Effects of sample survey design on the accuracy of classification tree models in species distribution models

We evaluated the effects of probabilistic (hereafter DESIGN) and non-probabilistic (PURPOSIVE) sample surveys on resultant classification tree models for predicting the presence of four lichen species in the Pacific Northwest, USA. Models derived from both survey forms were assessed using an independent data set (EVALUATION). Measures of accuracy as gauged by resubstitution rates were similar for each lichen species irrespective of the underlying sample survey form. Cross-validation estimates of prediction accuracies were lower than resubstitution accuracies for all species and both design types, and in all cases were closer to the true prediction accuracies based on the EVALUATION data set. We argue that greater emphasis should be placed on calculating and reporting cross-validation accuracy rates rather than simple resubstitution accuracy rates. Evaluation of the DESIGN and PURPOSIVE tree models on the EVALUATION data set shows significantly lower prediction accuracy for the PURPOSIVE tree models relative to the DESIGN models, indicating that non-probabilistic sample surveys may generate models with limited predictive capability. These differences were consistent across all four lichen species, with 11 of the 12 possible species and sample survey type comparisons having significantly lower accuracy rates. Some differences in accuracy were as large as 50%. The classification tree structures also differed considerably both among and within the modelled species, depending on the sample survey form. Overlap in the predictor variables selected by the DESIGN and PURPOSIVE tree models ranged from only 20% to 38%, indicating the classification trees fit the two evaluated survey forms on different sets of predictor variables. The magnitude of these differences in predictor variables throws doubt on ecological interpretation derived from prediction models based on non-probabilistic sample surveys.     

Locational Errors in Maps from Environmental Surveys and Their Implications for Information Extraction

1.Information on all maps, including those which depict characters of the natural environment, is subject to locational error. 2.Locational errors on field-sketched maps are attributable to inaccuracies both in the base map itself and in the method of locating and recording features onto the base map. 3.Two main sources of error associated with field sketch mapping were quantified using the River Corridor Survey maps as an example. First, channel widths are routinely exaggerated on these maps to allow recording of in-channel features. Distortions of river bank length of the order of 25% were shown to arise from a four-fold exaggeration of the width of a sinuous channel. Second, discrepancies in feature location of the order of 20% were found along a 500 m river stretch, although errors could be reduced to approximately 2% if undistorted, large-scale base maps were used. 4.An abundance scale appropriate to the inherent locational inaccuracy was devised to extract semi-quantitative information from River Corridor Surveys recorded on distorted base maps. Application of this scale to 29 River Corridor Survey maps of a 14·5 km river corridor produced a useful representation of environmental gradients within the corridor. 5.With the increasing potential to integrate and analyse environmental information within large computer databases including Geographic Information Systems, it is essential that the level of accuracy is recognised and quantified so that the errors can be allowed for in the development of methods of extracting information from the maps.     

Tolerating castration by hiding flowers in plain sight

A key challenge in the study of inter-specific cooperation, or mutualisms, is to understand the mechanisms that prevent cheating. However, many mutualisms are still invaded by parasites, and we propose that plant ‘tolerance strategies’, which allow an individual to re-grow and/or reproduce after damage, might have evolved to recover some of the fitness lost to parasitism. We focus on the ant plant Cordia nodosa and its protecting ant symbionts Allomerus octoarticulatus and Azteca spp. Allomerus is a castration parasite, destroying host flowers. However, some flowers are produced on new branch shoots, where they escape castration. Here, we ask whether C. nodosa tolerates castration by directing floral growth to new shoots. We find that C. nodosa produces four times more floral buds on the new shoots of Allomerus-inhabited plants, compared to Azteca-inhabited plants. Additionally, on Allomerus-inhabited plants, the production of floral buds is three times greater on new than on mature shoots, and more floral buds are grown on plants with new shoots than on those without. We conclude therefore that C. nodosa tolerates castration by re-allocating floral resources to new shoots. We also test whether tolerance exploits behavioural differences between the brood-tending ‘nurse’ ant worker caste, which is active on mature shoots, and the new shoot-protecting ‘patroller’ caste. Behavioural assay experiments reveal that nurse ants are strongly attracted to extracts of flowers, whereas patrollers are not, suggesting that nurses are the primary castrating caste. Thus, producing flowers on new shoots avoids the castrating caste. We finish by proposing that tolerance strategies can promote the evolution and maintenance of mutualism.     

Methane Fluxes from a Wetland using the Flux-Gradient Technique The Measurement of Methane Flux from a Natural Wetland Pond and Adjacent Vegetated Wetlands using a TDL-Based Flux-Gradient Technique

Methane emissions were measured from a bog andlake in the Experimental Lakes Area in Northern Ontario in 1992and 1993, prior to and following flooding. Bog fluxes were smallin 1992 (0.27 mg m^-2 d^-1) but increased 5-fold in 1993 afterflooding. Over the bog, there was a diel cycle of nighttimeemission and daytime uptake in 1992 in contrast to constantemission in 1993. Lake emissions decreased after flooding butwere much greater than bog emissions in both years (average = 7.3 mg m^-2 d^-1). Seasonally, the bog flux was correlated withground temperatures after flooding. In 1992, lake fluxes werecorrelated with air temperature on a daily basis. In contrast,seasonal lake fluxes were correlated with water and sedimenttemperatures in 1992, but only with sediment temperatures in1993. These results are explained with respect to the effects offlooding on lake and bog dynamics.     

Predicting regional spread of non-native species using oceanographic models: validation and identification of gaps

Predicting spread is a central goal of invasion ecology. Within marine systems, researchers have increasingly made use of oceanographic circulation models to estimate currents and track species dispersal. However, the accuracy of these models for predicting biological patterns, particularly for non-native species, has generally not been validated. Particularly, we wished to examine the ability of models to predict physical and biological processes, which jointly determine the spread of marine larval organisms. We conducted two empirical studies—a recruitment study and a drift card study—along the coast of New England, USA, focusing on two invaders of concern—the European green crab (Carcinus maenas) and the Asian shore crab (Hemigrapsus sanguineus), to explicitly evaluate the ability of oceanographic models to predict patterns of spread. We used data from the large-scale drift card study to validate our ability to capture dispersal patterns driven purely by physical processes. Next, we conducted a recruitment study to evaluate our ability to reproduce patterns of biological dispersal. We were generally capable of reproducing drift cards patterns—suggesting that the physical mechanics in the model were predictive. However, predicted biological patterns were inconsistent—we were able to predict dispersal patterns for H. sanguineus but not for C. maenas. Our results highlight the importance of validating models and suggest that more work is necessary before we can reliably use oceanographic models to predict biological spread of intertidal organisms.     

Climate vs. soil factors in local adaptation of two common plant species

Evolutionary theory suggests that divergent natural selection in heterogeneous environments can result in locally adapted plant genotypes. To understand local adaptation it is important to study the ecological factors responsible for divergent selection. At a continental scale, variation in climate can be important while at a local scale soil properties could also play a role. We designed an experiment aimed to disentangle the role of climate and (abiotic and biotic) soil properties in local adaptation of two common plant species. A grass (Holcus lanatus) and a legume (Lotus corniculatus), as well as their local soils, were reciprocally transplanted between three sites across an Atlantic-Continental gradient in Europe and grown in common gardens in either their home soil or foreign soils. Growth and reproductive traits were measured over two growing seasons. In both species, we found significant environmental and genetic effects on most of the growth and reproductive traits and a significant interaction between the two environmental effects of soil and climate. The grass species showed significant home site advantage in most of the fitness components, which indicated adaptation to climate. We found no indication that the grass was adapted to local soil conditions. The legume showed a significant home soil advantage for number of fruits only and thus a weak indication of adaptation to soil and no adaptation to climate. Our results show that the importance of climate and soil factors as drivers of local adaptation is species-dependent. This could be related to differences in interactions between plant species and soil biota.     

Characterization and growth response of bacteria in soil following application of carbofuran.

Enhanced biodegradation of carbofuran (2, 3-dihydro-2, 2 dimethyl-7-benzofuranyl methyl carbamate) is an economically significant, but poorly understood, microbial phenomenon in soil. A series of experiments was conducted to examine short term changes in soil bacterial populations stimulated by carbofuran application at field rates. In the field experiment, commercially formulated carbofuran and butylate (S-ethyl diisobutyl carbamothioate) were applied at 5.6 kg ai ha-1 and 8.4 kg ai ha-1, respectively, on a soil (Putnam silt loam) exhibiting enhanced degradation of carbofuran. In laboratory studies, technical grade carbofuran (20 mg kg-1 soil) was applied to samples of the field soil. Bacterial populations were estimated using non-selective (tryptic soy agar) and selective media containing carbofuran or butylate. Largest population increases in pesticide-treated soil were observed between 7 and 15 days after treatment (DAT) compared to populations in non-treated soil. Significant increases (P less than 0.05) in total bacterial populations and presumed carbofuran-degraders due to carbofuran application were associated with increased populations of Pseudomonas spp. and Flavobacterium spp. Application of carbofuran appeared to provide a competitive advantage to these species over actinomycetes persisting beyond 20 DAT. Growth responses of bacteria to carbofuran in the Putnam soil were compared to those in a native prairie soil (Mexico silt loam), which exhibited a much slower rate of carbofuran degradation. Bacterial population response to carbofuran was measurable, but small and short-lived. Perpetuation of the enhanced degradation phenomenon may lie in a persistent pesticide-induced competitive advantage given to a very small segment of the microbial population. This advantage may not be detectable after 20 days using conventional plating techniques.