species of the crust biota and that the litter can reduce the photosynthetic capacity of biological soil crusts. These results help to explain field observations of decreases in biological soil crust cover and changes in biological soil crust composition with increases in litter cover, and suggest that the landscape-wide invasion by B. tectorum may have substantial effects on biological soil crust performance and therefore their capacity to function in semiarid shrublands.

The Triggering Receptor Expressed on Myeloid Cells 2: “TREM-ming” the Inflammatory Component Associated with Alzheimer's Disease

Troy T. Rohn — Thu, 04 Apr 2013 13:11:11 PDT

Alzheimer's disease (AD) is an age-related neurodegenerative disorder characterized by a progressive loss of memory and cognitive skills. Although much attention has been devoted concerning the contribution of the microscopic lesions, senile plaques, and neurofibrillary tangles to the disease process, inflammation has long been suspected to play a major role in the etiology of AD. Recently, a novel variant in the gene encoding the triggering receptor expressed on myeloid cells 2 (TREM2) has been identified that has refocused the spotlight back onto inflammation as a major contributing factor in AD. Variants in TREM2 triple one's risk of developing late-onset AD. TREM2 is expressed on microglial cells, the resident macrophages in the CNS, and functions to stimulate phagocytosis on one hand and to suppress cytokine production and inflammation on the other hand. The purpose of this paper is to discuss these recent developments including the potential role that TREM2 normally plays and how loss of function may contribute to AD pathogenesis by enhancing oxidative stress and inflammation within the CNS. In this context, an overview of the pathways linking beta-amyloid, neurofibrillary tangles (NFTs), oxidative stress, and inflammation will be discussed.

Population Dynamics of the Southern Short-Tailed Opossum (Monodelphis dimidiata) in the Pampas of Argentina

Alejandro V. Baladrón et al. — Fri, 22 Feb 2013 13:57:35 PST

The genus Monodelphis is one of the most species rich among Neotropical marsupials. Despite this, little is known about most of the species. One of the most enigmatic species is M. dimidiata, a small terrestrial opossum that inhabits the Pampean region of Argentina, which is suspected to be a semelparous breeder. From 2005 to 2008, we conducted seasonal live trapping in near-pristine marshy grasslands and agroecosystems of the Pampean region in order to evaluate the population trends of this species and the occurrence of semelparity. M. dimidiata was characterised by a low abundance in the study area. The average density was higher in grasslands than in agroecosystems, and it appeared to be influenced by vegetative cover. The onset of the breeding season occurred during spring when the opossums showed a sudden increase in body size. Given that mature individuals were not found beyond autumn, the findings suggest an annual cycle for this species. In addition, this abrupt maturation resulted in a pronounced sexual dimorphism that, together with the strong reproductive seasonality and a likely polygynous mating system, supported previous claims that the species is semelparous. Our results also emphasise the importance of native grassland habitat for the maintenance of stable populations of M. dimidiata.

Variation in Root Architecture Among Switchgrass Cultivars Impacts Root Decomposition Rates

Marie-Anne de Graaff et al. — Fri, 22 Feb 2013 13:43:37 PST

Roots regulate soil carbon (C) input, but fine root decomposition rates and root impacts on soil organic C turnover (SOC) are uncertain. This uncertainty is, partly, caused by the heterogeneity of root systems, which vary in diameter distributions and tissue chemistry. Here, we evaluated how root diameter distributions affect root and SOC decomposition. Roots from eight Panicum virgatum (switchgrass) cultivars were analyzed for root diameter size-class distribution and C:N ratio. Roots from each cultivar were mixed with C₃ soil according to five root diameter treatments: (1) 0–0.5 mm, (2) 0.5–1 mm, (3) 1–2.5 mm, (4) a 1:1:1 mixture of roots from each diameter size class, and (5) a mixture combining diameter classes in proportions representing measured size distributions for each cultivar. All treatments were incubated for 90 days under laboratory conditions. Respired CO₂ was measured throughout and the microbial community structure was measured at termination of the experiment. Carbon-13 isotope techniques were used to partition respiration into root-derived C versus native SOC-derived C. Results indicated: (1) specific root length differed among the cultivars, (2) root decomposition rates within the three size classes varied by cultivar, but were not correlated with cultivar differences in root C:N ratios, (3) root diameter size class affected root and SOC decomposition, and (4) mixing roots of different diameters did not lead to synergistic increases in decomposition. We conclude that intraspecific variation in root architecture is significant and that fine root diameter size class distribution is an important trait for shaping decomposition processes.

New Species of Spartiella and Legeriosimilis from Mayflies and Other Arthropod-Associated Trichomycetes from Nova Scotia, Canada

Merlin M. White et al. — Fri, 22 Feb 2013 12:56:38 PST

The digestive tracts of non-predaceous, aquatic insects and other arthropods living in moist habitats harbour a group of fungal and protistan microorganisms known as trichomycetes or “gut fungi”. A former class of Zygomycota, “trichomycetes” now refers to an ecological group of gut microbes. This report adds to the growing inventory of gut fungi that have been described from Atlantic Canada, with two new fungal trichomycetes, Legeriosimilis hiemalis sp. nov. Strongman and M.M. White and Spartiella aurensis sp. nov. Strongman and M.M. White, both from Ephemeroptera (mayfly) nymphs. Legeriosimilis hiemalis is now the fourth of seven known species of the genus to be recorded only from Canadian sites. Spartiella aurensis displays an unusual feature, with thalli apparently able to grow from the hindgut back into the midgut of its host, a growth pattern not typically observed in other gut fungi. The potential significance of this development is discussed. Despite the focus on immature freshwater insects and their habitats, we also record a species of Orchesellaria from Collembola (springtails) and Astreptonema corophii from the amphipod crustacean Corophium volutator.

New Species of Smittium and Stachylina and Other Trichomycetes in Larval Diptera from Streams in Nova Scotia, Canada

Merlin M. White et al. — Fri, 22 Feb 2013 12:53:12 PST

The guts of non-predaceous invertebrates in aquatic and moist terrestrial habitats are often colonized by an ecological group of microorganisms called trichomycetes. Taxonomically, these endobionts are currently a diverse, polyphyletic assemblage including both zygomycetous fungi as well as protistan species. Trichomycetes are worldwide in distribution and are from varied habitats, but the species inventory of gut fungi from hosts in Canada is far from complete. We summarize the findings from our earliest surveys (from 1997 to 2005) and collections of candidate dipteran hosts in Nova Scotia. Nine new species of gut fungi are added to the inventory list, including the following seven Smittium spp.: Smittium aggregatum, Smittium gronthidium, Smittium papillum, Smittium pavocaudatum, Smittium radiculans, Smittium sparsum, and Smittium verticillatum, and the following two Stachylina spp.: Stachylina brevicellaris and Stachylina subgrandis. Four of the other 13 Harpellales, Pennella digitata, Smittium megazygosporum, Stachylina penetralis, and Zancudomyces culisetae are reported for the first time in Atlantic Canada. Also recorded is Paramoebidium curvum, with many more specimens of this genus from various locations and hosts included as Paramoebidium spp. only. We suggest that future collections of Diptera, to further document and discover trichomycetes, are warranted across the varied host habitats that abound not only in eastern Canada but the rest of the country as well.

When DNA Won't Work

Rick Visser et al. — Wed, 30 Jan 2013 12:24:18 PST

Within the criminal justice system, DNA (deoxyribonucleic acid) evidence has often been heralded as the gold standard of forensic science. In a 2009 U.S. Supreme Court decision, Chief Justice Roberts wrote that "DNA testing has an unparalleled ability both to exonerate the wrongly convicted and to identify the guilty. It has the potential to significantly improve both the criminal justice system and police investigative practices." The phrases “unparalleled ability” and “significantly improve” reflect the high standard that DNA has attained in both forensic science and the entire criminal justice system.

Forensic DNA technology has a major advantage over other forensic science fields because of its reliance on statistics and its historical development from medical science, which relies on double-blind testing, error analysis, and rigorous peer review. These factors distinguish DNA analysis from other forms of forensic analysis such as fingerprinting, ballistics, trace evidence, forensic anthropology (bones), handwriting analysis, and others. But every analytical field has its limits, and can be misappropriated. This article summarizes some of the key areas where the use of forensic DNA can be improved and includes proposed remedies.

Homoploid Hybrid Speciation in a Rare Endemic Castilleja from Idaho (Castilleja christii, Orobanchaceae)

Danielle L. Clay et al. — Wed, 30 Jan 2013 11:56:00 PST

• Premise of the study: Hybridization is an important evolutionary force in the history of angiosperms; however, there are few examples of stabilized species derived through homoploid hybrid speciation. Homoploid hybrid species are generally detected via the presence of genetic additivity of parental markers, novel ecological and spatial distinctions, and novel morphological traits, all of which may aid in the successful establishment of hybrid species from parental types. Speciation and diversification within the genus Castilleja (Orobanchaceae) has been attributed to high levels of hybridization and polyploidy, though currently there are no examples of homoploid hybrid speciation within the genus. We employed multiple lines of evidence to examine a putative hybrid origin in C. christii, a rare endemic, known only from 80 hectares at the summit of Mt. Harrison (Cassia Co., Idaho).

• Methods: We used granule-bound starch synthase II (waxy) sequences and 26 morphological characters to address hybridization between C. christii and widespread congeners C. miniata and/or C. linariifolia in an area of sympatry. Chromosomes of C. christii were also counted for the first time.

• Key results: All 230 direct-sequenced C. christii individuals had the additive genomes of both C. miniata and C. linariifolia. Castilleja christii shares traits with both parents but also has floral characters that are unique and transgressive. Cytological counts indicated that all three taxa are diploid.

• Conclusions: We conclude that C. christii is a stabilized homoploid hybrid derivative of C. linariifolia and C. miniata and is likely following an independent evolutionary trajectory from its progenitors.

Is Macroinvertebrate Drift a Density-Dependent Mechanism of the Benthos in the Lower Mississippi River?

Peter Koetsier et al. — Tue, 15 Jan 2013 10:30:12 PST

In the lower Mississippi River, we sampled drifting and benthic macroinvertebrates each month from November, 1984 to June, 1985. Drift was dominated by hydroids, Chaoborous punctipennis (Diptera), Taphromysis louisianae (Mysidacea), and decapod shrimp. The chief components of the benthic community were tubificid oligochaetes and chironomids. The species composition of the drift was significantly different from that of the benthos, for all but one month. We concluded that drift is not a density-dependent function of the bottom fauna in the lower Mississippi River. This information adds strength to the argument that, in very large rivers, drift may be a separate community from the benthos.

Benthos and Macroinvertebrate Drift in Six Streams Differing in Alkalinity

Peter Koetsier et al. — Tue, 15 Jan 2013 10:24:38 PST

The productive capacity of aquatic systems often is equated with the 'chemical richness' of the water. A primary objective of the present study was to relate macroinvertebrate benthos and drift to a streams' productive capacity as indicated by absolute levels of alkalinity. We tested this relationship in six 2nd–3rd order tributaries of the Salmon River, Idaho that ranged in alkalinity from 50 to 360 mg 1⁻¹. Benthic density and biomass, drift biomass, and benthic organic matter increased with increasing levels of alkalinity, although not all relationships were significant. The proportion of drift biomass to benthic biomass was similar among study streams suggesting that drift was primarily passive during the study period. The data suggest that spatial variations in landscape-scale geology may indirectly affect spatial patterns of macroinvertebrate benthic and drift standing crops among streams within a single river basin by mediating lotic chemical richness as found among tributaries of the Salmon River basin.

Short Term Benthic Colonization Dynamics in an Agricultural Stream Recovering from Slaughterhouse Effluents

Peter Koetsier — Mon, 14 Jan 2013 14:50:11 PST

The purpose of this study was to assess short term, macroinvertebrate colonization dynamics and biofilm accumulation in two agricultural streams, one of which had been recently exposed to chronic, intermittent organic effluents from a slaughterhouse. During the winter and summer, macroinvertebrates and biofilm were collected from brick substrates from four or three sites in the streams on a geometric time schedule (1, 2, 4, 8, 16, and 32 days of exposure). Invertebrate total densities stabilized quickly, but the mass of biofilm increased throughout the study periods. Invertebrate community indices (diversity, evenness, dominance, richness) differed between the unaffected, "agricultural reference" sites and the affected sites, below the point source. All sites were dominated by Baetis bicaudatus (mayfly), Hydrobia sp. (gastropod), and Dugesia tigrina (Turbellaria). Response of these taxa differed between seasons and exposure to organic effluents. Stream invertebrate colonization processes showed evidence of the perturbation after the inflow of organic effluents had stopped from the slaughterhouse. Chronic organic enrichment reduced the species richness in the potential pool of colonists. Three months after the organic inputs had stopped, colonization timing and community structure was not yet at levels evident in reference and upstream sites.

Response of a Stream Diatom Community to Top Predator Manipulations

Peter Koetsier — Mon, 14 Jan 2013 14:32:23 PST

I investigated the effects top predator manipulations have on the community structure of benthic diatoms in a small, third-ordered stream ecosystem. Following the concept of trophic cascades in food webs, changes in top predator abundance should, via herbivore elimination, influence community metrics and species composition of stream periphyton. Using in situ stream enclosures, I varied the density of two common stream predators, sculpin and a perlid stonefly larva. Over three weeks, in three seasons, I sampled both invertebrate prey and diatoms from tiles placed in each enclosure. Diatoms did respond to predator manipulations. Changes in diversity, species richness, evenness, and dominance varied with treatment and between seasons. Cluster analysis showed pronounced assemblage dissimilarities before and after predator manipulations. However, species composition did not change between treatments, though rankings of the ten most abundant species did shift. Top predators can alter the community composition and structure of stream benthic algae indirectly through grazer suppression and directly by disruption due to foraging activity. This study demonstrates that top predators can impact nonadjacent trophic levels and that predator type and abundance should be considered when comparing diatom communities temporally and spatially.

The Life History of the Utah (Desert) Valvata, Valvata utahensis, in the Snake River, Idaho

Steven Lysne et al. — Mon, 14 Jan 2013 14:26:27 PST

We describe the life history of the Utah (desert) valvata (Valvata utahensis, Call 1884) based on original research, field collected information, and review of the available literature. We report here the description, feeding, reproductive biology, life cycle, habitat use, and distribution and status of V. utahensis in the Snake River of southern Idaho, USA.

Caspase-Cleaved Glial Fibrillary Acidic Protein Within Cerebellar White Matter of the Alzheimer's Disease Brain

Troy T. Rohn et al. — Thu, 03 Jan 2013 13:43:31 PST

Although the cerebellum is generally thought of as an area spared of Alzheimer's disease (AD) pathology, recent evidence suggests that balance and mobility dysfunction may be magnified in affected individuals. In the present study, we sought to determine the degree of pathological changes within the cerebellum utilizing an antibody that specifically detects caspase-cleaved GFAP within degenerating astrocytes. Compared to control subjects, application of this antibody, termed the GFAP caspase-cleavage product (GFAPccp) antibody, revealed widespread labeling in cerebellar white matter with little staining observed in grey matter. Staining was observed within damaged astrocytes, was often localized near blood vessels and co-localized with other markers of apoptosis including TUNEL and caspase-cleaved tau. Of interest was the association of beta-amyloid deposition in white matter together with GFAPccp in cerebellar AD sections. In contrast, utilizing the tangle marker, PHF-1, neuritic pathology was completely absent in AD cerebellar sections. It is suggested that the observed pathological changes found in the white matter of the cerebellum may contribute to the declined motor performance in AD.

GOFAST: An Integrated Approach for Efficient and Comprehensive Membrane Proteome Analysis

Yanbao Yu et al. — Mon, 17 Dec 2012 15:34:50 PST

Membrane proteomics, the large-scale analysis of membrane proteins, is often constrained by the difficulties of achieving fully resolvable separation and resistance to proteolysis, both of which could lead to low recovery and low identification rates of membrane proteins. Here, we introduce a novel integrated approach, GELFrEE Optimized FASP Technology (GOFAST) for large-scale and comprehensive membrane proteins analysis. Using an array of sample preparation techniques including gel-eluted liquid fraction entrapment electrophoresis (GELFrEE), filter-aided sample preparation (FASP), and microwave-assisted on-filter enzymatic digestion, we identified 2 090 proteins from the membrane fraction of a leukemia cell line (K562). Of these, 37% are annotated as membrane proteins according to gene ontology analysis, resulting in the largest membrane proteome of leukemia cells reported to date. Our approach combines the advantages of GELFrEE high-loading capacity, gel-free separation, efficient depletion of detergents, and microwave-assisted on-filter digestion, minimizing sample losses and maximizing MS-detectable sequence coverage of individual proteins. In addition, this approach also shows great potential for the identification of alternative splicing products.

Spatial and Temporal Response of Stream Bacteria to Sources of Dissolved Organic Carbon in a Blackwater Stream System

Peter Koetsier et al. — Fri, 07 Dec 2012 14:33:04 PST

1. We hypothesized that changes in bacterial colony growth would be correlated to shifts in riparian vegetation (via leachate quality) along a river continuum of a south-eastern, blackwater stream (U.S.A.). Spatially, we expected bacterial assemblages from downstream reaches to utilize more sources of leachate and at higher concentrations than bacteria collected from headwater reaches. Temporally, we predicted higher colony growth on leachate from autumn-shed (senescent) leaves compared with leachate from fresh, green leaves.

2. We examined spatial differences in assemblage growth by culturing bacteria sampled along the stream continuum on gradient plates using leachates from four common riparian species (Taxodium distichum, Carya spp., Acer rubrum and Decumaria barbara). Bacteria from the lowest site were able to use all sources provided and at all concentrations, whereas bacteria from upper reaches could not. Colony density was correlated to relative leachate concentration at all sites along the continuum.

3. Leachates from fresh and senescent A. rubrum leaves were used to determine temporal differences. Winter assemblages of bacteria could not grow on fresh leaf leachate at any concentration but grew well on autumn leaf leachate at higher concentrations. Differential response of bacterial assemblages indicated local adaptation to potential sources of dissolved organic matter.

4. Growth response of stream bacterial colonies appeared to be dependent on the timing and source of leachate as well as on sources of dissolved organic carbon from further upstream. Growth of bacterial assemblages exhibited ‘generalist’ characteristics in headwater reaches and ‘specialist’ characteristics at the mouth of our study stream drainage. Thus, our findings lend support to the argument that variable resource habitats favour a small, generalist assemblage, while environments with stable resource supplies allow for highly diverse assemblages dominated by specialists.

The Effects of Disturbance Time Interval on Algal Biomass in a Small Idaho Stream

Peter Koetsier — Fri, 07 Dec 2012 11:45:20 PST

An experiment was designed to test the potential effect that disturbance frequency may have on benthic algal accumulation in a stream ecosystem. The stream was divided into segments. After measuring algal biomass in each segment, the stream substrate was left undisturbed, or physically disturbed once or twice per month. The highest levels of algal biomass were found in the segments that had the short between-disturbance intervals. Intervals may have been short enough to allow r-selected algal species to re-colonize, flourish and maximize biomass potential. Possible explanations for these results may be an increase in nutrient availability by the removal of senescent or competitor algal cells and the change to a disturbance-resistant community, or a release from invertebrate grazing as disturbance frequency increased.

Present Effects of Past Wildfires on the Diets of Stream Fish

Peter Koetsier et al. — Fri, 07 Dec 2012 11:20:40 PST

We investigated present indirect effects from a decade-old burn on the diets of stream fish. Based on soil instability and burn patterns from a 12–14-year-old wildfire complex, we separated 9 streams into 3 conditions: unburned, burned, and burned/scoured (i.e., experiencing a massive scour event 1 year post-burn). In the streams, we measured light levels and water temperatures, and we estimated fish density and biomass. We removed the digestive tracts from 9–15 rainbow trout (Oncorhynchus mykiss) from each stream and used a gravimetric procedure to analyze gut contents. Canopy cover development may dictate the composition of dietary items. Greater amounts of aquatic invertebrates and inorganic material were found in trout from streams with reduced overhead canopy. Further, these streams had lower amounts of terrestrial invertebrates and organic materials in the diets of fish. Although trout abundance was not different among the stream treatments, fire-induced, indirect effects on fish diets were still evident more than a decade after the burn. This suggests that recovery rates for trout assemblages may take longer than predicted and may depend on riparian recovery.