Karen H. Beard

Random Forests for Classification in Ecology

Classification procedures are some of the most widely used statistical methods in ecology. Random forests (RF) is a new and powerful statistical classifier that is well established in other disciplines but is relatively unknown in ecology. Advantages of RF compared to other statistical classifiers include (1) very high classification accuracy; (2) a novel method of determining variable importance; (3) ability to model complex interactions among predictor variables; (4) flexibility to perform several types of statistical data analysis, including regression, classification, survival analysis, and unsupervised learning; and (5) an algorithm for imputing missing values. We compared the accuracies of RF and four other commonly used statistical classifiers using data on invasive plant species presence in Lava Beds National Monument, California, USA, rare lichen species presence in the Pacific Northwest, USA, and nest sites for cavity nesting birds in the Uinta Mountains, Utah, USA. We observed high classification accuracy in all applications as measured by cross-validation and, in the case of the lichen data, by independent test data, when comparing RF to other common classification methods. We also observed that the variables that RF identified as most important for classifying invasive plant species coincided with expectations based on the literature.

Plant-soil feedbacks: a meta-analytical review.

Plants can change soil biology, chemistry and structure in ways that alter subsequent plant growth. This process, referred to as plant-soil feedback (PSF), has been suggested to provide mechanisms for plant diversity, succession and invasion. Here we use three meta-analytical models: a mixed model and two Bayes models, one correcting for sampling dependence and one correcting for sampling and hierarchical dependence (delta-splitting model) to test these hypotheses. All three models showed that PSFs have medium to large negative effects on plant growth, and especially grass growth, the life form for which we had the most data. This supports the hypothesis that PSFs, through negative frequency dependence, maintain plant diversity, especially in grasslands. PSFs were also large and negative for annuals and natives, but the delta-splitting model indicated that more studies are needed for these results to be conclusive. Our results support the hypotheses that PSFs encourage successional replacements and plant invasions. Most studies were performed using monocultures of grassland species in greenhouse conditions. Future research should examine PSFs in plant communities, non-grassland systems and field conditions.

A Meta-Analytic Review of Corridor Effectiveness

Using corridors for conservation is increasing despite a lack of consensus on their efficacy. Specifically, whether corridors increase movement of plants and animals between habitat fragments has been addressed on a case-by-case basis with mixed results. Because of the growing number of well-designed experiments that have addressed this question, we conducted a meta-analysis to determine whether corridors increase movement; whether corridor effectiveness differs among taxa; how recent changes in experimental design have influenced findings; and whether corridor effectiveness differs between manipulative and natural experiments. To conduct our meta-analysis, we analyzed 78 experiments from 35 studies using a conservative hierarchical Bayesian model that accounts for hierarchical and sampling dependence. We found a highly significant result that corridors increase movement between habitat patches by approximately 50% compared to patches that are not connected with corridors. We found that corridors were more important for the movement of invertebrates, nonavian vertebrates, and plants than they were for birds. Recent methodological advances in corridor experiments, such as controlling for the area added by corridors, did not influence whether corridors increased movement, whereas controlling for the distance between source and connected or unconnected recipient patches decreased movement through corridors. After controlling for taxa differences and whether studies controlled for distance in experimental design, we found that natural corridors (those existing in landscapes prior to the study) showed more movement than manipulated corridors (those created and maintained for the study). Our results suggest that existing corridors increase species movement in fragmented landscapes and that efforts spent on maintaining and creating corridors are worthwhile.

STRUCTURAL AND FUNCTIONAL RESPONSES OF A SUBTROPICAL FOREST TO 10 YEARS OF HURRICANES AND DROUGHTS

Little is known about ecosystem-level responses to multiple, climatic disturbance events. In the subtropical forests of Puerto Rico, the major natural disturbances are hurricanes and droughts. We tested the ecosystem-level effects of these disturbances in sites with different land use histories. From 1989 to 1992, data were collected to determine the effects of Hurricane Hugo and two droughts on litterfall inputs, fine-root biomass, and decomposition rates in three topographic locations (stream, riparian, upslope) within two watersheds. From 1994 to 1998, we added a third watershed and an experiment in which coarse-wood levels were manipulated to simulate hurricane inputs. Data were collected on tree and palm growth rates, litterfall inputs, fine-root biomass, and decomposition rates. From 1994 to 1998, four hurricanes and three droughts were recorded. Measured parameters had unique responses and recovery rates to hurricanes and droughts. Litterfall inputs returned to long-term mean rates within one month...

A depth-controlled tracer technique measures vertical, horizontal and temporal patterns of water use by trees and grasses in a subtropical savanna

• As described in the two-layer hypothesis, woody plants are often assumed to use deep soils to avoid competition with grasses. Yet the direct measurements of root activity needed to test this hypothesis are rare. • Here, we injected deuterated water into four soil depths, at four times of year, to measure the vertical and horizontal location of water uptake by trees and grasses in a mesic savanna in Kruger National Park, South Africa. • Trees absorbed 24, 59, 14 and 4% of tracer from the 5, 20, 50, and 120  cm depths, respectively, while grasses absorbed 61, 29, 9 and 0.3% of tracer from the same depths. Only 44% of root mass was in the top 20 cm. Trees absorbed tracer under and beyond their crowns, while 98% of tracer absorbed by grasses came from directly under the stem. • Trees and grasses partitioned soil resources (20 vs 5  cm), but this partitioning did not reflect, as suggested by the two-layer hypothesis, the ability of trees to access deep soil water that was unavailable to grasses. Because root mass was a poor indicator of root activity, our results highlight the importance of precise root activity measurements.

The effects of the frog Eleutherodactylus coqui on invertebrates and ecosystem processes at two scales in the Luquillo Experimental Forest, Puerto Rico

Determining the ubiquity of top-down control effects of predators on their prey and ecosystem processes is important for understanding community and ecosystem-level consequences that may result from predator loss. We conducted experiments at two spatial scales to investigate the effects of terrestrial frogs (Eleutherodactylus coqui )o n aerial and litter invertebrates, plant growth and herbivory, and litter decomposition. At both scales, frogs reduced aerial invertebrates and leaf herbivory, but had no effect on litter invertebrates. At the smaller scale, frogs increased foliage production rates, measured as the number of new leaves and new leaf area produced, by 80% and decomposition rates by 20%. The influence of E. coqui on increasing primary productivity and decomposition rates at the smaller scale appeared to be a result of elimination and excretion rather than of controlling prey. While the results provide evidence for frogs controlling herbivorous prey at both scales, species effects on ecosystem processes were only detectable at the smaller scale. The results highlight the difficulties in conducting experiments at large spatial scales. The findings from this study imply that the loss of amphibians and other species of higher trophic levels may affect nutrient cycling rates in tropical forests.

Plant–soil feedbacks provide an additional explanation for diversity–productivity relationships

Plant–soil feedbacks (PSFs) have gained attention for their role in plant community dynamics, but their role in productivity has been overlooked. We developed and tested a biomass-specific, multi-species model to examine the role of PSFs in diversity–productivity relationships. The model predicts a negative relationship between PSFs and overyielding: plants with negative PSFs grow more in communities than in monoculture (i.e. overyield), and plants with positive PSFs grow less in communities than in monoculture (i.e. underyield). This effect is predicted to increase with diversity and saturate at low species richness because the proportion of ‘self-cultivated’ soils rapidly decreases as species are added to a community. Results in a set of glasshouse experiments supported model predictions. We found that PSFs measured in one experiment were negatively correlated with overyielding in three-species plant communities measured in a separate experiment. Furthermore, when parametrized with our experimental PSF data, our model successfully predicted species-level overyielding and underyielding. The model was less effective at predicting community-level overyielding and underyielding, although this appeared to reflect large differences between communities with or without nitrogen-fixing plants. Results provide conceptual and experimental support for the role of PSFs in diversity–productivity relationships.

Nonnative Phragmites australis Invasion into Utah Wetlands

ABSTRACT. Phragmites australis (Cav.) Trin. ex Steud. (common reed), already one of the worlds most widespread plant species, has realized rapid range expansion in coastal wetlands of North America in the past century, but little is known about P. australis range expansion in inland wetland systems. We used genetic analyses, aerial photographs, field surveys, and a greenhouse experiment to study the extent and mechanism of nonnative P. australis invasion of Utah wetlands. We collected and genetically analyzed 39 herbarium samples across the state and 225 present-day samples from northern Utahs major wetland complexes. All samples collected before 1993 and all samples collected outside the major wetlands of northern Utah, including some as recent as 2001, were identified as native (haplotypes A, B, D, and H). Only 10 (4%) of the present-day samples were native, each from small, discrete, low-density stands; the remaining samples were nonnative (haplotype M). Our earliest nonnative sample was collected near the Great Salt Lake in 1993. Around the Great Salt Lake, which contains 40% of Utahs wetlands, P. australis cover has increased from 20% to 56% over the past 27 years—an increase that appears attributable to the nonnative strain. In a 3-month-long greenhouse experiment, the nonnative haplotype grew taller, had more aboveground biomass, and had a greater above- to belowground biomass ratio than the native haplotypes regardless of nitrogen, phosphorus, or water availability. Nonnative P. australis is rapidly invading the wetlands of northern Utah. Areas in Utah where the native P. australis remains should be identified and protected.

Diet of the Invasive Frog, Eleutherodactylus Coqui, in Hawaii

Abstract Because of their high densities and generalist feeding behaviors, the introduced frog, Eleutherodactylus coqui, has been hypothesized to consume and potentially reduce endemic invertebrates in Hawaii. To address this hypothesis, I compared E. coqui diets to invertebrate abundances in 11 sites on the Islands of Hawaii and Maui in the summer of 2004. At each site, I collected between 22 and 119 frogs from 20 × 20-m plots, and invertebrates from light traps, beating trays, and leaf litter samples. Prey items in frog stomachs were identified to order, and invertebrates collected in environmental samples were identified to the lowest taxonomic category possible. Multivariate analyses of diet content and invertebrates collected at each site suggest that most prey was from the leaf litter. Non-native ants (Hymenoptera: Formicidae) and amphipods (Amphipoda: Talitridae) comprised 30% and 22%, respectively, of the total prey items consumed. These non-native invertebrates were more abundant in stomachs of E. coqui than in the environment indicating a preference for these species. There was little evidence that E. coqui were reducing important invertebrate pests. No mosquitoes (Diptera: Culicidae) were found in stomachs, and termites (Isoptera) comprised <1% of the total prey items. Arthropod orders containing endemic species that appear most vulnerable to E. coqui predation include Acarina (mites), Coleoptera (beetles), Collembola (springtails), and Diptera (flies), which each made up >2% of the diet of E. coqui. Dominant prey items in frog stomachs differed among study sites suggesting that frogs are opportunistic feeders and forage on abundant prey items. Eleutherodactylus coqui management should focus on areas with endemic invertebrates of concern because it is these locations where E. coqui may have the greatest impact.

Biology and Impacts of Pacific Island Invasive Species. 5. Eleutherodactylus coqui , the Coqui Frog (Anura: Leptodactylidae)

Abstract: The nocturnal, terrestrial frog Eleutherodactylus coqui, known as the Coqui, is endemic to Puerto Rico and was accidentally introduced to Hawai‘i via nursery plants in the late 1980s. Over the past two decades E. coqui has spread to the four main Hawaiian Islands, and a major campaign was launched to eliminate and control it. One of the primary reasons this frog has received attention is its loud mating call (85–90 dB at 0.5 m). Many homeowners do not want the frogs on their property, and their presence has influenced housing prices. In addition, E. coqui has indirectly impacted the floriculture industry because customers are reticent to purchase products potentially infested with frogs. Eleutherodactylus coqui attains extremely high densities in Hawai‘i, up to 91,000 frogs ha-1, and can reproduce year-round, once every 1–2 months, and become reproductive around 8–9 months. Although the Coqui has been hypothesized to potentially compete with native insectivores, the most obvious potential ecological impact of the invasion is predation on invertebrate populations and disruption of associated ecosystem processes. Multiple forms of control have been attempted in Hawai‘i with varying success. The most successful control available at this time is citric acid. Currently, the frog is established throughout the island of Hawai‘i but may soon be eliminated on the other Hawaiian Islands via control efforts. Eradication is deemed no longer possible on the island of Hawai‘i.