Market interactions,farmers' choices,and the sustainability of growing advanced biofuels: a missing perspective?

Advanced biofuels such as cellulosic ethanol are of great interest in the USA. With agriculture being the major source of feedstock for advanced biofuels, how farmers would respond to markets and policy incentives in providing such feedstock can directly affect sufficient and sustainable supply of advanced biofuels and their environmental sustainability. In this study, we developed an economic model to examine farmers' production choices in a context where agricultural markets are linked to energy markets. We identified the economic conditions under which farmers could maximize their profits by converting current grain cropland to grow cellulosic biomass crops. An empirical illustration showed that with current technology, farmers are unlikely to grow switchgrass as a dedicated energy crop instead of corn on cropland. The biofuel incentives in the 2008 Farm Bill can improve the competitiveness of switchgrass, but may stimulate corn production as well, with corn residues as an alternative feedstock for advanced biofuels. The continuous, possibly expanding, corn production in future raises the same issues for advanced biofuels as for corn grain-based ethanol. To assure the environmental sustainability of advanced biofuel production, further research is needed to help design environmental policies alongside existing biofuel initiatives.     

Allelopathy,a chance for sustainable weed management

The exploitation of crop allelopathy against weeds may be useful to reduce issues related to the use of herbicides. Several crops, such as alfalfa, barley, black mustard, buckwheat, rice, sorghum, sunflower and wheat, demonstrate strong weed suppression ability, either by exuding allelochemical compounds from living plant parts or from decomposing residues. As well as the positive effect on weed reduction, the introduction in agronomic rotations of allelopathic crops, their use as a mulch to smother crops or as a green manure may also be helpful in reduction of other agricultural problems, such as environmental pollution, use of unsafe products and human health concerns, through a reduction in chemical inputs. Knowledge of allelopathic properties of crops may also be advantageous in mitigation of soil sickness. Moreover, information on weed allelopathy may be profitable in preventing serious crop damage if the weed biomass is buried in the soil, and a crop susceptible to allellochemicals is planned for the following year. The use of allelopathic traits from crops or cultivars with important weed inhibition qualities, together with common weed control strategies, can play an important role in the establishment of sustainable agriculture.     

Increased germination of diverse crop-wild hybrid sunflower seeds.

Gene flow from crop fields to wild populations produces hybrids that often differ from their wild counterparts in growth form, phenology, and life history characteristics. Germination and dormancy dynamics have a strong influence on population persistence, competitive dynamics, and ultimately, plant fitness. They may also play a role in modifying crop gene introgression, which has been of primary interest since the release of transgenic crops. We investigated how seed germination and dormancy were affected by sunflower crop wild hybridization in both laboratory and field experiments. Hybridization increased seed germination and decreased dormancy. Of the nine wild populations we assayed, most of their hybrids had higher germination than the wilds of the same population. However, absolute germination levels varied by population and testing environment. Hybrids produced by three different crop lines differed in germination, and their germination rankings shifted across populations. Increased germination in hybrids could accelerate crop gene introgression, provided that hybrids germinate in an appropriate period. Differences in relative germination of wild and hybrid seed indicated that the effect of germination on introgression will likely vary by population due, in part, to initial levels of dormancy in the population. Therefore, the implications of gene flow from crops with novel characteristics or from transgenic crops will also vary by population.     

Evaluating the outcomes of genetic rescue attempts

Augmenting gene flow is a powerful tool for the conservation of small, isolated populations. However, genetic rescue attempts have largely been limited to populations at the brink of extinction, in part due to concerns over negative outcomes (e.g., outbreeding depression). Increasing habitat fragmentation may necessitate more proactive genetic management. Broader application of augmented gene flow will, in turn, require rigorous evaluation to increase confidence and identify pitfalls in this approach. To date, there has been no assessment of best monitoring practices for genetic rescue attempts. We used genomically explicit, individual-based simulations to examine the effectiveness of common approaches (i.e., tests for increases in fitness, migrant ancestry, heterozygosity, and abundance) for determining whether genetic rescue or outbreeding depression occurred. Statistical power to detect the effects of gene flow on fitness was high (≥0.8) when effect sizes were large, a finding consistent with those from previous studies on severely inbred populations. However, smaller effects of gene flow on fitness can appreciably affect persistence probability but current evaluation approaches fail to provide results from which reliable inferences can be drawn. The power of the metrics we examined to evaluate genetic rescue attempts depended on the time since gene flow and whether gene flow was beneficial or deleterious. Encouragingly, the use of multiple metrics provided nonredundant information and improved inference reliability, highlighting the importance of intensive monitoring efforts. Further development of best practices for evaluating genetic rescue attempts will be crucial for a responsible transition to increased use of translocations to decrease extinction risk.     

Can domestic production of iLUC-free feedstock from arable land supply Sweden’s future demand for biofuels?

The increasing biofuel production from agricultural crops has been suggested to cause indirect land use change (iLUC). This increases interest in biofuel feedstocks that qualify as iLUC-free: (1) residues without a market, (2) crops from previously unused arable land, (3) additional crops and (4) biomass from intensified production. In the present study, biofuel potential from such feedstocks was quantified for Sweden and compared against the predicted biofuel demand from agricultural resources in 2030. The results indicate that straw (category 1) could cover up to 37% of future biofuel demand. Grass leys from intensified production (category 4), set-aside and abandoned land (category 2) and excess grass silage (category 1) could cover up to 79%. Intermediate and ecological focus area crops (category 3) could contribute up to 21%. To realize the biofuel targets, a high implementation rate of additional iLUC-free feedstock is needed. Future studies need to investigate impacts of low-iLUC policies.     

Targeted gene flow for conservation

Anthropogenic threats often impose strong selection on affected populations, causing rapid evolutionary responses. Unfortunately, these adaptive responses are rarely harnessed for conservation. We suggest that conservation managers pay close attention to adaptive processes and geographic variation, with an eye to using them for conservation goals. Translocating pre‐adapted individuals into recipient populations is currently considered a potentially important management tool in the face of climate change. Targeted gene flow, which involves moving individuals with favorable traits to areas where these traits would have a conservation benefit, could have a much broader application in conservation. Across a species’ range there may be long‐standing geographic variation in traits or variation may have rapidly developed in response to a threatening process. Targeted gene flow could be used to promote natural resistance to threats to increase species resilience. We suggest that targeted gene flow is a currently underappreciated strategy in conservation that has applications ranging from the management of invasive species and their impacts to controlling the impact and virulence of pathogens.     

Targeted gene flow and rapid adaptation in an endangered marsupial

Targeted gene flow is an emerging conservation strategy. It involves translocating individuals with favorable genes to areas where they will have a conservation benefit. The applications for targeted gene flow are wide-ranging but include preadapting native species to the arrival of invasive species. The endangered carnivorous marsupial, the northern quoll (Dasyurus hallucatus), has declined rapidly since the introduction of the cane toad (Rhinella marina), which fatally poisons quolls that attack them. There are, however, a few remaining toad-invaded quoll populations in which the quolls survive because they know not to eat cane toads. It is this toad-smart behavior we hope to promote through targeted gene flow. For targeted gene flow to be feasible, however, toad-smart behavior must have a genetic basis. To assess this, we used a common garden experiment, comparing offspring from toad-exposed and toad-naïve parents raised in identical environments, to determine whether toad-smart behavior is heritable. Offspring from toad-exposed populations were substantially less likely to eat toads than those with toad-naïve parents. Hybrid offspring showed similar responses to quolls with 2 toad-exposed parents, indicating the trait may be dominant. Together, these results suggest a heritable trait and rapid adaptive response in a small number of toad-exposed populations. Although questions remain about outbreeding depression, our results are encouraging for targeted gene flow. It should be possible to introduce toad-smart behavior into soon to be affected quoll populations.     

A simulation study of the medium-term effects of field patterns on cross-pollination rates in oilseed rape (Brassica napus L.)

Gene flow between cultivars within a landscape may lead to impurities that reduce harvest value. In OSR, as for most crops, impurity rates are expected to depend on the spatial distribution of crops over the landscape. However, in contrast to other well-studied crops such as maize, OSR crops generate seed banks in European agro-ecosystems. Gene flow is thus a spatio-temporal process which depends on cropping systems. We therefore aimed at identifying spatial variables that have an effect on regional or local harvest impurities, taking account of the time since the introduction of OSR crops in the regions and of cropping system. Gene flow was simulated over 36 field patterns cultivated with either 15% or 30% of OSR fields, among which 10% or 50% were GM, for three contrasted cropping systems, with the GeneSys software already used for EU co-existence studies. Through regression analyses, we determined spatial and agronomic factors that most affected harvest impurity rates of non-GM OSR after one or seven years of OSR cultivation. The cropping system was the main factor explaining regional harvest impurity rates. Its importance increased after six years of OSR cultivation. For a given cropping system, the regional impurity rate after one year increased linearly with the current proportion of GM crop. In contrast, impurity rates after six years largely depended on the proportions of OSR crop (GM or not) in the two preceding years. During the first year of OSR cultivation, local impurity rates were mostly explained by the distance to the closest GM field. After six years, these rates were mostly explained by the density of GM volunteers in the analysed field and, to a lesser degree, to that of volunteers in neighbour non-OSR fields. Cropping systems were most important in determining impurity rates and the way impurity rates related to regional or local factors. Determination of isolation distances to ensure harvest purity should thus consider past history of OSR cultivation in the area and, in particular, how current or future cropping systems will manage volunteers. Regression quantiles were fitted to the simulated data to determine regional rules (i.e. the maximum regional area of GM OSR and isolation distances between GM and non-GM crops) as a function of the risk accepted by the decision-maker (i.e. the % of situations exceeding harvest impurity thresholds), the cropping system and the volunteer infestation.     

A mark-recapture study of male<Emphasis Type="Italic"> Colletes cunicularius</Emphasis> bees: implications for pollination by sexual deception

An unusual pollination strategy is pollination by sexual deception in which orchids sexually attract male insects as pollinators. One gap in knowledge concerns the pattern and extent of pollinator movement among these sexually deceptive flowers and how this translates to pollen and gene flow. Our aim was to use mark and recapture techniques to investigate the behavior and movement of male Colletes cunicularius, an important bee pollinator of Ophrys. Our study site was located in northern Switzerland where a large population of the bees was nesting. Within two plots, (10×40 m), we marked bees with different colors and numbered tags. Seventeen percent of the 577 marked bees were recaptured over a period of 1 to a maximum of 11 days. However, the number of recaptures dropped dramatically after 3–5 days, suggesting an average lifetime of less than 10 days. Mark-recapture distances varied from 0 to 50 m, with a mean of 5 m. Our findings show that individual male bees patrol a specific and restricted region of the nesting area in search of mates. This mark-recapture study provides the first clues about the potential movement of pollen within populations of Ophrys orchids. We predict that orchid-pollen movements mediated by bees will be similar to the mark-recapture distances in this study. Parallel studies within orchid populations, including direct studies of pollen movement, are now required to better understand how pollinator mate-searching behavior translates to pollination success and pollen movement within sexually deceptive orchid populations.Communicated by R.F.A. Moritz     

When is an invasive not an invasive? Macrofossil evidence of doubtful native plant species in the Galápagos Islands

The Galápagos Islands are globally renowned for their ecological value and as a world symbol of scientific discovery; however the native biodiversity of this unique region is currently under threat. One of the primary concerns is the detrimental impact of approximately 750 nonnative plants introduced over the last 500 years of human presence in the archipelago. In addition to these known introduced species, there are an additional 62 vascular plants classified as "doubtful natives," where native status remains unclear. To help address the questions of provenance regarding these doubtfully native species and their impact on highland ecosystems over the past 500-1000 years, we analyzed plant macrofossils in sedimentary records. Appropriate species classification (native or introduced) was determined using baseline data of species presence on the islands. We confirmed that six plants (Ageratum conyzoides, Solanum americanum, Ranunculus flagelliformis, Brickellia diffusa, Galium canescens, and Anthephora hermaphrodita) once considered doubtful natives or introduced are actually native to the Galápagos flora. These results have relevance not just for the Galápagos but also many other oceanic islands in demonstrating the application of palaeobotanical data to conserving and restoring native biodiversity.     

Biofuels and Biodiversity: Principles for Creating Better Policies for Biofuel Production

Abstract:  Biofuels are a new priority in efforts to reduce dependence on fossil fuels; nevertheless, the rapid increase in production of biofuel feedstock may threaten biodiversity. There are general principles that should be used in developing guidelines for certifying biodiversity-friendly biofuels. First, biofuel feedstocks should be grown with environmentally safe and biodiversity-friendly agricultural practices. The sustainability of any biofuel feedstock depends on good growing practices and sound environmental practices throughout the fuel-production life cycle. Second, the ecological footprint of a biofuel, in terms of the land area needed to grow sufficient quantities of the feedstock, should be minimized. The best alternatives appear to be fuels of the future, especially fuels derived from microalgae. Third, biofuels that can sequester carbon or that have a negative or zero carbon balance when viewed over the entire production life cycle should be given high priority. Corn-based ethanol is the worst among the alternatives that are available at present, although this is the biofuel that is most advanced for commercial production in the United States. We urge aggressive pursuit of alternatives to corn as a biofuel feedstock. Conservation biologists can significantly broaden and deepen efforts to develop sustainable fuels by playing active roles in pursuing research on biodiversity-friendly biofuel production practices and by helping define biodiversity-friendly biofuel certification standards.     

Regional Consequences of Local Population Demography and Genetics in Relation to Habitat Management in Gentiana pneumonanthe

Abstract:  A joint demographic and population genetics stage-based model for a subdivided population was applied to Gentiana pneumonanthe , an early successional perennial herb, at a regional (metapopulation) scale. We used numerical simulations to determine the optimal frequency of habitat disturbance (sod cutting) and the intensity of gene flow among populations of G. pneumonanthe to manage both population viability and genetic diversity in this species. The simulations showed that even small populations that initially had near-equal allele frequencies could, if managed properly through sod cutting every 6 to 7 years, sustain their high genetic variation over the long run without gene flow. The more the allele frequencies in the small populations are skewed, however, the higher the probability that in the absence of gene flow, some alleles will be lost and within-population genetic variation will decrease even under proper management. This implies that although local population dynamics should be the major target for management, regional dynamics become important when habitat fragmentation and decreased population size lead to the loss of local genetic diversity. The recommended strategy to improve genetic composition of small populations is the introduction of seeds or seedlings of nonlocal origin.     

Cryptic species of Clavelina (Ascidiacea) in two different habitats: harbours and rocky littoral zones in the northwestern Mediterranean

Marinas and harbours provide ideal sites for the study of population genetics of marine invertebrates with restricted dispersal capabilities. They combine a confinement effect, particular ecological conditions (pollution, turbidity), and the possibility of high gene flow through ship-borne propagules, which greatly increases the natural dispersal capability of sexual and asexual propagules in many species with short-lived larvae. We studied the genetic structure of populations of the ascidian Clavelina lepadiformis living inside and outside harbours in the north-western Mediterranean. A 500-bp segment of the cytochrome c oxidase subunit I (COI) mitochondrial gene was sequenced in three populations from inside harbours (interior form) and in three populations from the rocky littoral (exterior form). Two congeneric Mediterranean species, Clavelina sp. and C. dellavallei, were used for comparison. We found that the interior and exterior forms of C. lepadiformis belong to two distinct clades, with a genetic divergence of 5%. Gene-flow values among these forms were insignificant. The lack of gene flow and the genetic divergence suggest that the interior and exterior forms of C. lepadiformis are in fact cryptic species rather than differentiated populations of the same species. Levels of gene flow were higher among interior habitats than among exterior habitats, a pattern likely maintained by genetic exchange through ships. We discuss the possible origins of the present-day distribution of these cryptic species. We contend that the study of species living both inside and outside these particular habitats will reveal more instances of genetic discontinuities allowing local adaptations.     

The Role of Hybrid Vigor in the Replacement of Pecos Pupfish by Its Hybrids with Sheepshead Minnow

Abstract:  Many species are jeopardized by hybridization and genetic introgression with closely related species. Unfortunately, the mechanisms that promote or retard gene flow between divergent populations are little studied and poorly understood. Like many imperiled fish species, the Pecos pupfish ( Cyprinodon pecosensis ) is threatened with replacement by its hybrids with a close congener. We examined swimming performance and growth rate of hybrid pupfish to determine the role of hybrid vigor in the genetic homogenization of C. pecosensis by its hybrids with sheepshead minnow ( C. variegatus ). The F1 hybrids, backcross hybrids, and purebred C. variegatus displayed greater swimming endurance than purebred C. pecosensis . In addition, F1 hybrids and C. variegatus grew more rapidly than C. pecosensis . The ecological superiority of hybrids probably promoted their rapid spread through and beyond the historic range of C. pecosensis . These results indicate that eradication of hybrids and restoration of C. pecosensis to its native range is unlikely. Extinction of unique species via genetic homogenization can result from human activities that increase gene flow between historically fragmented populations; conservation managers must weigh the potential for such a catastrophe against the presumed benefits of increased interpopulation gene flow. This example illustrates how, after hybridization has occurred, conflict may arise between formerly complementary conservation goals.     

Maximum feasible distance of windborne cross-pollination in Brassica napus: A ‘mass budget’ model

A theory of gene dispersal by wind pollination can make an important contribution to understanding the viability and evolution of important plant groups in the Earth's changing landscape and it can be applied to evaluate concerns about the spread of engineered genes from genetically modified (GM) crops into conventional varieties via windborne pollen. Here, we present a model of cross-pollination between plant populations due to the wind. We perform a ‘mass budget’ of pollen by accounting for the number of pollen grains from release in the source population, dispersal from the source to the sink population by the wind, and deposition on receptive surfaces in the sink population. Our model can be parameterised for any wind-pollinated species, but we apply it to Brassica napus (oilseed rape or canola) to investigate the threat posed by wind pollination to GM confinement in agriculture. Specifically, we calculate the maximum feasible distance at which a particular level of windborne gene dispersal could be attained. This is equivalent to the separation distance between populations or fields required to achieve a given threshold of gene dispersal or adventitious GM presence. As required, model predictions of the upper bounds on levels of wind-mediated gene dispersal exceed observations from a wide range of published studies. For a level of gene dispersal below 0.9%, which is the EU threshold for GM adventitious presence, we predict that the maximum feasible distance for agricultural fields of B. napus is 1000 m, regardless of field shape and direction of prevailing winds. For fields closer than 1000 m, our model results do not necessarily imply that the 0.9% threshold is likely to be breached, because in this instance we have conservatively set the values of parameters where current knowledge is limited. We also predict that gene dispersal is reduced by 50% when the lag in peak flowering between the source and sink populations is 13 days, and reduced by 90% when the lag is 24 days. We identify further measurements necessary to improve the accuracy of the model predictions.     

Patterns of Genetic Diversity in Remaining Giant Panda Populations

Abstract: The giant panda ( Ailuropoda melanoleuca ) is among the more familiar symbols of species conservation. The protection of giant panda populations has been aided recently by the establishment of more and better-managed reserves in existing panda habitat located in six mountain ranges in western China. These remaining populations are becoming increasingly isolated from one another, however, leading to the concern that historic patterns of gene flow will be disrupted and that reduced population sizes will lead to diminished genetic variability. We analyzed four categories of molecular genetic markers (mtDNA restriction-fragment-length polymorphisms [RFLP], mtDNA control region sequences, nuclear multilocus DNA fingerprints, and microsatellite size variation) in giant pandas from three mountain populations (Qionglai, Minshan, and Qinling) to assess current levels of genetic diversity and to detect evidence of historic population subdivisions. The three populations had moderate levels of genetic diversity compared with similarly studied carnivores for all four gene measures, with a slight but consistent reduction in variability apparent in the smaller Qinling population. That population also showed significant differentiation consistent with its isolation since historic times. From a strictly genetic perspective, the giant panda species and the three populations look promising insofar as they have retained a large amount of genetic diversity in each population, although evidence of recent population reduction—likely from habitat loss—is apparent. Ecological management to increase habitat, population expansion, and gene flow would seem an effective strategy to stabilize the decline of this endangered species.     

Genetic structure in native and non-native populations of the direct-developing gastropod Crepidula convexa

In many marine invertebrate species, larval development plays an important role in population connectivity and gene flow: species with direct benthic development generally show more genetic structure than those with planktonic development. We used nuclear markers (microsatellites) to determine population genetic structure of the direct-developing snail Crepidula convexa (Gastropoda: Calyptraeidae) in seven populations with 15–85 individuals each within its native range of the northwest Atlantic and compared it to Crepidula fornicata, a congener with planktonic development. Our results are consistent with general expectations and previous work in these species with other markers: C. convexa had greater population structure and even at a regional scale shows significant isolation-by-distance, in contrast to C. fornicata. We also genotyped a single population of C. convexa introduced to the northeastern Pacific to investigate the prediction of reduced genetic diversity following introduction (founder effect). We did not find a reduction in genetic diversity, suggesting that this non-native population may be characterized by multiple introductions. This pattern is consistent with many other introduced populations of marine invertebrates, including C. fornicata.     

Genetic diversity and population structure of the Chinese mitten crab <Emphasis Type="Italic">Eriocheir sinensis</Emphasis> in its native range

The Chinese mitten crab Eriocheir sinensis is an indigenous and economically important species in China, but can also be found as invasive species in Europe and America. Mitten crabs have been exploited extensively as a food resource since the 1990s. Despite its ecological and economic importance, the genetic structure of native mitten crab populations is not well understood. In this paper, we investigated the genetic structure of mitten crab populations in China by screening samples from ten locations covering six river systems at six microsatellite loci. Our results provide further evidence that mitten crabs from the River Nanliujiang in Southern China are a genetically differentiated population within the native range of Eriocheir, and should be recognized as a separate taxonomic unit. In contrast, extremely low levels of genetic differentiation and no significant geographic population structure were found among the samples located north of the River Nanliujiang. Based on the reproductive biology of mitten crabs and the geography of their habitat we argue that both natural and human-mediated gene flow are unlikely to fully account for the similar allele frequency distributions at microsatellite loci. Large population sizes of mitten crabs suggest instead that a virtual absence of genetic drift and significant homoplasy of microsatellite alleles have contributed to the observed pattern. Furthermore, a coalescent-based maximum likelihood method indicated a more than two-fold lower effective population size of the Southern population compared to the Northern Group and low but significant levels of gene flow between both areas.     

Hierarchical demographic approaches for assessing invasion dynamics of non-indigenous species: An example using northern snakehead (Channa argus)

Models of species’ demographic features are commonly used to understand population dynamics and inform management tactics. Hierarchical demographic models are ideal for the assessment of non-indigenous species because our knowledge of non-indigenous populations is usually limited, data on demographic traits often come from a species’ native range, these traits vary among populations, and traits are likely to vary considerably over time as species adapt to new environments. Hierarchical models readily incorporate this spatiotemporal variation in species’ demographic traits by representing demographic parameters as multi-level hierarchies. As is done for traditional non-hierarchical matrix models, sensitivity and elasticity analyses are used to evaluate the contributions of different life stages and parameters to estimates of population growth rate. We applied a hierarchical model to northern snakehead (Channa argus), a fish currently invading the eastern United States. We used a Monte Carlo approach to simulate uncertainties in the sensitivity and elasticity analyses and to project future population persistence under selected management tactics. We gathered key biological information on northern snakehead natural mortality, maturity and recruitment in its native Asian environment. We compared the model performance with and without hierarchy of parameters. Our results suggest that ignoring the hierarchy of parameters in demographic models may result in poor estimates of population size and growth and may lead to erroneous management advice. In our case, the hierarchy used multi-level distributions to simulate the heterogeneity of demographic parameters across different locations or situations. The probability that the northern snakehead population will increase and harm the native fauna is considerable. Our elasticity and prognostic analyses showed that intensive control efforts immediately prior to spawning and/or juvenile-dispersal periods would be more effective (and probably require less effort) than year-round control efforts. Our study demonstrates the importance of considering the hierarchy of parameters in estimating population growth rate and evaluating different management strategies for non-indigenous invasive species.     

Modeling water and soil quality environmental impacts associated with bioenergy crop production and biomass removal in the Midwest USA

The removal of corn stover or production of herbaceous crops such as switchgrass (Panicum virgatum) or big bluestem (Andropogon gerardii) as feedstocks for bioenergy purposes has been shown to have significant benefits from an energy and climate change perspective. There is potential, however, to adversely impact water and soil quality, especially in the United States Corn Belt where stover removal predominantly occurs and possibly in other areas with herbaceous energy crops depending upon a number of geo-climatic and economic factors. The overall goal of this research was to provide a thorough and mechanistic understanding of the relationship between stover and herbaceous crop production management practices and resulting range of impacts on soil and water quality, with a focus on eastern Iowa, USA. Comparisons of the production of herbaceous bioenergy crops to continuous corn (Zea mays L.) and corn-soybean (Glycine max L.) rotations on five different soils representative of the region were performed. Indices for total nutrient (nitrogen and phosphorus) loss to surface water and groundwater, total soil loss due to water and wind erosion, and cumulative soil carbon loss were derived to assess long-term sustainability. The Agricultural Policy/Environmental eXtender (APEX) agroecosystem model was used to quantify the sustainability indices and to generate sufficient data to provide a greater understanding of variables that affect water and soil quality than previously possible. The results clearly show the superiority of herbaceous crop production from a soil and water quality perspective. They also show, however, that compared to traditional cropping systems (e.g., corn-soybean rotations with conventional tillage), soil and water quality degradation can be reduced under certain conditions at the same time stover is removed.