Open Science with the Ocean Health Index [Nov 18, 2015]

The Ocean Health Index (OHI) is a framework to assess the state of our marine systems. With a definition of ‘healthy’ that includes sustainable human use, the OHI scores locations from 0-100 depending on how sustainably their waters provide a suite of benefits to people. The OHI framework was first used to assess all coastal nations globally, and was published in 2012 (Halpern et al. 2012, Nature).
Following the 2012 publication, the OHI framework has been used to assess smaller-scale locations, most often states or provinces within a single nation. These smaller spatial scales often have information that better represents local characteristics of marine systems and are also often the scale at which policy decisions are made.
To date, eleven assessments using the OHI framework have been completed at global, national, and regional scales, four of which have been led by independent academic or government groups. To facilitate these assessments, we have developed a suite of open-source tools and instruction. The OHI Toolbox provides structure for data organization and storage, with data processing and goal modeling done in the programming language R and RStudio for reproducibility and repeatability. The OHI Toolbox is stored on the open-source online platform GitHub, which allows for transparency and collaboration and also houses websites to display and communicate methods and results with interactive visualizations. More information can be found at (currently under a major restructuring and improvement, stay tuned!).
Julia Stewart Lowndes, PhD
Project Scientist, Ocean Health Index
National Center for Ecological Analysis and Synthesis (NCEAS)
University of California, Santa Barbara (UCSB)
735 State Street, Suite 300
Santa Barbara, CA, 93101, USA
ohi • ohi-science • github • twitter

Climate change, plant ecology and conservation: a case study of the SF Bay Area [Thurs, Nov 5]

Climate change is expected to profoundly impact terrestrial vegetation, and the mechanisms, rate and extent of change will influence biodiversity conservation and the ecological functions of natural ecosystems. The San Francisco Bay Area has steep climate gradients and rugged topography, supporting a wide range of natural habitats. Using a novel application of multinomial logistic regression, we have modeled the projected impacts of climate change on Bay Area vegetation. Model projections are evaluated over a wide range of possible future climates, allowing us to evaluate sensitivity of vegetation to changing climate, without choosing specific future climate scenarios. Sensitivity is highly variable across the Bay Area. Perhaps surprisingly, sensitivity to climate change is modeled to be greater on north-facing slopes and cooler locations. The model projections are best interpreted as the long-term equilibrium response to a particular degree of climate change, but they do not provide insight into how fast this equilibrium will be achieved or the transient states that may occur in response to rapid climate change. We combine model results with a discussion of the ecological mechanisms of vegetation change to better understand the challenges raised by disequilibrium dynamics and the implications for conservation biology in coming decades.

Dr. David D. Ackerly
Department of Integrative Biology
University of California, Berkeley


A Network Approach to Assessing Social-Ecological Systems in the Cook Islands (Nov 10)

A social-ecological system approach emphasizes the connectivity that exists between natural and human systems. This coupling is evident at a local scale, with people accessing natural resources for food provisioning and economic gain, and ecosystems providing services such as storm protection and food security. At a larger scale, institutions, and regional and global ecological processes influence how systems function. I present findings from research in Colombia and the Solomon Islands where social networks, institutions, livelihoods, and local ecological knowledge were analyzed to determine the factors that influence an individual’s motivation to comply with marine resource management and to withstand large-scale ecological disturbances. Finally, I propose a network-based approach to quantify social-ecological system interaction and assess the drivers of resilience in the Cook Islands.

Dr. Jaime Matera
Anthropology Program
California State University Channel Islands

Matera Pic

Progress towards developing a fisheries management strategy for data-limited species in Peru (Nov 3)

A majority of fisheries around the world lack the data and/or capacity to be scientifically assessed and managed. Scientifically assessed fish stocks are in better shape than those that are not, with small-scale, unassessed fisheries in worse shape with declining trends. While most of the assessment and management practices have been developed for large-scale, data-rich fisheries, there are many emerging options available for data and capacity limited fisheries. However, there is a challenge in navigating all of the available options, given their differences in data requirements, outputs, costs, and meeting different objectives. To address this, the SNAP Data-limited Fisheries working group is nearing completion of a Decision Support System (DSS) for data- and capacity-limited fisheries. The DSS is a process oriented approach to selecting the three components of a management strategy: 1) a monitoring plan; 2) assessment of the status of the resource; and 3) management decision rules. The DSS allows users to characterize the unique attributes of their fishery through a series of questions, which narrows down the management strategy options to those most cost-effective and relevant to the fishery.

In this round-table, I will present our progress towards applying this framework for a set of data-limited fisheries in Peru: 1) the Lorna Drum (Sciaena deliciosa) fishery; and 2) the Chita (Anisotremus scapularis) fishery. The project will be presented in the context of the Peruvian case study, but I hope this will stimulate discussion around the broader application of this framework and the use of decision support systems.

– – – – –
Dawn Dougherty
NCEAS Data-limited Fisheries SNAP Working Group

Protecting and predicting genetic diversity of whole communities – a case study of Hawaiian reefs

Conservation strategies increasingly call for preserving areas of high genetic diversity. This shift necessitates a look beyond single-species studies toward methods to predict and map community-level trends in genetic diversity. Theory suggests that genetic diversity primarily responds to habitat area and isolation, but ecology particular to each species nevertheless modify spatial patterns across co-distributed species. The balance and sources of convergent and divergent forces shaping genetic diversity of a community are largely unexplored.  With data for 47 reef species sampled across 16 Hawaiian Islands, we test a suite of hypotheses about drivers of biodiversity with a novel metric representing the emergent genetic diversity of the community. Results reassuringly support foundational theory on the relationship of diversity to habitat, but also suggest intriguing eco-genetic feedbacks and concerning signs that thermal stress has effected the genetic resilience of the whole reef community. I discuss the implications of these results for managing and protecting genetic diversity at the community level.

Kimberley Selkoe

Center Associate, NCEAS, UCSB /
Associate Research Biologist, Marine Science Institute, UCSB


Transitions of social-ecological subsistence systems in the Arctic

In this round-table, I will discuss how global change are transforming small-scale, native, resource-dependent communities in the Arctic. These social-ecological systems are increasingly exposed to global warming, industrial development and globalization, which subsequently alter the local SES dynamics. Subsistence use of fish and wildlife is a cornerstone in these communities. This traditional utilization of natural resources are commonly assumed to be donor-controlled, in which the users do not control the resource level but adapt to the fluctuating availability of fish and wildlife. A combination of increased harvest efficiency through the introduction of new technology, increased resource demand through population increase and commercialization, and reduced resource stocks by exogenous pressures such as climate change, is likely to increase the pressure on the stocks of fish and wildlife. The result could be a transition of the SES from a provisioning action situation, where the collective challenge is to secure subsistence on a local scale, to an appropriation action situation where the collective challenge is to avoid overuse of a common-pool resource on the scale of the resource stock. We applied cross-national comparison of Arctic Alaska, Canada and Greenland, synthesized secondary data from documents, official statistics and grey and scientific literature, and asked: What are the evidence for SES transitions in the Arctic? Which exogenous pressures are associated with transitions, and what conditions might prevent transitions? How does the transitions change the focus and sustainability challenges faced by the governance systems?

Although the results I will present are from the Arctic, I hope the talk will stimulate a more general discussion on how global change might transform local social-ecological systems.

Dr Per Fauchald

NCEAS visiting scientist

Senior researcher at the Norwegian Institute for Nature Research


What kind of science do we need to create sustainable pathways in the Arctic? (Oct 14)

Globalization processes coupled to the new sea transport routes, resource and infrastructure development and market integration are changing the arctic social-ecological systems at an accelerating pace. The increase in global connectedness will change the local resource-use systems thereby altering landscapes, fish and wildlife populations, and other ecosystem services important to Arctic people. While there is a rich body of research focusing on the direct effects of global warming and adaptions to climate-related changes, we have a limited understanding about how globalization and the adoption of new lifestyles, practices, technologies and institutional innovations could influence causal pathways and sustainability in the Arctic. Despite of these large gaps in understanding, researchers are expected to deliver knowledge that could enable actions and adaptations to environmental changes.

In this roundtable, I hope to spur an informal discussion about what kinds of science are needed and which research gaps we need to fill before providing reliable advice about sustainable pathways. While I will briefly introduce sustainability challenges in the Arctic by presenting the Belmont Forum project CONNECT, this roundtable will benefit from the participants broad experience from research outside the Arctic. I also encourage participants to bring their mobile or laptop in case we will use interactive polling to facilitate discussions (no software need to be installed).

Dr. Vera Helene Hausner
NCEAS Visiting Scientist
Associate Professor in Sustainability Science, UiT-The Arctic University of Norway

NCEAS / UCSB role as the new LTER Network Communications Office (Oct 7)

The National Science Foundation recently awarded the Long Term Ecological Research (LTER) Network Communications Office (NCO) to UCSB and NCEAS (PI Frank Davis; Co-PIs Carol Blanchette, Jenn Caselle, Stacy Rebich Hespanha, Matt Jones, and Mark Schildhauer). The NCO is conceived as an integrated set of activities in three areas – Communication and Outreach, Synthesis Research, and Education and Training – that builds on NCEAS’ longstanding relationship with LTER scientists, leverages existing staff capacity and infrastructure, and takes advantage of UCSB’s strengths and resources in ecology, environmental science and management, environmental communication and media, and environmental informatics.

In this Roundtable I will summarize the key feaures of the NCO and what it will mean for NCEAS, UCSB, and the broader LTER community. I will leave ample time for discussion of NCO needs and priorities.

Frank W. Davis
Director, NCEAS
Professor, Bren School of Environmental Science and Management, UCSB

When does hypoxia affect management performance of fisheries? A MSE of Dungeness crab fisheries in Hood Canal, WA

Hypoxia [dissolved oxygen (DO) < 2 mg/L] is one of the key threats to some of the most productive regions of the marine environment (e.g., estuaries). Although mortality can occur, mobile organisms have the potential to avoid the most severe low oxygen conditions, but suffer ecologically significant indirect and sublethal impacts as a result. In Washington State, USA, a fjord estuary of the Puget Sound marine ecosystem, known as Hood Canal (110 km), regularly experiences seasonal hypoxia. My dissertation addresses several important gaps in the current knowledge pertaining to the non-lethal biological effects of hypoxia on the mobile benthic and pelagic species of Hood Canal – for the sake of time and your sanity, I’ll be focusing on the benthos. Using acoustic telemetry, I quantified movement patterns and distributional shifts of Dungeness crab (Metacarcinus magister), an abundant and widely distributed species. Although highly mobile, Dungeness crab displayed more localized, rather than large-scale, directional movement relative to hypoxia. More specifically, the tagged crabs showed significant distributional shifts towards shallower waters. As one of the most important fisheries in Puget Sound, I wanted to then investigate the generalized relationship between hypoxia and the Dungeness crab harvest (3-S) management strategy. Inferred by the shoaling behavior from the field, an age-structured population model was constructed to test several hypoxia-scenarios with other stressors, including harvest, illegal crab fishing, and incidental capture mortality. It was found that the 3-S management strategy is most sensitive to the influence of hypoxia when other sources of demographic restrictions are considered, underscoring the uncertainty associated with a data-poor species under multiple anthropogenic and environmental stressors.

FieldWork_2010_HoodCanal Tagged_Crab


Halley E. Froehlich, Ph.D. (Halley is the untagged one on the left)

Postdoctoral Researcher

National Center for Ecological Analysis & Synthesis
University of California, Santa Barbara



Introduction to Spatial Analysis in R

Jamie Afflerback (NCEAS Assistant Specialist)
Wed Sept 23
Note location change to Main Conference Room
Ever wonder how to work with your spatial data in R? Now’s the time to learn! I will lead an informal, participatory workshop on how to do some spatial analysis in R. This session will use RStudio to introduce some of the most commonly used spatial packages/libraries to work with both raster and vector data types.

– Your own personal laptop
– Familiarity with R and RStudio. This is not an introduction to R so participants should already be using R.
– The most up to date versions of R and RStudio

The workshop is set up to walk through a script I prepared, line by line. Participants can choose to code as we go along, or just step through the coded script. If you’d like to participate please send an email to by Monday September 21. More details will be sent out next Tuesday.

For a preview, you can find all code and data held in this GitHub repository. Please note that being familiar with GitHub is not a requirement to participate.