Systems Biology Commons^™

Joint Fire Science Program – Lake Mead National Recreation Area Revegetating Burned Arid Lands: Identifying Successful Native Species Using Trait And Competition Analysis: Quarterly Progress Report, Time Period: May 1 — June 30, 2010, Margaret N. Rees

Fire Science

• Article entitled “Competitive Hierarchy of Native Desert Plants with Red Brome (Bromus rubens): Towards Identifying Invasion-Reducing Species" was submitted to the Invasive Plant Science and Management journal.
• Maintained nursery plots and added installment of nitrogen treatment.
• Took measurements in nursery (competition) plots and harvested biomass.

Comparison Of Two Zooplankton Sampling Gears In Shallow, Homogeneous Lakes, Maude E. Livings, Casey W. Schoenebeck, Michael L. Brown

The Prairie Naturalist

We compared two zooplankton collection gears, Wisconsin nets and column samplers, to evaluate the effectiveness of each gear in quantifying inshore and offshore zooplankton density and size structure in shallow, homogeneous lakes. Zooplankton densities (within gear) did not differ (P > 0.05) between inshore and offshore sites in either study lake, with the exception of Wisconsin-netted Cyclops sp. in Lake Goldsmith. Wisconsin net samples produced a higher mean zooplankton density than column samplers for Bosmina sp., Cyclops sp., and Daphnia sp. in East Oakwood Lake and for Cyclops sp. (inshore), Daphnia sp., and Diaptomus sp. in Lake Goldsmith. Zooplankton densities had …

Climatological Factors Influencing Yellow Perch Production In Semi-Permanent Wetlands, Christopher M. Longhenry, Michael L. Brown, Todd R. St. Sauver

The Prairie Naturalist

Climatological factors such as temperature, wind, and precipitation have been reported to affect fish reproduction and recruitment in large lakes; however, little is known about these relationships in shallow, semi-permanent wetlands. We utilized age-O yellow perch (Perca flavescens) aquacultural harvest data to model climate effects on variability of juvenile yellow perch year class strength in semi-permanent wetlands. Overall, March through May precipitation, April air temperature, and a wetland parameter (i.e., intrinsic characteristics) provided the best-supported model. These results potentially indicate that spring weather patterns have an influence on yellow perch year class strength in semi-permanent wetlands.

Ring-Necked Pheasant Nest Parasitism Of Sharp-Tailed Grouse Nests In Southwest North Dakota, Benjamin A. Geaumont, Kevin K. Sedivec, Christopher S. Schauer

The Prairie Naturalist

Numerous investigators have reported observations of ring-necked pheasant (RNP; Phasianus colchicus) eggs in nests of other gamebirds and waterfowl species (Errington and Hamerstrom 1938, Westemeier et al. 1998, Hagen et al. 2002, Krakauer and Kimball 2009). Previously recorded hosts include wild turkey (Meleagris gallopavo; Schmutz 1988), northern bobwhite (Colinus virginianus; Westemeier et al. 1989), greater prairie-chickens (Tyrnpanuchus cupido; Westemeier et al. 1998), and lesser prairie-chickens (T. pallidicinctus; Hagen et al. 2002). The reported occurrence of nest parasitism during these studies has generally been low with the highest reported occurrences found in …

In Situ Development Of Western Prairie Fringed Orchid Seeds, Protocorms, And Seedlings In Grazed And Non-Grazed Prairie Habitat, Bonnie Warner Alexander, Donald Kirby, Mario Biondini, Edward Dekeyser

The Prairie Naturalist

In 1989, the U.S. Fish and Wildlife Service listed the western prairie fringed orchid (Platanthera praeclara) as threatened. Although this orchid has been monitored for years, there is little scientific documentation of its biology, ecology, and phenology, nor the impacts of management activities on its populations. Our objectives were to document seed germination and seedling production rates after one year in situ, and compare seed germination in grazed and non-grazed prairie habitat in the Sheyenne National Grassland (SNG) in southeastern North Dakota. Of 18,717 planted seeds, we recovered 1,561 swollen embryos, 94 protocorms, and 51 seedlings. We documented no difference …

Early Winter Feeding On Elm Bark By Eastern Fox Squirrels Near The Western Range Terminus, Dessa K. Montgomery, Raymond S. Matlack

The Prairie Naturalist

Fox squirrels (Sciurus niger) feed on >30 different types of food across their extensive range ~Korschgen 1981) including tree buds, flowers, fruits, seeds, and, on occasion, bark. For a large portion of the year, fox squirrels rely heavily on tree seeds (Koprowski 1991). For three consecutive years (2007-2009), we observed fox squirrels feeding on bark of elm trees ( Ulmus sp.) on the campus of West Texas A&M University, Canyon, Texas. Squirrels began feeding on bark in late November shortly after leaves had fallen off the trees and continued almost daily throughout the winter. In late February, when …

Seed Production And Maturation Of The Western Prairie Fringed Orchid, Bonnie Warner Alexander, Donald Kirby, Mario Biondini, Edward Dekeyser

The Prairie Naturalist

A population of threatened western prairie fringed orchid (Platanthera praeclara) was selected in 2004 on the Sheyenne National Grassland in southeastern North Dakota to study seed production and maturation for future use in population viability modeling. We randomly collected 30 seed capsules from the population under a permit from the U.S. Fish and Wildlife Service to: 1) identify capsule parameters that might be correlated with seed number and viability, 2) estimate an appropriate sample size to obtain accurate seed production estimates, 3) quantify seed production and viability per seed capsule, and 4) document temporal patterns in seed embryo …

Cattle Grazing Reduces Survival And Reproduction Of The Western Prairie Fringed Orchid, Bonnie Warner Alexander, Donald Kirby, Mario Biondini, Edward Dekeyser

The Prairie Naturalist

QuantifYing impacts of livestock grazing and prairie management strategies on the threatened western prairie' fringed orchid (Platanthera praeclara) is difficult due to the erratic appearance of the orchid above-ground. We monitored above-ground survival of orchids from flowering to mature seed capsule production, comparing plant height, flower numbers, and seed capsule numbers from 2002-2004 in rotationally grazed pastures and non-grazed sites. Orchid survival differed significantly between grazed and non-grazed pastures, with the proportion of plants surviving from flower to capsule production consistently lower in grazed pastures. Mean orchid survival in grazed and non-grazed areas was 40% and 87%, respectively. …

Bat Survey Along The Missouri River In Central South Dakota, Alyssa M. Kiesow, Joshua A. Kiesow

The Prairie Naturalist

ats are efficient predators of night-flying insects (Whitaker 1993), particularly in urban, agricultural, and forested areas in South Dakota (Kiesow 2004). In South Dakota, 6 bat species are considered rare and presently monitored by the South Dakota Natural Heritage Program (SDNHP; South Dakota Natural Heritage Program 2002). Because bats serve a vital ecosystem function there is an increased need to conserve bats and their habitats. Hence, the objectives of this project were to determine bat species richness along the Missouri River in central South Dakota. We conducted surveys of bats using mist-nets and acoustic detection from early May to early …

Use Of Late Season Standing Corn By Female White-Tailed Deer In The Northern Great Plains During A Mild Winter, Troy W. Grovenburg, Christopher N. Jacques, Christopher C. Swanson, Robert W. Klaver, Jonathan Jenks

The Prairie Naturalist

Winter habitat and resource use of white-tailed deer (Odocoileus virginianus) have been studied extensively throughout their northern range. However, limited information exists on deer use of late season standing corn. We evaluated standing corn use by female white-tailed deer on winter range in north-central South Dakota during winter 2005-2006. Results indicate that cover type selection occurred at the population (P < 0.001) and home range (P < 0.001) levels. PopUlation level analysis indicated selection for standing corn (vi> = 4.31) and Conservation Reserve Program (CRP) grasslands (vi> = 2.81). Similarly, at the home range level, deer selected for standing corn (vi> = 1.35) and CRP grasslands (vi> = 1.44). Deer disproportionately increased use of standing corn and CRP …

Potential Importance Of Competition, Predation, And Prey On Yellow Perch Growth From Two Dissimilar Population Types, Casey W. Schoenebeck, Michael L. Brown

The Prairie Naturalist

Our objective was to describe the influence of population dynamics, inter- and intra-specific competition, predation, prey abundance, and prey size structure on yellow perch (Perca flavescens) growth for two perch population types (high-quality and low-quality) commonly found in South Dakota glacial lakes. We selected Lake Cochrane as a low quality yellow perch population and Lake Madison as a high quality perch population. Sunfish (Lepomis spp.) relative abundance was greater (P < 0.05) in Lake Cochrane than Lake Madison, suggesting interspecific competition may have a large influence on yellow perch growth. Indices of available sizes and densities of zooplankton were lower (P < 0.05) in Lake Cochrane than Lake Madison, suggesting that increased competition for large zooplankton may have reduced zooplankton size structure and density. Zooplankton may be a limiting resource in South Dakota glacial lakes when both yellow perch and sunfish are feeding primarily on zooplankton which may explain differences in perch growth rates between population types .

Evaluating The Impacts Of Black-Tailed Prairie Dogs On Vegetation In Traditional And Non-Traditional Habitats, Erin M. Lehmer, Laurel Hartley, Jesse Lanci, Charlie Kolb

The Prairie Naturalist

The wildland-urban interface (WUI), defined as areas where human development meets undeveloped wildland (Radeloff et al. 2005), is a focal area for humanwildlife interactions in many communities of the western United States, particularly in those areas that have experienced rapid and expansive human population growth. Since 1960, conversion of rural to urban land has more than doubled in the United States (Theobald 2001). The eastern front range of the Rocky Mountains has experienced one of the most rapid urban expansions in the country, with approximately 110,000 hectares of undeveloped rural land being converted to human-developed land every year between 1992 …

The Prairie Naturalist, Volume 42, No. 1/2 June 2010, The Great Plains Natural Science Society

The Prairie Naturalist

CHANNEL CATFISH DIETS INCLUDE SUBSTANTIAL VEGETATION IN A MISSOURI RIVER RESERVOIR • J. D. Dagel, M. R. Wuellner, and D. W. Willis

USE OF LATE SEASON STANDING CORN BY FEMALE WHITE-TAILED DEER IN THE NORTHERN GREAT PLAINS DURING A MILD WINTER • T. W. Grovenburg, C. N. Jacques, C. C. Swanson, R. W. Klaver, and J. A. Jenks

COMPARISON OF TWO ZOOPLANKTON SAMPLING GEARS IN SHALLOW, HOMOGENOUS LAKES • M. E. Livings, C. W. Schoenebeck, and M. L. Brown

VEGETATION TRENDS ON A WASTE ROCK REPOSITORY CAP IN THE NORTHERN BLACK HILLS • A. C. Korth, G. E. Larson, L. …

Channel Catfish Diets Include Substantial Vegetation In A Missouri River Reservoir, Jonah D. Dagel, Melissa R. Wuellner, David W. Willis

The Prairie Naturalist

Channel catfish (Ictalurus punctatus) are native to Lake Sharpe, a Missouri River mainstem reservoir, and are common in angler catches. Channel catfish growth has declined since the formation of the reservoir in 1963. Mean lengths at time of capture for channel catfish ages 9, 10, II, and 12 have decreased by 69, 55, 115, and 21S mm, respectively, since impoundment. The objective of this study was to document monthly food habits of channel catfish throughout the growing season (May-August) in Lake Sharpe to assess potential effects of diet on growth. Although channel catfish consumed both macro invertebrates and …

Observations Of Little Blue Herons Nesting In North Dakota, And An Instance Of Probable Natural Hybridization Between A Little Blue Heron And A Cattle Egret, Alisa J. Bartos, Lawrence Igl, Marsha A. Sovada

The Prairie Naturalist

The little blue heron (Egretta caerulea) is native to North America and most commonly breeds along the coast of the southeastern United States and the Gulf of Mexico through Central America and into South America (Rodgers and Smith 1995). In North America, little blue herons rarely nest outside their coastal range. However, nesting has been documented at several locations in the northern plains including Brown, Kingsbury, and Charles Mix counties, South Dakota (Naugle et al. 1996, Tallman et al. 2002); Pope County, Minnesota (Green and Janssen 1975); and possibly in southeastern Saskatchewan (Nero and Lein 1971, Smith et al. 1996). …

A Novel Gene Network Inference Algorithm Using Predictive Minimum Description Length Approach, Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold which defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to …

Vegetation Trends On A Waste Rock Repository Cap In The Northern Black Hills, Andrew C. Korth, Gary E. Larson, Lan Xu, Thomas E. Schumacher

The Prairie Naturalist

We assessed successional trends, long-term vegetation sustainability, and soil surface protection during the 2005-2007 growing seasons on the 32-ha Ruby Gulch Waste Rock Repository cap. The cap consisted of 150 cm of rock and soil covering a polyethylene membrane which in turn covered mining waste rock in order to prevent leaching of heavy metals and acidic water into streams. Following construction in 2003, a contractor applied a grass-forb seed mixture to provide soil-surface protection especially for steeply sloped portions of the cap. In 2005, we established 56, 1-m² plots, and 20, 20-m transects to annually measure canopy cover, basal …

Joint Fire Science Program – Lake Mead National Recreation Area Revegetating Burned Arid Lands: Identifying Successful Native Species Using Trait And Competition Analysis: Quarterly Progress Report, Time Period: January 1 — April 30, 2010, Margaret N. Rees

Fire Science

• Article entitled “Competitive Hierarchy of Native Desert Plants with Red Brome (Bromus rubens): Towards Identifying Invasion-Reducing Species" was submitted to the Invasive Plant Science and Management journal
• Maintained nursery plots and added installment of nitrogen treatment.
• Took measurements in nursery (competition) plots and harvested biomass.

29 Years Of Vegetation Community Change Across Environmental Gradients In A Mojave Desert Mountain Range, Christopher L. Roberts, James S. Holland, Scott R. Abella

Graduate Research Symposium (2010 - 2017)

There is a great deal of uncertainty as to how biological communities respond to changes in land use and climate change, a situation particularly relevant in protected areas such as national parks that were designated to conserve specific biological features. Utilizing extant vegetation data sets with repeatable methodology can provide opportunities for insight into previous vegetation change and provide base line data for long-term monitoring projects useful for modeling vegetation community trajectories. We have relocated and resurveyed 106 sites from a vegetation community study initiated in 1979 in the Newberry Mountains, southern Nevada, within Lake Mead National Recreation Area managed …

A Toolkit For Rapid Gene Mapping In The Nematode Caenorhabditis Briggsae, Daniel C. Koboldt, Julia E. Staisch, Bavithra Thillainathan, Karen Haines, Scott Everet Baird, Helen M. Chamberlin, Eric S. Haag, Raymond D. Miller, Bhagwati P. Gupta

Biological Sciences Faculty Publications

Background

The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

Results

We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 …