Modelling plant species richness using functional groups

Conservation biologists increasingly rely on spatial predictive models of biodiversity to support decision-making. Therefore, highly accurate and ecologically meaningful models are required at relatively broad spatial scales. While statistical techniques have been optimized to improve model accuracy, less focus has been given to the question: How does the autecology of a single species affect model quality? We compare a direct modelling approach versus a cumulative modelling approach for predicting plant species richness, where the latter gives more weight to the ecology of functional species groups. In the direct modelling approach, species richness is predicted by a single model calibrated for all species. In the cumulative modelling approach, the species were partitioned into functional groups, with each group calibrated separately and species richness of each group was cumulated to predict total species richness. We hypothesized that model accuracy depends on the ecology of individual species and that the cumulative modelling approach would predict species richness more accurately. The predictors explained plant species richness by ca. 25%. However, depending on the functional group the deviance explained varied from 3 to 67%. While both modelling approaches performed equally well, the models of the different functional groups highly varied in their quality and their spatial richness pattern. This variability helps to improve our understanding on how plant functional groups respond to ecological gradients.     

A Protocol for Plant Conservation by Translocation in Threatened Lowland Fynbos

Abstract: A form of lowland, sandplain Fynbos restricted to the Cape Flats near the city of Cape Town is the South African vegetation type most threatened by urban and agricultural development. Cape Flats Fynbos remnants, totaling 4.8 km², contain 14 plant species endemic to the Cape Flats scattered through four protected areas and 11 unprotected vegetation fragments on public land. Despite their small size and management problems, the remaining protected areas are under pressure from the public and developers to function as "lifeboats," or places of safety, for attractive indigenous plant species from the unprotected areas destined for development because the popular perception is that any indigenous plant population threatened by habitat destruction should be saved by being transplanted into a protected area. The urgency for dealing with the issue of plant rescue in the Cape Town metropolitan area was the catalyst for a workshop held at the University of Cape Town in 1998 to develop protocols for Fynbos plant species translocations. We report on points raised by managers and academics at the workshop, including the selection of target taxa, individuals, and establishment sites, and methods for introduction, and present case histories illustrating possible solutions to the problems encountered.     

Determination of antimony in human blood with inductively coupled plasma-mass spectrometry

A method is presented for the determination of antimony in whole human blood samples with an ICP-MS instrument using a quadrupole mass analyzer. A nitric acid/hydrogen peroxide open digestion procedure was employed for the blood sample treatment and preparation for analysis. The precision and accuracy of the method were evaluated by analyzing several Seronorm trace elements whole blood reference materials. The precision of the method at various antimony levels was better than 4% RSD and the recovery was greater than 92% at all levels. The detection limit, calculated as three times the standard deviation of the blank (3sigma, n= 12), was 0.03 microg L(-1). The method was successfully applied for the determination of antimony in blood samples from school children in rural areas of Kwazulu/Natal, South Africa and adults from Dearborn, Michigan. Blood antimony levels ranged from <0.03 to 3.82 microg L(-1) in children and 1.40 to 4.35 microg L(-1) for adults.     

Relative density of finds for assessing similarity-based maps of orchid occurrence

Similarity-based mapping of the expected distribution of 10 orchid species was conducted in a study area covering 300 km² in south-eastern Estonia. The observation track and species finds were recorded during fieldwork. Absence locations were generated on the line of observation track. Both presence and absence sites having an in-between distance of at least 100 m were used as training data. Expected presence/absence of a species was calculated according to similarity between the predictable location and selected observations (examples) of presence and absence sites. For each species, the machine learning system identified the best predictive sets by selecting the most useful variables out of 136 map and remote sensing features. Similarity-based estimations were evaluated both by training fit and by independent verification data. Reliability of the predictive maps was expressed also by usefulness ratios—the densities of validation find sites (1) in the predicted presence area relative to the density of those in the predicted absence area, and (2) relative to the share of the observation track in the predicted presence area and in the predicted absence area. The predictive mapping was most efficient for Dactylorhiza incarnata, D. russowii, Epipactis palustris, and Goodyera repens. We conclude that the profound coverage of observations on any larger area is unrealistic and the reliability of similarity-based predictive maps depends on the representativity of existing records relative to the diversity of the study area. The investigation showed that the studied species are much more common in nature than the records in the national database indicate.     

Controls of spatial variation in the prevalence of trematode parasites infecting a marine snail

Geographic variability in abundance can be driven by multiple physical and biological factors operating at multiple scales. To understand the determinants of larval trematode prevalence within populations of the marine snail host Littorina littorea, we quantified many physical and biological variables at 28 New England intertidal sites. A hierarchical, mixed-effects model identified the abundance of gulls (the final hosts and dispersive agents of infective trematode stages) and snail size (a proxy for time of exposure) as the primary factors associated with trematode prevalence. The predominant influence of these variables coupled with routinely low infection rates (21 of the 28 populations exhibited prevalence <12%) suggest broad-scale recruitment limitation of trematodes. Although infection rates were spatially variable, formal analyses detected no regional spatial gradients in either trematode prevalence or independent environmental variables. Trematode prevalence appears to be predominantly determined by local site characteristics favoring high gull abundance.     

Bayesian spatial prediction

This paper presents a complete Bayesian methodology for analyzing spatial data, one which employs proper priors and features diagnostic methods in the Bayesian spatial setting. The spatial covariance structure is modeled using a rich class of covariance functions for Gaussian random fields. A general class of priors for trend, scale, and structural covariance parameters is considered. In particular, we obtain analytic results that allow easy computation of the predictive distribution for an arbitrary prior on the parameters of the covariance function using importance sampling. The computations, as well as model diagnostics and sensitivity analysis, are illustrated with a set of precipitation data.     

Setting Conservation Priorities: The Importance of Endemism and Phylogeny in the Southern African Orchid Genus Herschelia

The southern and south-central African terrestrial orchid genus Herschelia contains several rare and endangered species. The distribution patterns of the species were assessed and classified into the Rabinowitz rarity categories. The degree of rarity was correlated with habitat types and with the phylogenetic history. Of the 16 species recognized, two are too poorly known to be assessed further. Of the remainder, three species are shown to be "metaspecies," which can be interpreted as being ancestral to five narrowly endemic species. A. strong correlation between the age of the habitats, the relative age of the species, and the degree of rarity was demonstrated. I review the phylogenetic criteria for prioritizing species for conservation, and I develop a new criterion, the ability of a species to speciate into "new" environments. This suggests that it might be better to conserve metaspecies, which are found in the mountains, rather than the autapomorphic daughter species, which are found in the ephemeral habitats of the lowlands.     

A Screening-Level Assessment of Lead, Cadmium, and Zinc in Fish and Crayfish from Northeastern Oklahoma, USA

The objective of this study was to evaluate potential human and ecological risks associated with metals in fish and crayfish from mining in the Tri-States Mining District (TSMD). Crayfish (Orconectes spp.) and fish of six frequently consumed species (common carp, Cyprinus carpio; channel catfish, Ictalurus punctatus; flathead catfish, Pylodictis olivaris; largemouth bass, Micropterus salmoides; spotted bass, M. punctulatus; and white crappie, Pomoxis annularis) were collected in 2001--2002 from the Oklahoma waters of the Spring River (SR) and Neosho River (NR), which drain the TSMD. Samples from a mining-contaminated site in eastern Missouri and from reference sites were also analyzed. Individual fish were prepared for human consumption in the manner used locally by Native Americans (headed, eviscerated, and scaled) and analyzed for lead, cadmium, and zinc. Whole crayfish were analyzed as composite samples of 5--60 animals. Metals concentrations were typically higher in samples from sites most heavily affected by mining and lowest in reference samples. Within the TSMD, most metals concentrations were higher at sites on the SR than on the NR and were typically highest in common carp and crayfish than in other taxa. Higher concentrations and greater risk were associated with fish and crayfish from heavily contaminated SR tributaries than the SR or NR mainstems. Based on the results of this and previous studies, the human consumption of carp and crayfish could be restricted based on current criteria for lead, cadmium, and zinc, and the consumption of channel catfish could be restricted due to lead. Metals concentrations were uniformly low in Micropterus spp. and crappie and would not warrant restriction, however. Some risk to carnivorous avian wildlife from lead and zinc in TSMD fish and invertebrates was also indicated, as was risk to the fish themselves. Overall, the wildlife assessment is consistent with previously reported biological effects attributed to metals from the TSMD. The results demonstrate the potential for adverse effects in fish, wildlife, and humans and indicate that further investigation of human health and ecological risks, to include additional exposure pathways and endpoints, is warranted.This study was conducted by the Columbia Environmental Research Center (CERC) of the U.S. Geological Survey (USGS) and cooperating organizations and government agencies. All field and laboratory procedures conformed to the “Guidelines for the use of fishes in research” of the American Fisheries Society (AFS), Institute of Fishery Research Biologists (AIFRB), and American Society of Ichthyologists and Herpetologists (ASIH) Use of Fishes in Research Committee (AFS, AIFRB, and ASIH 2004), and with all USGS and CERC guidelines for the humane treatment of test organisms during culture and experimentation. Use of trade names does not constitute USGS or U.S. government endorsement.