Generalized site occupancy models allowing for false positive and false negative errors

Site occupancy models have been developed that allow for imperfect species detection or "false negative" observations. Such models have become widely adopted in surveys of many taxa. The most fundamental assumption underlying these models is that "false positive" errors are not possible. That is, one cannot detect a species where it does not occur. However, such errors are possible in many sampling situations for a number of reasons, and even low false positive error rates can induce extreme bias in estimates of site occupancy when they are not accounted for. In this paper, we develop a model for site occupancy that allows for both false negative and false positive error rates. This model can be represented as a two-component finite mixture model and can be easily fitted using freely available software. We provide an analysis of avian survey data using the proposed model and present results of a brief simulation study evaluating the performance of the maximum-likelihood estimator and the naive estimator in the presence of false positive errors.     

Species identity dominates the relationship between predator biodiversity and herbivore suppression

Agricultural pest suppression is an important ecosystem service that may be threatened by the loss of predator diversity. This has stimulated interest in the relationship between predator biodiversity and biological control. Multiple-predator studies have shown that predators may complement or interfere with one another, but few experiments have determined if the resulting effects on prey are caused by changes in predator abundance, identity, species richness, or some combination of these factors. We experimentally isolated the effect of predator species richness on the biological control of an important agricultural pest, the green peach aphid. We found no evidence that increasing predator species richness affects aphid biological control; overall there was no strong complementarity or interference among predator species that altered the strength of aphid suppression. Instead, our experiments revealed strong effects of predator species identity, because predators varied dramatically in their per capita consumption rates. Our results are consistent with other multiple-predator studies finding strong species-identity effects and suggest that, for the biological control of aphids, conservation strategies that directly target key species will be more effective than those targeting predator biodiversity more broadly.     

A trait-based test for habitat filtering: convex hull volume

Community assembly theory suggests that two processes affect the distribution of trait values within communities: competition and habitat filtering. Within a local community, competition leads to ecological differentiation of coexisting species, while habitat filtering reduces the spread of trait values, reflecting shared ecological tolerances. Many statistical tests for the effects of competition exist in the literature, but measures of habitat filtering are less well-developed. Here, we present convex hull volume, a construct from computational geometry, which provides an n-dimensional measure of the volume of trait space occupied by species in a community. Combined with ecological null models, this measure offers a useful test for habitat filtering. We use convex hull volume and a null model to analyze California woody-plant trait and community data. Our results show that observed plant communities occupy less trait space than expected from random assembly, a result consistent with habitat filtering.     

Dining on disease: how interactions between infection and environment affect predation risk

Despite growing interest in ecological interactions between predators and pathogens, few studies have experimentally examined the consequences of infection for host predation risk or how environmental conditions affect this relationship. Here we combined mesocosm experiments, in situ foraging data, and broad-scale lake surveys to evaluate (1) the effects of chytrid infection (Polycaryum laeve) on susceptibility of Daphnia to fish predators and (2) how environmental characteristics moderate the strength of this interaction. In mesocosms, bluegill preferred infected Daphnia 2-5 times over uninfected individuals. Among infected Daphnia, infection intensity was a positive predictor of predation risk, whereas carapace size and fecundity increased predation on uninfected individuals. Wild-caught yellow perch and bluegill from in situ foraging trials exhibited strong selectivity for infected Daphnia (3-10 times over uninfected individuals). In mesocosms containing water high in dissolved organic carbon (DOC), however, selective predation on infected Daphnia was eliminated. Correspondingly, lakes that supported chytrid infections had higher DOC levels and lower light penetration. Our results emphasize the strength of interactions between parasitism and predation while highlighting the moderating influence of water color. P. laeve increases the conspicuousness and predation risk of Daphnia; as a result, infected Daphnia occur predominantly in environments with characteristics that conceal their elevated visibility.     

Adding infection to injury: synergistic effects of predation and parasitism on amphibian malformations

We explored the importance of interactions between parasite infection and predation in driving an emerging phenomenon of conservation importance: amphibian limb malformations. We suggest that injury resulting from intraspecific predation in combination with trematode infection contributes to the frequency and severity of malformations in salamanders. By integrating field surveys and experiments, we evaluated the individual and combined effects of conspecific attack and parasite (Ribeiroia ondatrae) infection on limb development of long-toed salamanders (Ambystoma macrodactylum). In the absence of Ribeiroia, abnormalities involved missing digits, feet, or limbs and were similar to those produced by cannibalistic attack in experimental trials. At field sites that supported Ribeiroia, malformations were dominated by extra limbs and digits. Correspondingly, laboratory exposure of larval salamanders to Ribeiroia cercariae over a 30-day period induced high frequencies of malformations, including extra digits, extra limbs, cutaneous fusion, and micromelia. However, salamander limbs exposed to both injury and infection exhibited 3-5 times more abnormalities than those exposed to either factor alone. Infection also caused significant delays in limb regeneration and time-to-metamorphosis. Taken together, these results help to explain malformation patterns observed in natural salamander populations while emphasizing the importance of interactions between parasitism and predation in driving disease.     

Biological invasions: recommendations for U.S. policy and management.

The Ecological Society of America has evaluated current U.S. national policies and practices on biological invasions in light of current scientific knowledge. Invasions by harmful nonnative species are increasing in number and area affected; the damages to ecosystems, economic activity, and human welfare are accumulating. Without improved strategies based on recent scientific advances and increased investments to counter invasions, harm from invasive species is likely to accelerate. Federal leadership, with the cooperation of state and local governments, is required to increase the effectiveness of prevention of invasions, detect and respond quickly to new potentially harmful invasions, control and slow the spread of existing invasions, and provide a national center to ensure that these efforts are coordinated and cost effective. Specifically, the Ecological Society of America recommends that the federal government take the following six actions: (1) Use new information and practices to better manage commercial and other pathways to reduce the transport and release of potentially harmful species; (2) Adopt more quantitative procedures for risk analysis and apply them to every species proposed for importation into the country; (3) Use new cost-effective diagnostic technologies to increase active surveillance and sharing of information about invasive species so that responses to new invasions can be more rapid and effective; (4) Create new legal authority and provide emergency funding to support rapid responses to emerging invasions; (5) Provide funding and incentives for cost-effective programs to slow the spread of existing invasive species in order to protect still uninvaded ecosystems, social and industrial infrastructure, and human welfare; and (6) Establish a National Center for Invasive Species Management (under the existing National Invasive Species Council) to coordinate and lead improvements in federal, state, and international policies on invasive species. Recent scientific and technical advances provide a sound basis for more cost-effective national responses to invasive species. Greater investments in improved technology and management practices would be more than repaid by reduced damages from current and future invasive species. The Ecological Society of America is committed to assist all levels of government and provide scientific advice to improve all aspects of invasive-species management.     

Litter and dead wood dynamics in ponderosa pine forests along a 160-year chronosequence.

Disturbances such as fire play a key role in controlling ecosystem structure. In fire-prone forests, organic detritus comprises a large pool of carbon and can control the frequency and intensity of fire. The ponderosa pine forests of the Colorado Front Range, USA, where fire has been suppressed for a century, provide an ideal system for studying the long-term dynamics of detrital pools. Our objectives were (1) to quantify the long-term temporal dynamics of detrital pools; and (2) to determine to what extent present stand structure, topography, and soils constrain these dynamics. We collected data on downed dead wood, litter, duff (partially decomposed litter on the forest floor), stand structure, topographic position, and soils for 31 sites along a 160-year chronosequence. We developed a compartment model and parameterized it to describe the temporal trends in the detrital pools. We then developed four sets of statistical models, quantifying the hypothesized relationship between pool size and (1) stand structure, (2) topography, (3) soils variables, and (4) time since fire. We contrasted how much support each hypothesis had in the data using Akaike's Information Criterion (AIC). Time since fire explained 39-80% of the variability in dead wood of different size classes. Pool size increased to a peak as material killed by the fire fell, then decomposed rapidly to a minimum (61-85 years after fire for the different pools). It then increased, presumably as new detritus was produced by the regenerating stand. Litter was most strongly related to canopy cover (r2 = 77%), suggesting that litter fall, rather than decomposition, controls its dynamics. The temporal dynamics of duff were the hardest to predict. Detrital pool sizes were more strongly related to time since fire than to environmental variables. Woody debris peak-to-minimum time was 46-67 years, overlapping the range of historical fire return intervals (1 to > 100 years). Fires may therefore have burned under a wide range of fuel conditions, supporting the hypothesis that this region's fire regime was mixed severity.     

Crown ratio influences allometric scaling in trees

Allometric theories suggest that the size and shape of organisms follow universal rules, with a tendency toward quarter-power scaling. In woody plants, however, structure is influenced by branch death and shedding, which leads to decreasing crown ratios, accumulation of heartwood, and stem and branch tapering. This paper examines the impacts on allometric scaling of these aspects, which so far have been largely ignored in the scaling theory. Tree structure is described in terms of active and disused pipes arranged as an infinite branching network in the crown, and as a tapering bundle of pipes below the crown. Importantly, crown ratio is allowed to vary independently of crown size, the size of the trunk relative to the crown deriving from empirical results that relate crown base diameter to breast height diameter through crown ratio. The model implies a scaling relationship in the crown which reduces to quarter-power scaling under restrictive assumptions but would generally yield a scaling exponent somewhat less than three-quarters. For the whole tree, the model predicts that scaling between woody mass and foliage depends on crown ratio. Measurements on three boreal tree species are consistent with the model predictions.     

Globalization of the Amazon Soy and Beef Industries: Opportunities for Conservation

Abstract:  Amazon beef and soybean industries, the primary drivers of Amazon deforestation, are increasingly responsive to economic signals emanating from around the world, such as those associated with bovine spongiform encephalopathy (BSE, "mad cow disease") outbreaks and China's economic growth. The expanding role of these economic "teleconnections" (coupled phenomena that take place in distant places on the planet) led to a 3-year period (2002–2004) of historically high deforestation rates. But it also increases the potential for large-scale conservation in the region as markets and finance institutions demand better environmental and social performance of beef and soy producers. Cattle ranchers and soy farmers who have generally opposed ambitious government regulations that require forest reserves on private property are realizing that good land stewardship—including compliance with legislation—may increase their access to expanding domestic and international markets and to credit and lower the risk of "losing" their land to agrarian reform. The realization of this potential depends on the successful negotiation of social and environmental performance criteria and an associated system of certification that are acceptable to both the industries and civil society. The foot-and-mouth eradication system, in which geographic zones win permission to export beef, may provide an important model for the design of a low-cost, peer-enforced, socioenvironmental certification system that becomes the mechanism by which beef and soy industries gain access to markets outside the Amazon.