Philip M. Dixon

A new method to measure spatial association for ecological count data

Abstract A new method is introduced to assess the spatial association between two sets of count data. This features a measure of local association for counts, defined for each sample unit. The new measure is based on a comparison of the spatial SADIE clustering index of the two sets at each sample unit; the mean of the measure is represented by the simple correlation coefficient between the clustering indices of the two sets. The randomization method allows the construction of a test and critical values. For the first time, spatial association may be mapped for count data; clusters of units with positive association or negative dissociation may be identified. The method is exemplified by analysis of spatial pattern and spatial association of counts of male and female tupelo trees from three plots in a South Carolina swamp forest. In addition, methods are presented to distinguish larger-scale apparent association between the sexes, caused by indirect effects, from direct smaller-scale association. No tendency was found for the sexes to occur together at the small-scale, only an apparent affinity caused through their co-location in particular subareas of each plot. The conversion from mapped to count data requires a choice of unit size; the conclusions of these analyses were not affected greatly by changes in unit size.

Bootstrapping the Gini Coefficient of Inequality

Despite current interest in the causes and consequences of plant size hierarchies, there are different opinions about the best way to evaluate a size distribution. Weiner and Solbrig (1984) have argued that size hierarchy means size inequality, and that the Gini coefficient of inequality (Sen 1973) is more relevant than skewness or variance of plant size (e.g., Turner and Rabinowitz 1983) for most ecological questions. Weiner (1985) presents a formula to estimate the population Gini coefficient (G) from a sample and states that reasonable confidence intervals for the population Gini coefficient can be obtained by a bootstrapping procedure (Efron 1982). This note evaluates the accuracy of these bootstrap confidence intervals. We find that they are reasonably accurate when calculated from samples of 50 or more individuals, but that they are too narrow when calculated from smaller samples. The bootstrap procedure uses the observed data to estimate the theoretical and usually unknown distribution from which the data came (Efron 1982, Meyer et al. 1986). Bootstrap samples of the same size as the original sample are repeatedly drawn by sampling with replacement from the observed data. The test statistic, e.g., the Gini coefficient, is calculated for each bootstrap sample. The distribution of Gs obtained from bootstrap sampling can be used to estimate the standard deviation and set confidence limits on the observed statistic (Efron 1982). The bootstrap procedure does not require any knowledge of the distribution of the statistic in question, may have certain optimal properties (Efron 198 1, but see Schenker 1985, Wu 1986), and can be used when the standard deviation or confidence intervals for the statistic are unknown or difficult to calculate analytically. The accuracy of any method for computing confidence intervals can be evaluated by generating data from a known distribution with a known parameter. If many samples of data from the known distribution are generated and a confidence interval calculated from each, the number of confidence intervals that include the parameter can be determined. An accurate confidence interval includes the known parameter the stated percentage of the time; for example, a 95% confidence interval should include the true value in 95% of the random samples of data. Although in some situations bootstrap confidence intervals are relatively accurate (Efron 1982:79), in other situations they are too narrow (Schenker 1985, Meyer et al. 1986).

WOODY PLANT REGENERATION IN FOUR FLOODPLAIN FORESTS

Between 1987 and 1990, we estimated seedfall and recorded age, growth, and survival of 10 933 tree and vine seedlings growing in the understories of four bottom- land hardwood forests in South Carolina. The forests differed in flood frequency, soils, and vegetation structure but had a number of woody plant species in common. Several demographic processes were consistent for all four forests as well as for flood- plain forests described in other published studies. Smaller seeded species had larger numbers of seeds dispersed, germinants, and established seedlings. Seed size, however, was not clearly related to seedling survival. Published rankings of shade and flood tolerances were also unrelated to survival, at least during the first growing season after germination. Seedling survival rates were least during the first growing season and greater in subsequent years. Within a growing season, early germinants had greater survival. For some species, survival was negatively related to basal area of neighboring conspecific adult trees. Some aspects of the regeneration process were more site specific. Within species, seedfall densities relative to adult tree abundance differed across forests by an order of magnitude. First-year seedling mortality rates were significantly affected by site and site x species interactions. Mortality in subsequent years was also significantly affected by site. Although the role of flooding in site-specific mortality was not clear, small elevation changes within flooded sites were correlated with changes in germination and survival for some species.

Global amphibian population declines

The decline and disappearance of relatively undisturbed populations of amphibians in several high-altitude regions since the 1970s suggests that they may have suffered a global decline, perhaps with a common cause or causes. Houlahan et al. examined means of trends for 936 amphibian populations and concluded that global declines began in the late 1950s, peaked in the 1960s, and have continued at a reduced rate since. Here we re-analyse their data using a method that accounts for the sampling of different populations over different time periods, and find evidence of a mean global decline in monitored populations only in the 1990s. However it is calculated, the global mean not only masks substantial spatial and temporal variation in population trends and sampling effort, but also fails to distinguish between a global decline with global causes and the cumulative effects of local declines with local causes.

Effects of past land use on spatial heterogeneity of soil nutrients in southern Appalachian forests

We examined patterns of nutrient heterogeneity in the mineral soil (0-15 cm depth) of 13 southern Appalachian forest stands in western North Carolina .60 yr after abandonment from pasture or timber harvest to investigate the long-term effects of land use on the spatial distribution and supply of soil resources. We measured soil carbon (C), nitrogen (N), acid-extractable phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) concentrations and pools, and potential net N mineralization and nitrification rates to evaluate differences in mean values, variance at multiple scales, and fine-scale spatial structure. While comparisons of averaged values rarely indicated that historical land use had an enduring effect on mineral soil or N cycling, differences in variance and spatial structure suggested that former activities continue to influence nutrient distributions by altering their spatial heterogeneity. Patterns differed by element, but generally variance of soil C, N, and Ca decreased and variance of soil P, K, and Mg increased with intensive past land use. Changes in variance were most conspicuous and consistent locally ( ,28 m), but C, Ca, P, and Mg also exhibited appreciable differences in variance at coarser scales ( .150 m). High variability in soil compaction resulted in some changes in scale-dependent patterns of nutrient pool variance compared with nutrient concentration variance. It also affected the variance of N cycling rates, such that mass-based rates varied less and area-based rates varied more in intensively used areas than in reference stands. Geostatistical analysis sug- gested that past land use homogenized the spatial structure of soil C, K, and P in former pastures. In contrast, logged stands had highly variable spatial patterning for Ca. These results suggest that land use has persistent, multi-decadal effects on the spatial heterogeneity of soil resources, which may not be detectable when values are averaged across sites. By interacting with patterns of variability in the plant and heterotrophic biota, differences in nutrient distribution and supply could alter the composition and diversity of forest ecosystems. Scale-dependent changes in nutrient heterogeneity could also complicate efforts to determine biogeochemical budgets and cycling rates.

Are many little hammers effective? Velvetleaf (Abutilon theophrasti) population dynamics in two- and four-year crop rotation systems

Abstract To improve understanding of relationships between crop diversity, weed management practices, and weed population dynamics, we used data from a field experiment and matrix models to examine how contrasting crop rotations affect velvetleaf. We compared a 2-yr rotation system (corn–soybean) managed with conventional rates of herbicides with a 4-yr rotation (corn–soybean–triticale + alfalfa–alfalfa) that received 82% less herbicide. In November 2002, a pulse of velvetleaf seeds (500 seeds m−2) was added to 7- by 7-m areas within replicate plots of each crop phase–rotation system combination. Velvetleaf seed, seedling, and reproductive adult population densities, seed production, and seed losses to predators were measured during the next year. Velvetleaf seed production was greater in the 4-yr rotation than in the 2-yr rotation (460 vs. 16 seeds m−2). Averaged over 12 sampling periods from late May to mid-November 2003, loss of velvetleaf seeds to predators also was greater in the 4-yr rotation than in the 2-yr rotation (32 vs. 17% per 2 d). Modeling analyses indicated that velvetleaf density in the 4-yr rotation should decline if cumulative losses of seeds produced in the soybean phase exceeded 40%. Achieving such a level of predation appears possible, given the observed rates of velvetleaf seed predation. In addition, no tillage occurs in the 4-yr rotation for 26 mo after soybean harvest, thus favoring seed exposure on the soil surface to predators. Models that included estimates of seed predation indicated that to prevent increases in velvetleaf density, weed control efficacy in soybean must be ≥ 93% in the 2-yr rotation, but could drop to 86% in the 4-yr rotation. These results support the hypothesis that diverse rotations that exploit multiple stress and mortality factors, including weed seed predation, can contribute to effective weed suppression with less reliance on herbicides. Nomenclature: Velvetleaf, Abutilon theophrasti Medicus ABUTH; alfalfa, Medicago sativa L.; corn, Zea mays L.; soybean, Glycine max (L.) Merr.; triticale, Triticosecale spp.

Evolution of Porcine Reproductive and Respiratory Syndrome Virus during Sequential Passages in Pigs

ABSTRACT Porcine reproductive and respiratory syndrome (PRRS) viruses are recognized as possessing a high degree of genetic and antigenic variability. Viral diversity has led to questions regarding the association of virus mutation and persistent infection in the host and has raised concerns vis-à-vis protective immunity, the ability of diagnostic assays to detect novel variants, and the possible emergence of virulent strains. The purpose of this study was to describe ongoing changes in PRRS virus during replication in pigs under experimental conditions. Animals were inoculated with a plaque-cloned virus derived from VR-2332, the North American PRRS virus prototype. Three independent lines of in vivo replication were maintained for 367 days by pig-to-pig passage of virus at 60-day intervals. A total of 315 plaque-cloned viruses were recovered from 21 pigs over the 367-day observation period and compared to the original plaque-cloned virus by virus neutralization assay, monoclonal antibody analysis, and sequencing of open reading frames (ORFs) 1b (replicase), 5 (major envelope protein), and 7 (nucleocapsid) of the genome. Variants were detected by day 7 postinoculation, and multiple variants were present concurrently in every pig sampled over the observation period. Sequence analysis showed ORFs 1b and 7 to be highly conserved. In contrast, sequencing of ORF 5 disclosed 48 nucleotide variants which corresponded to 22 amino acid variants. Although no epitopic changes were detected under the conditions of this experiment, PRRS virus was shown to evolve continuously in infected pigs, with different genes of the viral genome undergoing various degrees of change.

DETECTING TRENDS IN SPECIES COMPOSITION

Species composition reflects a combination of environmental and historical events at a site; hence, changes in species composition can provide a sensitive measure of ecologically relevant changes in the environment. Here, we consider the analysis of species composition when multiple sites are followed through time. Analyses of temporal trends in species composition either summarize species composition into a few metrics (indices or axis scores) or analyze the similarity among sites. We develop and illustrate the similarity approach. Each pair of samples represents a pair of replicates, a pair from the same site at different times, a pair from different sites at the same time, or an unrelated pair. Differences among times can be estimated by comparing average temporal dissimilarity to average replicate dissimilarity. Temporal trends can be described by one of three statistics that measure progressive change, the correlation of temporal dissimilarity with the length of time between samples. These methods are illustrated using data on changes in a South Carolina zooplankton assemblage following disturbance, and changes in bird species composition on Skokholm Island, Wales. It is difficult to define and interpret temporal trends. Some definitions of interesting trends, like increasing divergence from another set of sample plots, place additional requirements on the sampling design. Including replicate samples or clustering sample plots and including “control” plots for comparison with sentinel sites would contribute to an understanding of changes in species composition.

Testing Spatial Segregation Using a Nearest-Neighbor Contingency Table

Segregation of species occurs when a species tends to be found near conspecifics. This is frequently investigated using a contingency table, classifying each point by its species and the species of its nearest neighbor. Pielou proposed using a 1-df chi-square test of independence as a test of segregation. This test is inappropriate if all locations within a study area are mapped. For completely mapped data, I derive the expectations and variances of the cell counts in the nearest-neighbor contingency table under the null hypothesis that species labels are randomly assigned to points. The properties of the cell counts suggest a new 2-df chi-square test of spatial segregation, a pair of species-specific tests, and a pair of species-specific measures of segregation. In small samples, the proposed tests have the appropriate size, unlike the Pielou test. The new test is illustrated with three examples: Pielous Douglas-fir/ponderosa pine data, a realization of a mother-daughter process, and the locations of male and female water tupelo trees. 24 refs., 4 figs., 6 tabs.

Germination and Sporulation of Colletotrichum acutatum on Symptomless Strawberry Leaves

ABSTRACT The germination and sporulation of Colletotrichum acutatum were characterized over time on strawberry leaves (cv. Tristar) and plastic coverslips incubated at 26 degrees C under continuous wetness. Conidia germinated within 3 h after inoculation and formed melanized appressoria with pores by 9 h after inoculation. Host penetration was not observed up to 7 days after inoculation. Production of secondary conidia on conidial and hyphal phialides began within 6 h after inoculation. Secondary conidiation was responsible for up to a threefold increase in the total number of conidia within 7 days after inoculation. Primary conidia and hyphae began to collapse 48 h after inoculation, whereas melanized appressoria remained intact. These findings suggest that appressoria and secondary conidia of C. acutatum produced on symptomless strawberry foliage may be significant sources of inoculum for fruit infections.