Integrating patterns across multiple genetic markers to infer spatial processes

Landscape geneticists can take considerable advantage of differences in the action of evolutionary forces (mutation, migration, selection, and drift) on different loci within the genome. Appropriate comparisons among loci allow researchers to isolate and study the effects of these processes. For example, the organelles are typically inherited maternally (but occasionally paternally), and so will experience migration only when females or seeds disperse (males or pollen in the paternally inherited organelles). Thus, the comparison with biparentally inherited loci allows inferences about the differential migration rates of male vs. female animals or of seeds vs. pollen in plants. Conversely, all biparentally inherited nuclear loci should experience the same levels of migration and drift. Thus, loci that show unusually large levels of variation across the landscape (as compared with the bulk of loci) may be reflecting the action of spatially varying natural selection (local adaptation). Such comparisons are conceptually straightforward, but are complicated by the high intrinsic variability of stochastic neutral processes. Careful statistical analysis is needed to avoid over-interpreting differences among loci. Inferences will be most robust when both genetic and non-genetic data can be integrated, and the collaboration of landscape ecologists with geneticists promises to be particularly fruitful.     

Comparison of the Sensitivity of Landscape-fire-succession Models to Variation in Terrain, Fuel Pattern, Climate and Weather

The purpose of this study was to compare the sensitivity of modelled area burned to environmental factors across a range of independently-developed landscape-fire-succession models. The sensitivity of area burned to variation in four factors, namely terrain (flat, undulating and mountainous), fuel pattern (finely and coarsely clumped), climate (observed, warmer & wetter, and warmer & drier) and weather (year-to-year variability) was determined for four existing landscape-fire-succession models (EMBYR, FIRESCAPE, LANDSUM and SEM-LAND) and a new model implemented in the LAMOS modelling shell (LAMOS(DS)). Sensitivity was measured as the variance in area burned explained by each of the four factors, and all of the interactions amongst them, in a standard generalised linear modelling analysis. Modelled area burned was most sensitive to climate and variation in weather, with four models sensitive to each of these factors and three models sensitive to their interaction. Models generally exhibited a trend of increasing area burned from observed, through warmer and wetter, to warmer and drier climates with a 23-fold increase in area burned, on average, from the observed to the warmer, drier climate. Area burned was sensitive to terrain for FIRESCAPE and fuel pattern for EMBYR. These results demonstrate that the models are generally more sensitive to variation in climate and weather as compared with terrain complexity and fuel pattern, although the sensitivity to these latter factors in a small number of models demonstrates the importance of representing key processes. The models that represented fire ignition and spread in a relatively complex fashion were more sensitive to changes in all four factors because they explicitly simulate the processes that link these factors to area burned. The US Government's and the Canadian Government's right to retain a non-exclusive, royalty-free license is acknowledged     

Exploring Patterns of Exotic Earthworm Distribution in a Temperate Hardwood Forest in South-Central New York, USA

Exotic earthworms invading forests in Canada and northeastern United States that were naturally devoid of large detritivores cause major changes in ecosystem function. To assess their long-term impacts, studies are needed to elucidate the factors that control the patterns of earthworm invasion at the landscape level. We analyzed the distribution patterns of exotic earthworms in a northern hardwood forest in south-central New York (USA), as explained by landscape variables thought to be important in determining earthworm distribution. Forest type, slope angle, elevation, and the distance to agricultural clearings and wet refugia were significant predictors of earthworm presence, whereas local wetness index and the distance to streams and roads were not. Forest type and distance to agricultural clearings were the two most significant predictors. Our data suggest that areas close to agricultural clearings, dominated by mixed hardwoods, and located towards valley bottoms or on gentle slopes are very likely to support communities of exotic earthworms. Steeper slopes, areas dominated by American beech or eastern hemlock, and locations in the core of extensive forest landscapes have lower probabilities of invasion by exotic earthworms. When applied to a nearby area, our statistical model correctly predicted earthworm presence for 67% of 377 sampling points. Most of the mistakes were incorrect predictions of earthworm absence, suggesting that our statistical model slightly underestimated earthworm presence, possibly because of the pervasive influence of active agricultural fields adjacent to the test site.     

Pineapple organic acid metabolism and accumulation during fruit development

Developmental changes in pineapple (Ananas Comosus (L.) Merrill) fruit acidity was determined for a ‘Smooth Cayenne’ high acid clone PRI#36-21 and a low acid clone PRI#63-555. The high acid clone gradually increased in fruit acidity from 1.4 meq/100 ml 6 weeks from flowering, and peaked a week before harvest at ca 10 meq/100 ml. In contrast, the low acid clone increased in acidity 6 to 8 weeks after flowering, peaked 15 weeks after flowering at ca. 9 meq per/100 ml and then sharply declined in 2 weeks to 6 meq/100 ml. The increased in total soluble solids (TSS) of the low acid clone began 6 weeks after flowering and for the high acid clone at 12 weeks after flowering. The increase in titratable fruit acidity (TA) paralleled the changes in the citric acid content of both clones. Citric acid content increased from less than 1 mg/g at 6 weeks after flowering to 6 to 7 mg/g, 9 weeks later. The malic acid concentration in both clones varied between 3 and 5 mg/g and showed no marked changes just before harvest. The developmental changes in fruit potassium were significantly correlated with fruit acidity and fruit total soluble solids in both the high and low acid clones. Developmental changes in acid-related enzymatic activities showed an increase in citrate synthase (EC 4.1.3.7) activity that occurred a week before harvest, coincided with the peak in citric acid in the high acid clone. An increase in aconitase (ACO, EC 4.2.1.3) activity was observed just before harvest as the decline in acidity occurred in the low acid clone. The activities of phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31), malate dehydrogenase (MDH, EC 1.1.1.37) and malic enzyme (ME, EC 1.1.1.40) did not parallel any changes in fruit acidity. The results indicated that the change in pineapple fruit acidity during development was due to changes in citric acid content. The major difference in acid accumulation occurred in the low acid clone just before harvest when acidity declined by one-third. The activities of citrate synthase and aconitase possibly played a major role in pineapple fruit acidity changes.     

Neutral models for testing landscape hypotheses

Neutral landscape models were originally developed to test the hypothesis that human-induced fragmentation produces patterns distinctly different from those associated with random processes. Other uses for neutral models have become apparent, including the development and testing of landscape metrics to characterize landscape pattern. Although metric development proved to be significant, the focus on metrics obscured the need for iterative hypothesis testing fundamental to the advancement of the discipline. We present here an example of an alternative neutral model and hypothesis designed to relate the process of landscape change to observed landscape patterns. The methods and program, QRULE, are described and options for statistical testing outlined. The results show that human fragmentation of landscapes results in a non-random association of land-cover types that can be describe by simple statistical methods. Options for additional landscape studies are discussed and access to QRULE described in the hope that these methods will be employed to advance our understanding of the processes that affect the structure and function in human dominated landscapes.     

Determining landscape extent for succession and disturbance simulation modeling

Dividing regions into manageable landscape units presents special problems in landscape ecology and land management. Ideally, a landscape should be large enough to capture a broad range of vegetation, environmental and disturbance dynamics, but small enough to be useful for focused management objectives. The purpose of this study was to determine the optimal landscape size to summarize ecological processes for two large land areas in the southwestern United States. We used a vegetation and disturbance dynamics model, LANDSUMv4, to simulate a set of nine scenarios involving systematically varied topography, map resolution, and model parameterizations of fire size and fire frequency. Spatial input data were supplied by the LANDscape FIRE Management Planning System (LANDFIRE) prototype project, an effort that will provide comprehensive and scientifically credible mid-scale data to support the National Fire Plan. We analyzed output from 2,000 year simulations to determine the thresholds of landscape condition based on the variability of burned area and dominant vegetation coverage. Results show that optimal landscape extent using burned area variability is approximately 100 km² depending on topography, map resolution, and model parameterization. Variability of dominant vegetation area is generally higher and the optimal landscape sizes are larger in comparison to those features determined from burned area. Using the LANDFIRE project as a case study, we determined landscape size and map resolution for a large mapping project, and showed that optimal landscape size depends upon geographical, ecological, and management context. This paper was written and prepared by U.S. Government employees on official time, and therefore is in the public domain and not subject to copyright. The use of trade or firm names in this paper is for reader information and does not imply endorsement by the U.S. Department of Agriculture of any product or service.     

Complementary host–pathogen genetic analyses of the role of fumonisins in the Zea mays–Gibberella moniliformis interaction

Zea mays often is colonized with the fungus Gibberella moniliformis, which produces fumonisin toxins. The role of fumonisins in seedling colonization and blight was studied using complementary genetic analyses of host and pathogen. Only one of two fumonisin B1 (FB1)-insensitive maize backcross lines was more resistant than the FB1-sensitive parent to seedling blight, indicating that the increase in FB1-insensitivity was not associated with an increase in resistance. FB1-producing and nonproducing isogenic fungal strains did not differ in ability to cause seedling blight, but the FB1-producing strain was more effective in systemic colonization of seedlings in reciprocal strain challenge tests. Together, these and previous results indicate that the role of fumonisins depends on complex environmental and genetic contexts in this host–pathogen interaction.     

Alanine aminotransferase apoenzyme in dogs

Unusually low serum activity of alanine aminotransferase (ALT) was detected in a Rottweiler dog with gastric dilatation-volvulus. Activity of ALT in the same sample was found to be much higher (estimated increase of 14,225%) when measured by methods adding the cofactor pyridoxal-5'-phosphate (P5P), indicating that nearly all serum ALT was in the apoenzyme form. An investigation was undertaken to determine the frequency of high serum aminotransferase apoenzyme levels in dogs. Eighty canine serum samples submitted to the Clinical Pathology Laboratory at Cornell University were assayed for ALT and aspartate aminotransferase (AST) in the presence or absence of exogenous P5P. In 79 dogs, inclusion of P5P in the LAT assay resulted in a median decrease in AST activity of -6.3% (range -33.3% to 25.0%) in all 80 dogs. One dog had an increase of 336% in ALT activity after inclusion of P5P in the assay, but lacked a similar increase in AST activity. The reason for the high levels of ALT apoenzyme in the 2 dogs was not determined.     

DETECTION OF PORTAL BLOOD FLOW USING PER-RECTAL 99mTc-PERTECHNETATE SCINTIGRAPHY IN NORMAL CATS

This study reports data obtained from per-rectal ^99mTc-pertechnetate portal scintigraphy in normal cats. It examines the effects of chemical restraint and the methods employed in defining regions of interest (ROIs) on the shunt index derived from this data. Six normal cats were used for the study; all six were chemically restrained for imaging using propofol and later four of them were manually restrained for comparison. Portal blood flow was studied and the mean shunt index was found to be 5.9%± 3.9 when ROIs were operator defined and 9.2%± 4.4 when ROIs were defined using an isocontour program. In cats that were restrained using propofol and operator defined ROIs, the mean value for the time between detection of radioactivity in the liver and in the heart was 14 ± 1 seconds.     

RADIOGRAPHIC ASPECTS OF Pneumocystis carinii PNEUMONIA IN THE MINIATURE DACHSHUND

The thoracic radiographic changes of Pneumocystis carinii in 7 miniature Dachshunds were reviewed. The dogs were 7–12 months old and presented with polypnea, exercise intolerance and clinical signs suggestive of immune-incompetence. P. carinii pneumonia was diagnosed in all the dogs using transtracheal aspirate cytology and confirmed at postmortem in 3 dogs that died. Radiographically, diffuse pulmonary changes were present and varied from a mild interstitial and bronchial pattern to an alveolar pattern. Radiographic evidence of cor pulmonale was present in 1 dog. The most severe radiographic changes were seen in 2 of the dogs that died.