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Reptiles and amphibians play important roles in ecological communities and can be extremely sensitive indicators of environmental change, despite their cryptic and secretive habits. To estimate herpetofaunal community dynamics potentially attributable to either natural or anthropogenic environmental variation, herpetofaunal biodiversity managers will require specific, standardized, and efficient field sampling methods. One such method involves using arrays of wood and tin coverboards and is the subject of this paper. Studies were conducted on the Savannah River Site in the Upper Coastal Plain of South Carolina from January 1988 to August 1991. Compared with a drift fence/pitfall trap array, the coverboard technique requires less maintenance and sampling effort, but only those reptiles and amphibians using the coverboards at the time of an array check could be encountered. In contrast, live-trapping methods integrate over a longer time period and thereby generate many more encounters per trap. Nonetheless, large numbers of encounters with cryptic reptiles and amphibians can result from coverboard sampling depending upon the study site, coverboard age, time of day, and type of coverboard (i.e., wood or tin). Detailed analyses of hydric and thermal microclimates beneath coverboards suggest specific mechanisms to explain observed differences in herpetofaunal coverboard use. We conclude that the coverboard technique can provide a useful means to quantify patterns in herpetofaunal relative abundance and biodiversity. However, array design and sampling protocol should be carefully selected to minimize sampling biases in encounter probabilities due to subtle differences among herpetofauna in their hygrothermal microclimate preferences.

Little is known about the feeding ecology and breeding success of the Lesser Flamingo (Phoeniconaias minor) and Greater Flamingo (Phoenicopterus ruber roseus) on the ephemeral salt lake of the Makgadikgadi, Botswana. Some observations of large numbers of both species have been recorded breeding on the Makgadikgadi salt pans, and it is believed that this site is among the most important breeding sites for both species of flamingo in Africa. This paper addresses the importance of the Makgadikgadi salt pans by revising some of the observations made in the past and also introduces a long-term research project that is currently underway to determine more about the ecology of the pans and the flamingo breeding success at this important site.

We studied foraging habitat use of Wood Storks (Mycteria americana) from three coastal colonies using United States Fish and Wildlife Service National Wetlands Inventory data within a geographic information system (GIS). Observers followed storks from breeding colonies to foraging sites in a fixed-winged aircraft. The main objectives of the study were to estimate the foraging range of each Wood Stork colony, determine what wetland types were used in relation to their availability and spatial distribution, and determine how foraging habitat use was related to tidal stage. Storks foraged in tidal creeks during lower tide levels when prey were concentrated in shallower water, and foraged more in palustrine (freshwater) wetlands when tide levels were high. Predictability of foraging habitat use based on habitat distribution varied among colonies and depended on how wetland types were aggregated. Foraging locations were spatially clustered, in some cases by habitat type (estuarine vs. palustrine). These spatial clusterings may be explained by the proximity of a foraging location to the colony and by the habitat types around the colony. Storks also flew longer distances to forage in palustrine sites than in estuarine sites. Received 29 July 1997, accepted 1 January 1998.

We used the seedling emergence method to evaluate the influence of the dominant vegetation (herbaceous, shrubby, forested) and the surrounding landscape on seed bank composition in seven Carolina bays. Landscape influence was evaluated indirectly by determining whether seed banks in wetlands close to clearcuts had more upland weedy species than those farther from clearcuts. Seed bank species composition and richness differed among forested, shrubby and herbaceous bays. DECORANA ordination identified a gradient of species composition from herbaceous bays, to shrubby bays, to forested bays. Bays near clearcuts had significantly more upland weedy species in their seed banks, with bays 20 m from clearcuts containing 79% more weedy species on average than bays 100 m from clearcuts. Within a bay, drier vegetation zones had 2.4 times more weedy species than did deep water zones. These results illustrate the potential contributions from surrounding landscape units to bay seed banks and highlight the need for further studies directly assessing the impact of adjacent clearcuts on bay vegetation dynamics.

Neighborhood (spatial) models of plant populations have assumed implicitly that competition between adjacent individuals is the primary determinant of observed dynamics. In contrast, non-spatial models now routinely test this assumption against the null hypothesis that individual differences in intrinsic growth rate alone can explain observed patterns. In a widely-used neighborhood model (Pacala and Silander 1990), competition is modelled as a direct effect of neighbors on target plant biomass, which in turn affects plant fecundity. We have developed a statistical null model for Pacala and Silander's (1990) neighborhood model for plant monocultures that explicitly incorporates variation in plant growth rate, and permits a test of the hypothesis that neighborhood competition controls plant ground area occupied (= rosette diameter) and biomass. An additional alternative hypothesis to our model is that neighbors can affect fecundity independently of their effects on plant diameter and biomass. We tested these three hypotheses (1) no effect of competition (null); (2) neighborhood competition directly affecting plant diameter and biomass, and indirectly affecting fecundity (Pacala and Silander 1990); (3) neighborhood competition directly affecting plant diameter, biomass, and fecundity by replicating, with appropriate controls, Silander and Pacala's (1985) experiments with the rosette-forming crucifer, Arabidopsis thaliana. Neighborhood competition in dense stands resulted in simultaneous changes in plant diameter, biomass, and fecundity relative to plants grown in the absence of competition. There also were apparent effects of neighbors on plant fecundity independent of their effects on plant size alone. The null model was not supported, but Pacala and Silander's model did not fit the data as well as the model that incorporated direct effects of neighbors on plant fecundity.

were used to quantify shade tolerance and successional status of individual species. In all plots, small stem density decreased and large stem density increased, an indication that the forests were in mid-successional phases where competition is expected to be intense. Shade tolerant species, especially small tree life forms, had the greatest ratios of ingrowth to mortality. Large differences in population flux, even among shade tolerant species, indicated that different mechanisms can account for increases in populations of late-successional species. Within some species, ratios of ingrowth to mortality varied significantly across the gradient reflecting flooding or soil moisture effects on succession.

Genotypic frequencies at 8 enzyme loci were examined in a population of mosquitofish, Gambusia affinis (Baird and Girard) during acute arsenate exposure. Genotypes at 2 loci (fumarate hydratase and glucose-phosphate isomerase-2) and multiple locus heterozygosity (male fish) were significantly correlated with time to death (TTD). The results from arsenate exposures were contrasted with those reported earlier for acute inorganic mercury exposure. Earlier TTD were associated with a rare homozygous genotype for the Gpi -2 locus in both arsenate and inorganic mercury exposures; however, no other single locus effect-on TTD was common to both toxicants. The results of acute exposures of mosquitofish to mercury and arsenate suggest that most of the effects of multiple locus heterozygosity can be attributed to the summation of single locus effects.

Genetic plasticity in a mosquitofish (Gambusia affinis Baird and Girard) population was examined relative to acute mercury toxicity. Genotypes at eight loci (isocitrate dehydrogenase-1 and -2, mannosephosphate isomerase, glucosephosphate isomerase-2, fumarate hydratase, malate dehydrogenase-1, leucylglycylglycine peptidase and phenylalanylproline peptidase) were scored using starch gel electrophoresis. Two null hypotheses were tested: (a) time to death does not differ between genotypes at individual loci and (b) time to death does not differ with multiple-locus heterozygosity. Genotypes at three of the eight loci displayed significant effects on mosquitofish time to death. Multiple-locus heterozygosity also had a significant effect on time to death. Significant amounts of genetic plasticity were found in a population of mosquitofish with no previous exposure to inorganic mercury.

We examined herbivore damage in a natural association in order to evaluate the hypothesis that herbivory is generally greater in the shade (Maiorana 1981). Damage was measured in relation to habitat, adult plant distribution, and plant size for 13 species of native herbaceous forbs that cross the natural shade/sun ecotone at the interface of montane meadow and aspen (Populus tremuloides) woodland. Eight of the 13 species had statistically significant differences in leaf area damaged between sun and shade individuals (p

Left-censoring of data sets complicates subsequent statistical analyses. Generally, substitution or deletion methods provide poor estimates of the mean and variance of censored samples. These substitution and deletion methods include the use of values above the detection limit (DL) only, or substitution of 0, DL/2 or the DL for the below DL values during the calculation of mean and variance. A variety of statistical methods provides better estimators for different types of distributions and censoring. Maximum likelihood and order statistics methods compare favorably to the substitution or deletion methods. Selected statistical methods applicable to left-censoring of environmental data sets are reviewed with the purpose of demonstrating the use of these statistical methods for coping with Type I (and Type II) left-censoring of normally and log-normally distributed environmental data sets. A PC program (UNCENSOR) is presented that implements these statistical methods. Problems associated with data sets with multiple DLs are discussed relative to censoring methods for life and fatigue tests as recently applied to water quality data sets.

Sparse species have chronically small local population sizes, even though they occur in several habitats over a wide geographic range. Greenhouse de Wit replacement series with seven species of sparse and common perennial grasses of tallgrass prairie were performed with seedlings and tiller fragments for 5, 10, and 15, mo. As younger and older seedlings, sparse grasses overyielded and were advantaged by the interaction with common grasses. The common grasses underyielded and were disadvantaged in mixture with sparse grasses. As tillers, the interaction was less antagonistic, and both common and sparse grasses either overyielded or were unaffected by the interaction. Seedlings of sparse species were largest when planted in low proportion, surrounded by individuals of a common grass. Because the sparse species are not disadvantaged by interactions with their common neighbors, their competitive abilities are not implicated as a cause of their local rarity. Rather, the good competitive abilities of these spar...

Background Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of the genome assembly for the black legged tick, Ixodes scapularis, and transcriptome datasets for multiple species of ticks offers an opportunity to assess the contribution of gene duplication to the genome. Here we developed a bioinformatics pipeline to identify and analyze duplicated genes (paralogs) using gene models from the prostriate tick, I. scapularis IscaW1.1 annotation and expressed sequence tags (ESTs) from I. scapularis and the metastriate ticks, Rhipicephalus microplus (southern cattle tick), R. appendiculatus (brown ear tick) and Amblyomma variegatum (tropical bont tick). Results Approximately 1-2 % of I. scapularis gene models and 2-14 % of ESTs from the four species represent duplicated genes. The ratio of non-synonymous to synonymous nucleotide substitution rates suggests ~ 25 % of duplicated genes are under positive selection pressure in each species. Analyses of synonymous substitution rates provide evidence for two duplication events in I. scapularis and R. microplus involving several hundred genes. Conservative molecular clock estimates based on synonymous substitution rates for species of Anopheles mosquitoes and the fruit fly, Drosophila melanogaster, suggest these events occurred within the last 50 MYA. Mapping of paralogs to the I. scapularis genome assembly supports tandem, or possibly segmental duplication events. Conclusions The present study marks the first genome-level analyses of gene duplication for the Ixodidae and provides insights into mechanisms shaping genome evolution in this group. At least two duplication events involving hundreds of genes may have occurred independently in the lineages prostriata and metastriata, with tandem and segmental duplication the most likely mechanisms for paralog generation. Duplicated genes under positive selection pressure may be linked to emerging functions in the tick and represent important candidates for further study. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2350-2) contains supplementary material, which is available to authorized users.