Jeffrey J. Steiner

A hybrid genetic algorithm for multiobjective problems with activity analysis-based local search

The objective of this research was the development of a method that integrated an activity analysis model of profits from production with a biophysical model, and included the capacity for optimization over multiple objectives. We specified a hybrid genetic algorithm using activity analysis as a local search method, and NSGA-II for calculation of the multiple objective Pareto optimal set. We describe a parallel computing approach to computation of the genetic algorithm, and apply the algorithm to evaluation of an input tax to regulate pollution from agricultural production.

RFLP marker analysis supports tetrasonic inheritance in Lotus corniculatus L.

Abstract Lotus corniculatus is a tetraploid (2n=4x=24) perennial forage legume and has been reported to have tetrasomic inheritance for several traits, although it has also been reported to show disomic inheritance. Molecular markers were used to clarify whether tetrasomic inheritance, disomic inheritance, or a combination of both, was found within an F2 population arising from a cross between two diverse L. corniculatus accessions. The inheritance of ”tetra-allelic” RFLP markers (markers with four segregating bands) indicated that disomic inheritance could not account for the phenotypic F2 classes observed, and that only tetrasomic inheritance would explain the observed results. Goodness of fit tests for ”tetra-allelic” and ”tri-allelic” (three segregating bands) RFLP marker data suggested support for chromosomal-type tetrasomic inheritance. RFLP genotypes interpreted from autoradiographic signal intensity provided additional support for tetrasomic inheritance and the occurrence of preferential pairing between parental chromosomes. Bivalent pairing was predominant in the two parental lines and their F1 hybrid in cytological analyses. L. corniculatus has been classified as both an autotetraploid and an allotetraploid species. RFLP evidence of tetrasomic inheritance gives support for L. corniculatus being classified as an autotetraploid species. Even though bivalent pairing occurs, as seen in other autotetraploid species, pairing between any of the four homologous chromosomes is possible. Preferential pairing in the F1 hybrid suggests that genome differentiation appears to be minimal between homologs within an accession, while genome differentiation is greater between homologs from different accessions of this genetically diverse species.

Mineral concentration in selected native temperate grasses with potential use as biofuel feedstock

Stands of native grasses along roadways, in buffer strips, riparian zones and grass prairies have potential utility as feedstock for bioenergy production. The sustainability of harvesting these stands is reliant, in part, on knowledge of the mineral concentration of the harvested grasses because removal of mineral nutrients such as phosphorus (P) and potassium (K) can impact subsequent biomass production and ecosystem services associated with these stands. Mineral content of biomass, particularly that of silicon (Si), chlorine (Cl), and sulfur (S) also impacts thermochemical conversion approaches that convert grasses into bioproducts. This study quantified Cl, S, Si, P and K in Bromus marginatus, Elymus glaucus, Poa secunda, Pseudoroegneria, Elymus lanceolatus, Elymus trachycaulus, Leymus cinereus, Leymus triticoides, and Pseudoroegneria spicata collected at three growth developmental stages from four plant introduction stations located in the western US. Differences (P< or =0.05) in mineral concentrations were associated with developmental stage, species, and location. Variability was greatest in Si concentrations which ranged from 1847 to 28620 mg kg(-1), similar to those recorded in other grasses. Variability in Cl and S concentrations also occurred, but at less magnitude than that of Si. Concentrations of P and K, two mineral fertilizer components, varied approximately threefold among these grasses. Differences in mineral concentrations among these grasses were not completely dependent upon soil mineral content. Long-term evaluations of available soil mineral concentrations under contrasting management practices are needed to quantify how local conditions impact mineral cycling, and in turn, the sustainability of harvesting these stands. The data presented here establish baselines for these species in locations subject to contrasting environmental and microbiological conditions that affect mineral cycling and availability.

High resolution characterization of soil biological communities by nucleic acid and fatty acid analyses

Fatty acid methyl ester (FAME) and length heterogeneity-polymerase chain reaction (LH-PCR) analyses were used to generate ‘fingerprints’ of FAMEs and eubacterial 16S rDNA sequences characteristic of agricultural soil communities. We hypothesized that pooling data from two methods that characterized different components of soil biological communities would improve the resolution of fingerprints characterizing the effects of contrasting tillage and ground cover practices. By using supervised classifications of FAME and LH-PCR, a discriminant analysis procedure distinguished soils from contrasting tillage and ground cover management and predicted the origin of soil samples. Used independently, FAME provided higher resolution of tillage, ground cover, and field location than LH-PCR, but LH-PCR was effective at identifying field location. Pooling data from both methods did not enhance the predictive power. A comparison of linear discriminant analysis, quadratic discriminant analysis, and nonparametric density estimation demonstrated that minimizing assumptions about data distribution improved the capacity of FAME analysis to resolve differences in soil types. Use of a purely statistical Bayesian method to select a subset of fatty acids (FA’s) as variables in discriminant analyses identified FA’s that represented signature FA’s for specific groups of organisms. Published by Elsevier Science Ltd.

Nitrate-nitrogen, land use/land cover, and soil drainage associations at multiple spatial scales.

Managing non-point-source pollution of water requires knowledge of land use/land cover (LULC) influences at altering watershed scales. To gain improved understanding of relationships among LULC, soil drainage, and dissolved nitrate-N dynamics within the Calapooia River Basin in western Oregon, we selected 44 watersheds ranging in size between 3 and 33 km(2) for monthly synoptic sampling of surface water quality between October 2003 and September 2004. Seasonal associations were examined between dissolved nitrate-N and proportion of woody vegetation or poorly drained soils at differing scales (10, 20, 30, 60, 90, 150, 300 m, and entire watershed), which we defined as influence zones (IZs), surrounding stream networks. Correlations between nitrate-N and proportion woody vegetation or poorly drained soil at each IZ were analyzed for differences using the Hotelling-Williams test. We observed negative correlations (r = -0.81 to -0.94) between nitrate-N and proportion of woody vegetation during winter and spring. Poorly drained soils had positive correlations (r = 0.63-0.87) with nitrate-N. Altering the scale of analysis significantly changed correlations between nitrate-N and woody vegetation, with IZs <150 m being stronger than the watershed scale during winter. However, absolute differences in correlation values were small, indicating minimal ecological consequence for significant differences among scales. In contrast, nitrate-N correlations with poorly drained soil were stronger at the watershed scale than the 10- through 90-m IZs during winter and spring, and absolute differences were sufficient to suggest that scale is ecologically important when determining associations between dissolved nitrate-N and poorly drained soils.

Conservation Practices in Western Oregon Perennial Grass Seed Systems

Rapid changes in practices used to produce perennial grass seed crops in the U.S. Pacific Northwest region and shortened lengths of time that perennial grass seed fields remain in production have increased the need for additional rotation crops that are adapted to the poorly drained soils found in western Oregon. This research was conducted at three sites to determine ways to manage meadowfoam (Limnanthes alba Hartw. ex Benth.) as a component in perennial grass seed rotation systems. Experiments were conducted in 1997, 1998, and 2001 to investigate combinations of spring-applied herbicide and N fertilizer and times of applications, direct-seeded and conventional tillage establishment methods, and previous crop residue management on meadowfoam seed yield, seed oil concentration, and oil yield. No spring-applied fertilizer or herbicide produced responses for all yield components as great as or greater than any other treatment combination. Direct-seeded meadowfoam yielded more oil than the conventional establishment treatment. There was no effect of residue management amounts from grass seed grown in the previous rotation sequence on meadowfoam production; however, maximal residue management, especially if used in combination with direct-seeded meadowfoam, should reduce annual soil erosion. Meadowfoam is suited to low-input production and is adapted to the use of conservation practices including direct seeding and maximal residue management in perennial grass seed systems.

WebGRMS: Prototype software for web-based mapping of biological collections

Biological collections are gaining recognition as priceless sources of information about the historic distribution and diversity of life. The Internet is emerging as the major venue for sharing biodiversity information since it supports globalization and broad-scale interoperability. This research demonstrates how a Web-based mapping application for biological collections was developed using WebGD, an open-source software development tool, and illustrates how simple spatial analysis help collection users describe the range of ecogeographic variation in collections and customize the selection of accessions based on georeferenced variables. Our prototype can be viewed at http://www.yukon.een.orst.edu/ greene/ms_apps/home/index.htm. The demonstration site has three functional areas: (i) Query, (ii) Analyze Collections, and (iii) Add Data. The application was developed relatively quickly and at a low cost, since the complex workings for delivering GIS functions over the Web were an internal part of the WebGD framework. Because it was based on open-source code, costs were greatly decreased compared to commercially available software. In its current form, the prototype WebGRMS application provides users interested in Medicago and Trifolium germplasm with an innovative method to better understand the germplasm collections. More importantly, we hope the prototype provides a glimpse into the future of Web-based spatial analysis of biological collections.