Tag Archives: ecology

A primer on natural history collection digitization and data sharing.

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Natural history collections contain both historical and contemporary
information about the ecology of our natural and urban areas. The
research and instructive potential of these data are rapidly becoming
more relevant as more and more collections become digitized.

I managed the digitization of over 3 million plant and insect
specimens for the National Science Foundation Tri-Trophic Thematic
Collection Network project from 2011 until 2015. The focus of this
high-throughput digitization effort was on the hemipteran herbivorous
insects (aphids, scales, hoppers, cicadas, and true bugs), their host
plants, and related parasitoids.  At this NCEAS roundtable, I plan to
present to review of contemporary standards in natural history
collection digitization, highlight some of the exciting derivative
research, and outline many of the ongoing challenges natural history
collection digitization still faces.

Katja Seltmann, PhD
Katherine Esau Director / Entomology Curator
Cheadle Center for Biodiversity & Ecological Restoration (CCBER)
seltmann@ccber.ucsb.edu

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Development at NCEAS, Fundraising for Ecology [Jan 13, 2016]

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This round-table will be led by Jeanne Kearns who is the new Director of Development at NCEAS. Jeanne will be discussing what development is, in the context of NCEAS and how the NCEAS community can contribute to its development. In particular, Jeanne will present on:

1) Who I am and why I do what I do?
2) What is Development and What does Development look like at UCSB?
3) How does NCEAS fit into this picture?
and then answer any questions and hopefully have a fruitful discussion!
Jeanne Kearns

Director of Development

National Center for Ecological Analysis and Synthesis

University of California Santa Barbara

735 State Street, Suite 300
Santa Barbara, CA 93101
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Synthetic ecology across scales: a follow-up discussion on hurdles to synthesis

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This will be a follow-up to a round-table last July on hurdles to synthesis (here). Look forward to an informal discussion on the process of data synthesis, based on a poster presentation by the GoA group at the CERF meeting last November in Portland, OR. A list of questions for discussion will be posted before the round-table on Wed, Jan 6th.

Here’s a link to the full poster (pdf): CERF 2015_Poster_Large

Abstract:
Large-scale ecological syntheses are increasingly important to understanding patterns, processes, and effects at an ecosystem scale.  However, conducting such syntheses requires lots of data which frequently is considered either large data (large-scale, designed to identify broad patterns not mechanisms, often many investigators or organizational) or small data (intensive, designed to identify mechanisms, often single/few investigators).  We explored a case where we integrated large and small data to examine questions across spatial and temporal scales in the Gulf of Alaska, focusing on the impacts of the Exxon Valdez oil spill.  However, for this discussion we will be focusing on the process of synthesizing disparate datasets rather than the actual data themselves.  Key to integrating data for synthetic analyses is the availability of informative documentation of the data.  We used Ecological Metadata Language (EML), online code sharing (GitHub), and an online data repository (DataONE) to document the data we used and to aid in transparency of these analyses.  Some of the hurdles encountered included a wide variety of poorly documented data formats, and fragmented research (through space and time).  Potential solutions include standardization of data formatting and storage across organizations, and better integration of research efforts by large organizations (government agencies, academia, etc.).  We hope to foster a discussion about these hurdles and potential solutions to synthesizing ecological data across scales.

Rachael Blake, NCEAS Post Doc
Jessica Couture, NCEAS Research Associate
Colette Ward, NCEAS Post Doc

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

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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 ohi-science.org (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
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Transitions of social-ecological subsistence systems in the Arctic

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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

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Looking for hotspots while the world gets hotter: multi-species genetic data inform landscape-scale conservation in the face of climate change in the San Joaquin Desert of California.

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Global climate change can create patterns of biodiversity where once-widespread species become restricted to small islands of persistence, commonly called climate refugia. Species can subsequently recolonize the intervening spaces between the islands, masking the historical range restriction. Advances in molecular genetic technology now allow us to see the signature of these historical restriction events. In our ongoing study of desert vertebrates in the San Joaquin Valley, we are layering patterns of population subdivision from multiple species into a composite map of historical population centers. We have significant population subdivison as well as pattern concordance among some species, suggesting past refuges in the Panoche Hills and the Carrizo Plain. A parallel study projecting the distribution of the blunt-nosed leopard lizard following the current climate change event shows both spots as potential refugia, suggesting the tantalizing possibility that contemporary hotspots may serve as future redoubts.

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Michael Westphal
Bureau of Land Management
Hollister Field Office, CA

Do synthesis centers produce novel, potentially transformative research? Research publication diversity as an indicator of novelty and transformative capacity

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20150223AAASposterTopicsCrop


a few of the topics that emerged in our analysis

For this Roundtable, I will present a poster that I presented at the recent AAAS meeting in San Jose. The project is an outgrowth of a working group jointly supported by NCEAS and NESCent and led by Ed Hackett and John Parker. Please read the abstract below for a bit of background, and then come prepared to discuss how you think academic publications (including yours!) produced through synthesis center work might be measurably different from other publications in the field. Then we’ll see if your intuitions are supported by the data we have available. Prepare yourselves to either be really proud of your keen intuitions, or to be surprised by our results!

 

You can access the poster on figshare using this link: http://dx.doi.org/10.6084/m9.figshare.1314918

Update: To initiate discussion prior to the meeting, I’ve put a question up on Tricider, and I welcome you to use the link below to add your ideas, comment on others’ ideas, and/or vote on the ideas that have been suggested. The question is the following:

“How would you expect academic publications that report on synthesis research to differ from publications resulting from other research approaches?”
Here is the link:
http://www.tricider.com/brainstorming/35cVP1jgQRp
Synthesis is an emerging synthetic method for producing transformative research, and publications centers to promote synthesis are on the rise in the US and around the world. New analytic tools and techniques are needed to assess the originality and transformative potential of synthesis. We propose that research outputs produced within synthesis centers will exhibit distinctive qualities that distinguish them from other publications in their fields. To explore this possibility, we conducted a topical analysis of titles, abstracts, and keywords for approximately 400,000 articles published in 108 leading journals from the fields of Ecology, Evolutionary Biology, Biodiversity Conservation, Forestry, and Fisheries. We then described each document as a proportional combination of the discovered topics, and used the Rao-Stirling heuristics to estimate, for each document, various measures that illuminate contrasting aspects of diversity (i.e. variety, balance, and disparity). We then compare diversity metrics for the synthesis center documents with those for all other documents in our corpus to evaluate whether and how the measured diversity of synthesis center publications differs from that of other publications in the relevant fields.