marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R

Greetings OpenChannels Community Members,

A new package for the Open Source statistical package, R, for analyzing bathymetric and topographic data has appeard in a recent article in PLoS ONE. marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R may be downloaded for free, as well as the R package and the marmap module itself.

Happy reading!
-Nick Wehner, OpenChannels Project Manager

Table of Contents

Journal Articles

When does fishing lead to more fish? Community consequences of bottom trawl fisheries in demersal food webs​. ​Proc. R. Soc. B 22 October 2013 vol. 280 no. 1769 20131883 doi: 10.1098/rspb.2013.1883​. P. Daniel van Denderen, Tobias van Kooten and Adriaan D. Rijnsdorp​.

Free: marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R. Pante E, Simon-Bouhet B (2013) PLoS ONE 8(9): e73051. doi:10.1371/journal.pone.0073051.

Free: Juvenile King Scallop, Pecten maximus, Is Potentially Tolerant to Low Levels of Ocean Acidification When Food Is Unrestricted. Sanders MB, Bean TP, Hutchinson TH, Le Quesne WJF (2013) PLoS ONE 8(9): e74118. doi:10.1371/journal.pone.0074118.

Reefs of last resort: Locating and assessing thermal refugia in the wider Caribbean. Biological Conservation; Volume 167, November 2013, Pages 179–186. Iliana Chollett, Peter J. Mumby.

Exploring the science–policy interface for Integrated Coastal Management in New Zealand. Ocean & Coastal Management; Volume 84, November 2013, Pages 107–118. Scott Bremer, Bruce Glavovic.

Fish as indicators of diving and fishing pressure on high-latitude coral reefs. Ocean & Coastal Management, Volume 84, November 2013, Pages 130–139. C. Floros, M.H. Schleyer, J.Q. Maggs.

Exploring fisheries dependency and its relationship to poverty: A case study of West Sumatra, Indonesia. Ocean & Coastal Management; Volume 84, November 2013, Pages 140–152. Richard J. Stanford, Budy Wiryawan, Dietriech G. Bengen, Rudi Febriamansyah, John Haluan.

Valuing marine and coastal ecosystem services: An integrated participatory framework. Ocean & Coastal Management, Volume 84, November 2013, Pages 153–162. Rita Lopes, Nuno Videira.

Lessons learned from developing integrated ecosystem assessments to inform marine ecosystem-based management in the USA. Samhouri, J. F., Haupt, A. J., Levin, P. S., Link, J. S., and Shuford, R. 2013. ICES Journal of Marine Science, doi:10.1093/icesjms/fst141.

Incorporating Socioeconomic and Political Drivers of International Collaboration into Marine Conservation Planning. BioScience 63(7):547-563. 2013. Noam Levin , Ayesha I. T. Tulloch , Ascelin Gordon , Tessa Mazor , Nils Bunnefeld , and Salit Kark.

Marine conservation planning in practice: lessons learned from the Gulf of California. Aquatic Conservation: Marine and Freshwater Ecosystems; Volume 23, Issue 4, pages 483–505, August 2013. Jorge G. Álvarez-Romero, Robert L. Pressey, Natalie C. Ban, Jorge Torre-Cosío, Octavio Aburto-Oropeza.


Free: Evaluating the Effectiveness of Fish Stock Rebuilding Plans in the United States. The National Academies Press, 2013; 292 pages; ISBN 978-0-309-29227-6

When does fishing lead to more fish? Community consequences of bottom trawl fisheries in demersal food webs

Bottom trawls are a globally used fishing gear that physically disturb the seabed and kill non-target organisms, including those that are food for the targeted fish species. There are indications that ensuing changes to the benthic invertebrate community may increase the availability of food and promote growth and even fisheries yield of target fish species. If and how this occurs is the subject of ongoing debate, with evidence both in favour and against. We model the effects of trawling on a simple ecosystem of benthivorous fish and two food populations (benthos), susceptible and resistant to trawling. We show that the ecosystem response to trawling depends on whether the abundance of benthos is top-down or bottom-up controlled. Fishing may result in higher fish abundance, higher (maximum sustainable) yield and increased persistence of fish when the benthos which is the best-quality fish food is also more resistant to trawling. These positive effects occur in bottom-up controlled systems and systems with limited impact of fish feeding on benthos, resembling bottom-up control. Fishing leads to lower yields and fish persistence in all configurations where susceptible benthos are more profitable prey. Our results highlight the importance of mechanistic ecosystem knowledge as a requirement for successful management.

marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R

In this communication we introduce marmap, a package designed for downloading, plotting and manipulating bathymetric and topographic data in R. marmap can query the ETOPO1 bathymetry and topography database hosted by the NOAA, use simple latitude-longitude-depth data in ascii format, and take advantage of the advanced plotting tools available in R to build publication-quality bathymetric maps. Functions to query data (bathymetry, sampling information…) are available interactively by clicking on marmap maps. Bathymetric and topographic data can also be used to calculate projected surface areas within specified depth/altitude intervals, and constrain the calculation of realistic shortest path distances. Such information can be used in molecular ecology, for example, to evaluate genetic isolation by distance in a spatially-explicit framework.

Juvenile King Scallop, Pecten maximus, Is Potentially Tolerant to Low Levels of Ocean Acidification When Food Is Unrestricted

The decline in ocean water pH and changes in carbonate saturation states through anthropogenically mediated increases in atmospheric CO2 levels may pose a hazard to marine organisms. This may be particularly acute for those species reliant on calcareous structures like shells and exoskeletons. This is of particular concern in the case of valuable commercially exploited species such as the king scallop, Pecten maximus. In this study we investigated the effects on oxygen consumption, clearance rates and cellular turnover in juvenile P. maximus following 3 months laboratory exposure to four pCO2 treatments (290, 380, 750 and 1140 µatm). None of the exposure levels were found to have significant effect on the clearance rates, respiration rates, condition index or cellular turnover (RNA: DNA) of individuals. While it is clear that some life stages of marine bivalves appear susceptible to future levels of ocean acidification, particularly under food limiting conditions, the results from this study suggest that where food is in abundance, bivalves like juvenile P. maximus may display a tolerance to limited changes in seawater chemistry.

Reefs of last resort: Locating and assessing thermal refugia in the wider Caribbean

Ocean temperature increase is recognised as one of the major threats to the future of coral reefs. During the past 50 years, global mean temperatures have risen by 0.13 °C/decade, but in the Caribbean warming trends are greater, and are of the order of 0.29 °C/decade. In light of this threat, some researchers have proposed that reefs may survive better in locations of naturally low thermal stress, and have hypothesised that such refugia may be located in: (1) deep areas; (2) areas of high currents; (3) upwelling; and (4) high-latitude areas. These regions have been targeted as priorities for conservation activities; however, with the exception of deep reefs, formal assessment of the efficacy of these potential refugia is lacking. Here we tested the three remaining hypotheses in the wider Caribbean region using remotely sensed data and hydrodynamic model outputs. We began by determining the location of the hypothesised refugia, and then quantified the extent to which they minimise acute and chronic thermal stress in a significant and consistent manner through time. Furthermore, recognising the increasing sea warming and the concern that high temperatures could frequently exceed lethal thresholds for many organisms in the future, we assessed the ability of these areas to slow the rates of increase of temperatures. We show that the proposed areas do not constitute meaningful refugia from acute thermal stress. However, upwelling areas in the Caribbean have conservation utility because rates of thermal warming are lower.

Exploring the science–policy interface for Integrated Coastal Management in New Zealand

Integrated Coastal Management has seen an on-going debate on the best way of integrating knowledge with political decision-making across the so-called ‘science–policy interface’. This paper engages with this debate by presenting an empirical study into practice at the science–policy interface supporting coastal management in New Zealand. The research takes as its point of departure a notional dichotomy in the Integrated Coastal Management literature between two broad traditions; one espousing a ‘science-based interface’, the other a ‘participatory interface’. Structured according to this conceptual framework, the research describes and analyses the diverse ways in which these two traditions have found practical expression across New Zealand, both at the national scale and according to a comprehensive survey of coastal managers across all 16 regional councils. The analysis extends to the relationship between these two traditions, and how this relationship has determined the evolution of the science–policy interface.

This paper describes the traditional dominance of science-based coastal management in New Zealand, but highlights an important paradox; while science is valorised as the most robust knowledge for decision-making under the statutory decision-making process, there are pervasive financial, procedural and institutional barriers to its collection, meaning that many decisions are made under significant uncertainty. Against the background of this paradox, local government has increasingly departed from the statutory process, according to a philosophy of co-management. This extends to new strategies for mobilising knowledge, both through knowledge partnerships to generate more science, and participatory approaches to mobilise other forms of traditional and local knowledge. These participatory interfaces take many forms, but typically see scientists engaged alongside other knowledge holders within an inclusive decision-making process. All knowledge systems form a common pool of evidence on which to base decisions, and science is used strategically to fill knowledge gaps identified by a participatory process. Therefore, while science-based coastal management remains dominant in New Zealand, it is increasingly couched within a participatory tradition that valorises other knowledge systems as well.

Fish as indicators of diving and fishing pressure on high-latitude coral reefs

Despite the proclamation of South Africa's coral reef marine protected areas (MPAs) more than 20 years ago, the effects of human activities on the fish communities have not been investigated. This study used a multi-species Fish-index to compare ecological indicators such as biomass, abundance, trophic structure and reproductive potential between multiple-use and no-take sanctuary zones. Seven study reefs were surveyed; six in South Africa and a non-MPA reef in southern Mozambique. Randomly stratified underwater visual censuses (UVC) using the point count technique were used to survey fish communities. Environmental variables and habitat characteristics were also recorded. Nonmetric multidimensional scaling ordinations were similar for abundance and biomass trends and revealed a high degree of overlap between all zones, except for the no-take Sanctuaries. The latter formed discrete clusters and were significantly different (Analysis of Similarity) to the other zones. Total abundance and biomass were highest in the Sanctuary zones and lowest in the Open zone. Differences in trophic composition between zones were largely due to predatory species. This was supported by similarity percentages analysis (SIMPER) which identified six discriminating species. Length-frequency analysis of these species revealed consistent trends with higher numbers of large individuals in the Sanctuary zones and reduced numbers of small individuals in zones open to human activity. These results along with those of the Generalised Linear Models (GLM) demonstrate that human activities are affecting the southern African coral reef fish communities. Marginal differences between the multiple-use MPA zones on the South African reefs and the non-MPA reef in southern Mozambique suggest that MPA management objectives require re-evaluation.

Exploring fisheries dependency and its relationship to poverty: A case study of West Sumatra, Indonesia

Like many nations Indonesia is pressing ahead with a marine spatial planning process intended to bring coherence to marine management. As a contribution to this, broad scale oceanographic surveys are being undertaken at considerable cost to the tax payer. While the desire to deepen understanding of the marine environment is admirable, the limited social and economic component of this process is regrettable. Ironically, these social–economic data are routinely collected and it is the process of integrating these data that is missing. As a step in the right direction, this paper outlines a simple methodology using social–economic statistics consistently collected by government agencies and applies it to one coastal province of Indonesia, West Sumatra. Two indices are developed to map fisheries dependence and incidences of poverty amongst fishers at three spatial scales. Using census data of employment and poverty across all economic sectors, incidences of poverty amongst fishers are placed in the wider poverty context in order to begin to answer the question of whether ‘fishery truly rhymes with poverty’ using empirical data. This study identified the following trends; 1) that the number of fishers in a state of poverty is increasing, 2) fishing together with crop farming are the two sectors in which incidences of poverty are greatest, 3) there is no significant correlation between high fishing dependency and high proportions of poverty amongst fishers, 4) there is a significant correlation between agricultural dependence and total percentage poverty in coastal communities and 5) there are inverse correlations between the strength of other economic sectors and poverty in the agricultural sector. Implications for poverty alleviation initiatives and policy recommendations are briefly discussed. The methodology described in this paper is instantly applicable to the ongoing implementation of the national marine spatial planning program.

Valuing marine and coastal ecosystem services: An integrated participatory framework

The complex nature of marine and coastal ecosystems combined with the inaccessibility and invisibility of the majority of their goods and services call for tailored approaches to valuation. Furthermore, a deliberative approach is necessary to support emerging policy initiatives and decision-making processes, and this paper presents a participatory framework for valuing marine and coastal ecosystem services. The framework provides a coherent process for the identification and valuation of these services through the active involvement of stakeholder groups. The process begins with "set the scene", a stage in which institutional analysis and procedures for stakeholder involvement are deployed. A value elicitation stage, "deepen understanding", follows to determine the impacts of policy and/or project proposals. This stage involves the identification of the affected ecosystem services, the variations on the flow of services and the associated ecological, social and economic values. The final stage of "articulate values" fosters the integration of knowledge into policy and decision-making processes. The proposed framework adds communicative and informative features to valuation by advancing an approach that integrates deliberative methods for articulating the multiple values of ecosystem services affected by marine and coastal management decisions.

Lessons learned from developing integrated ecosystem assessments to inform marine ecosystem-based management in the USA

Borne out of a collective movement towards ecosystem-based management (EBM), multispecies and multi-sector scientific assessments of the ocean are emerging around the world. In the USA, integrated ecosystem assessments (IEAs) were formally defined 5 years ago to serve as a scientific foundation for marine EBM. As outlined by the US National Oceanic Atmospheric Administration in 2008, an IEA is a cyclical process consisting of setting goals and targets, defining indicators, analysing status, trends, and risk, and evaluating alternative potential future management and environmental scenarios to enhance information needed for effective EBM. These steps should be hierarchical, iterative, non-prescriptive about technical implementation, and adaptable to existing information for any ecosystem. Despite these strengths and some initial successes, IEAs and EBM have yet to be fully realized in the USA. We propose eight tenets that can be adopted by scientists, policy-makers, and managers to enhance the use of IEAs in implementing EBM. These tenets include (i) engage with stakeholders, managers, and policy-makers early, often, and continually; (ii) conduct rigorous human dimensions research; (iii) recognize the importance of transparently selecting indicators; (iv) set ecosystem targets to create a system of EBM accountability; (v) establish a formal mechanism(s) for the review of IEA science; (vi) serve current management needs, but not at the expense of more integrative ocean management; (vii) provide a venue for EBM decision-making that takes full advantage of IEA products; and (viii) embrace realistic expectations about IEA science and its implementation. These tenets are framed in a way that builds on domestic and international experiences with ocean management. With patience, persistence, political will, funding, and augmented capacity, IEAs will provide a general approach for allowing progressive science to lead conventional ocean management to new waters.

Incorporating Socioeconomic and Political Drivers of International Collaboration into Marine Conservation Planning

International collaboration can be crucial in determining the outcomes of conservation actions. Here, we propose a framework for incorporating demographic, socioeconomic, and political data into conservation prioritization in complex regions shared by multiple countries. As a case study, we quantitatively apply this approach to one of the world's most complex and threatened biodiversity hotspots: the Mediterranean Basin. Our analysis of 22 countries surrounding the Mediterranean Sea showed that the strongest economic, trade, tourism, and political ties are clearly among the three northwestern countries of Italy, France, and Spain. Although economic activity between countries is often seen as a threat, it may also serve as an indicator of the potential of collaboration in conservation. Using data for threatened marine vertebrate species, we show how areas prioritized for conservation shift spatially when economic factors are used as a surrogate to favor areas where collaborative potential in conservation is more likely.

Marine conservation planning in practice: lessons learned from the Gulf of California

  1. Overfishing, pollution, coastal development and climate change threaten marine biodiversity globally and compromise the services that marine ecosystems provide. Systematic conservation planning (SCP) provides a framework to identify areas where actions can be effective in addressing these threats, while minimizing the costs of interventions. This study investigated the application of SCP in the Gulf of California, a marine hotspot where seven prioritization exercises have been undertaken.
  2. The review of planning exercises showed that the use of SCP methods has progressed slowly (gaps include planning for land–sea connections and ecosystem services) and highlighted benefits and difficulties of applying SCP principles and tools.
  3. Despite some convergence, important spatial differences were found in priorities between plans. Convergence was evident in well-studied shallow and benthic marine ecosystems. There were also important differences related to the planning approach, methods and extent. Divergence between methodological and spatial similarities between plans suggests that additional factors (e.g. manually delineating priority areas, incorporating updated datasets, random error), in addition to data and objectives, play an important role in defining the distribution of conservation priorities.
  4. According to expert opinion, the implementation of new marine protected areas (MPAs) in the region has been influenced by some of the planning exercises. However, uptake of planning outputs has progressed slowly for many reasons (e.g. conflicting mandates and interests between organizations, limited technical capacities and resources, insufficient political commitment). Other benefits of planning included: developing institutional skills and knowledge; improving collaboration and coordination between organizations (including agencies, and local, regional and national NGOs); converging on the need to assess priorities for marine conservation in regional context; and building trust among organizations.
  5. The existence of multiple marine conservation plans in the Gulf of California also highlighted some of the complexities and benefits of having multiple sets of priorities.

Evaluating the Effectiveness of Fish Stock Rebuilding Plans in the United States

In the United States (U.S.), the Fishery Conservation and Management Act of 1976, now known as the Magnuson-Stevens Fishery Conservation and Management Act (MSFCMA), was the first major legislation to regulate federal fisheries in the U.S. Fishery Conservation Zone (later designated as the U.S. exclusive economic zone). The re-authorization of the MSFCMA passed by Congress in 2006 included additional mandates for conserving and rebuilding fish stocks and strengthening the role of scientific advice in fisheries management. Approximately 20% of the fisheries that have been assessed are considered overfished according to the September 2012 stock status Report to Congress prepared by the U.S. National Oceanic and Atmospheric Administration (NOAA). Overfished refers to a stock that is below the minimum stock size threshold, commonly set to half the stock size at which maximum sustainable yield (MSY) is achieved. Under the provisions of the MSFCMA, rebuilding plans for overfished stocks should take no more than 10 years, except when certain provisions apply. Rebuilding mandates have led to substantial reductions in catch and effort for many fisheries, raising concerns about the consequent social and economic impacts to the fishing communities and industry.

Evaluating the Effectiveness of Fish Stock Rebuilding Plans in the United States reviews the technical specifications that underlie current federally-implemented rebuilding plans, and the outcomes of those plans. According to this report, fisheries management has evolved substantially since 1977 when the U.S. extended its jurisdiction to 8 200 miles, in the direction of being more prescriptive and precautionary in terms of preventing overfishing and rebuilding overfished fisheries. However, the trade-offs between precaution and yield have not been fully evaluated. Evaluating the Effectiveness of Fish Stock Rebuilding Plans in the United States discusses the methods and criteria used to set target fishing mortality and biomass levels for rebuilding overfished stocks, and to determine the probability that a particular stock will rebuild by a certain date. This report will be of interest to the fishing industry, ecology professionals, and members of Congress as they debate the renewal of the Magnuson-Stevens Fishery Conservation and Management Act.