Triggers and maintenance of multiple shifts in the state of a natural community

Ecological communities can undergo sudden and dramatic shifts between alternative persistent community states. Both ecological prediction and natural resource management rely on understanding the mechanisms that trigger such shifts and maintain each state. Differentiating between potential mechanisms is difficult, however, because shifts are often recognized only in hindsight and many occur on such large spatial scales that manipulative experiments to test their causes are difficult or impossible. Here we use an approach that focuses first on identifying changes in environmental factors that could have triggered a given state change, and second on examining whether these changes were sustained (and thus potentially maintained the new state) or transitory (explaining the shift but not its persistence). We use this approach to evaluate a community shift in which a benthic marine species of filter feeding sea cucumber (Pachythyone rubra) suddenly came to dominate subtidal rocky reefs that had previously supported high abundances of macroalgae, persisted for more than a decade, then abruptly declined. We found that a sustained period without large wave events coincided with the shift to sea cucumber dominance, but that the sea cucumbers persisted even after the end of this low wave period, indicating that different mechanisms maintained the new community. Additionally, the period of sea cucumber dominance occurred when their predators were rare, and increases in the abundance of these predators coincided with the end of sea cucumber dominance. These results underscore the complex nature of regime shifts and illustrate that focusing separately on the causes and maintenance of state change can be a productive first step for analyzing these shifts in a range of systems

Sublethal toxicant effects with dynamic energy budget theory: application to mussel outplants

We investigate the effectiveness of a sublethal toxic effect model embedded in Dynamic Energy Budget (DEB) theory for the analysis of field data. We analyze the performance of two species of mussels, Mytilus galloprovincialis and M. californianus, near a diffuser discharging produced water in the Southern California Bight, California. Produced water is a byproduct of oil production consisting of fossil water together with compounds added during the extraction process, and generally contains highly elevated levels of pollutants relative to sea water. Produced water negatively affects the production of somatic and reproductive biomass in both mussel species; we show that these negative effects can be quantified with our DEB-based modeling framework through the estimation of toxic effect scaling parameters. Our analyses reveal that the toxic impact of produced water on growth and reproduction of M. californianus is substantially higher than for M. galloprovincialis. Projections of the expected lifetime production of gonad biomass indicate that the environmental impact of produced water can be as large as 100%, whereas short-term assessment without the use of DEB theory projects a maximum effect of only 30%

Coral Reef Monitoring by Scuba Divers Using Underwater Photogrammetry and Geodetic Surveying

Underwater photogrammetry is increasingly being used by marine ecologists because of its ability to produce accurate, spatially detailed, non-destructive measurements of benthic communities, coupled with affordability and ease of use. However, independent quality control, rigorous imaging system set-up, optimal geometry design and a strict modeling of the imaging process are essential to achieving a high degree of measurable accuracy and resolution. If a proper photogrammetric approach that enables the formal description of the propagation of measurement error and modeling uncertainties is not undertaken, statements regarding the statistical significance of the results are limited. In this paper, we tackle these critical topics, based on the experience gained in the Moorea Island Digital Ecosystem Avatar (IDEA) project, where we have developed a rigorous underwater photogrammetric pipeline for coral reef monitoring and change detection. Here, we discuss the need for a permanent, underwater geodetic network, which serves to define a temporally stable reference datum and a check for the time series of photogrammetrically derived three-dimensional (3D) models of the reef structure. We present a methodology to evaluate the suitability of several underwater camera systems for photogrammetric and multi-temporal monitoring purposes and stress the importance of camera network geometry to minimize the deformations of photogrammetrically derived 3D reef models. Finally, we incorporate the measurement and modeling uncertainties of the full photogrammetric process into a simple and flexible framework for detecting statistically significant changes among a time series of models

Indirect effects of species interactions on habitat provisioning

Species that shelter in a biogenic habitat can influence their refugia and, in turn, play an essential role in shaping local patterns of biodiversity. Here we explore a positive feedback loop between the provisioning rate of habitat-forming branching corals and their associated fishes and show how interactions between two groups of fish—the planktivorous damselfish and predatory hawkfish—altered the feedback. A field experiment confirmed that skeletal growth of branching coral (genus Pocillopora) increased substantially with increasing numbers (biomass) of resident fishes, likely because they greatly increased the interstitial concentrations of nutrients. Because there is a positive relationship between colony size and number (biomass) of associated fishes (primarily damselfishes in the Family Pomacentridae), a structure–function feedback loop exists in which increasing numbers of damselfish enhance coral growth and larger corals host greater abundances (and species richness) of fish. However, interactions between damselfishes and arc-eye hawkfish, Paracirrhites arcatus, a largely solitary resident, can disrupt this positive feedback loop. Field surveys revealed a marked pattern of fish occupancy related to coral size: Pocillopora colonies of sufficient size to host fish (>40 cm circumference) had either groups of damselfish or an arc-eye hawkfish; only larger colonies (>75 cm) were occupied by both the damselfish and hawkfish. Subsequent short- and long-term experiments revealed that on intermediate-sized Pocillopora colonies, arc-eye hawkfish prevented the establishment of damselfish by suppressing their recruitment. The demographic consequences to the host coral were substantial; in a 1-year-long experiment, intermediate-size Pocillopora occupied by hawkfish grew at half the rate of corals that hosted groups of damselfish. These findings indicate that: (1) species which occupy a biogenic habitat can enhance the provisioning rate of their habitat; (2) such positive feedbacks between community structure and ecosystem function can be disrupted by a strong interactor; (3) even substantial consequences on ecosystem processes that arise can be difficult to discern

Analysis of Abrupt Transitions in Ecological Systems

The occurrence and causes of abrupt transitions, thresholds, or regime shifts between ecosystem states are of great concern and the likelihood of such transitions is increasing for many ecological systems. General understanding of abrupt transitions has been advanced by theory, but hindered by the lack of a common, accessible, and data-driven approach to characterizing them. We apply such an approach to 30–60 years of data on environmental drivers, biological responses, and associated evidence from pelagic ocean, coastal benthic, polar marine, and semi-arid grassland ecosystems. Our analyses revealed one case in which the response (krill abundance) linearly tracked abrupt changes in the driver (Pacific Decadal Oscillation), but abrupt transitions detected in the three other cases (sea cucumber abundance, penguin abundance, and black grama grass production) exhibited hysteretic relationships with drivers (wave intensity, sea-ice duration, and amounts of monsoonal rainfall, respectively) through a variety of response mechanisms. The use of a common approach across these case studies illustrates that: the utility of leading indicators is often limited and can depend on the abruptness of a transition relative to the lifespan of responsive organisms and observation intervals; information on spatiotemporal context is useful for comparing transitions; and ancillary information from associated experiments and observations aids interpretation of response-driver relationships. The understanding of abrupt transitions offered by this approach provides information that can be used to manage state changes and underscores the utility of long-term observations in multiple sentinel sites across a variety of ecosystems.Organismic and Evolutionary Biolog

Herbivory, Connectivity, and Ecosystem Resilience: Response of a Coral Reef to a Large-Scale Perturbation

Coral reefs world-wide are threatened by escalating local and global impacts, and some impacted reefs have shifted from coral dominance to a state dominated by macroalgae. Therefore, there is a growing need to understand the processes that affect the capacity of these ecosystems to return to coral dominance following disturbances, including those that prevent the establishment of persistent stands of macroalgae. Unlike many reefs in the Caribbean, over the last several decades, reefs around the Indo-Pacific island of Moorea, French Polynesia have consistently returned to coral dominance following major perturbations without shifting to a macroalgae-dominated state. Here, we present evidence of a rapid increase in populations of herbivorous fishes following the most recent perturbation, and show that grazing by these herbivores has prevented the establishment of macroalgae following near complete loss of coral on offshore reefs. Importantly, we found the positive response of herbivorous fishes to increased benthic primary productivity associated with coral loss was driven largely by parrotfishes that initially recruit to stable nursery habitat within the lagoons before moving to offshore reefs later in life. These results underscore the importance of connectivity between the lagoon and offshore reefs for preventing the establishment of macroalgae following disturbances, and indicate that protecting nearshore nursery habitat of herbivorous fishes is critical for maintaining reef resilience

Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium

Abstract Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions

Integrated genomic characterization of oesophageal carcinoma

Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist