Impacts of anthropogenic stressors in vegetated coastal habitats

Anthropogenic stressors are increasingly changing conditions in coastal areas and impacting important habitats.  But, when multiple stressors act simultaneously, their effects on ecosystems become more difficult to project.  Stressors from climate change, coastal development, and pollution are currently impacting coastal habitats, but understanding the interaction of these stressors is critical to knowing how vulnerable coastal habitats and the critical ecosystem functions they provide may be maintained or changed in the future. Seagrass bed and saltmarshes are two habitats that are vulnerable to stressors yet provide many things we humans value.

My research to date has shown that stressors can impact foundation plant species in predictable ways, but those impacts can vary with temporal and spatial scales.  In addition, the composition and diversity of these communities varies but can buffer certain ecosystem properties against stressor impacts.  Overall, in these habitats stressors can be context specific, non-interactive, and vary with spatial and temporal scales.

Rachael E. Blake


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


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:

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:
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.

When big data and complex workflows meet the reality of finite data storage: a discussion of best practices for data management

"tapes, backup" CC-BY-SA 2.0 by Martin Abblegen via flickr

“tapes, backup” CC-BY-SA 2.0 by Martin Abblegen via flickr

Scientific workflows — for many of us, it’s a love/hate relationship. We love the fact that they help us keep our stuff organized, but hate the overhead required to maintain them. And then when we find out that our meticulously maintained workflow hasn’t captured some important detail? Oh the frustration!!

This discussion will be broadly about managing scientific workflows, and I hope to hear from everyone about the tools and tricks you have for keeping track of which outputs match with which inputs to an analysis, with which models, and which parameters, which figures, papers, and projects all of those things are connected to. It would be great to hear about a wide range of strategies ranging from how you organize and name your files to how you’ve implemented a workflow management tool like Kepler.

I also hope that we can spin up ideas for workflow management problems people may be facing, so if you have a workflow-related issue or question that you’d like to get input on, please let me know. I’ll make sure you get a few minutes to describe your problem or question so that you can get ideas from the crowd.

And if you’re reading this and thinking “I’m a workflow management pro, and don’t need any help with or ideas for managing my workflow,” then please come to the discussion! We (well, at least I) need your help. I have a homegrown scripted workflow management system for the text analyses I do, which does a great job of capturing a lot of details and documenting relationships between inputs and outputs, but requires me to purge unused outputs (e.g., outputs for all but selected runs of a model) manually. How do the rest of you keep track of which files you can throw away down the line and which need to be kept indefinitely? I need to downsize my data storage and am a little worried about making mistakes when I do this manually, so would love to hear ideas about how to build functions like this into my system.

Hope to see you all for a fun discussion!

Research in the coastal temperate rainforest, by Dr. Allison Bidlack

Juvenile Bald Eagle in Tree near Haines

Juvenile Bald Eagle in Tree near Haines

Join us for our March 11th Roundtable with Dr. Allison Bidlack from the Alaska Coastal Rainforest Center!

The north Pacific coastal temperate rainforest (PCTR) ecosystem extends from central British Columbia to southcentral Alaska, includes the largest remaining old-growth forests in North America, supports some of the most robust fisheries on the continent, and is home to tens of thousands of people who depend on a resource and tourism-based economy for their livelihoods. It is also a region characterized by an intricate geologic and evolutionary past, a rich cultural history, and complex linkages among ecosystem components. The social-ecological systems of the PCTR are being transformed by climate change, as well as by global economic drivers such as tourism, energy prices, and timber demand.  Given the current rates of ecosystem change and the potential for profound systemic shifts and economic upheaval in the region and beyond, a more holistic understanding of these patterns, processes and impacts is essential for the effective management of resources and the resilience of communities. This talk will provide a brief introduction to the region and some of the integrative work being performed, with an emphasis on regional projects involving existing datasets.


From the top of the mountain to the top of the world: vegetation change in the tundra

Join us for our roundtable discussion on March 4th with Dr. Anne Bjorkman from he German Center for Integrative Biodiversity Research (iDiv).

Abstract: Identifying large-scale patterns in functional traits has become a hot topic in community ecology over the past decade, as understanding current biogeographical patterns can help us predict future shifts under climate warming. In the Arctic, where temperatures are warming faster than anywhere else on the planet, shifts in vegetation and associated functional traits can have direct consequences for ecosystem function. For example, increases in shrub cover could affect summer and winter soil temperatures and thus influence the depth of permafrost thaw, while specific leaf area (SLA) and leaf nitrogen concentration can influence decomposition rates, relative growth rates, photosynthetic rates, and carbon fixation, all of which in turn influence carbon cycling and net primary productivity (NPP).

As part of an international synthesis effort based at the German Centre for Integrative Biodiversity Research (“iDiv” – the German equivalent of NCEAS, or at least we like to think so), we are investigating patterns of functional traits across climate space and over time by combining a circumpolar vegetation database with a large and growing tundra plant trait database. This is very much a work in progress, so I will present some of our work so far and would love to have your feedback!

Anne at her study site

Anne at her study site

A roundtable on roundtables

We have had a few informal discussions here at NCEAS on round-tables and the form/structure that they could take in order to be both engaging and useful. There is a dichotomy apparent, between ‘talks’ and ‘discussions.’

The more one-way, information providing ‘talks’ are a very useful way for researchers in different fields to explain and learn about on-going work, though time constraints generally mean that this leaves less room for questions and discussion.

On the other hand, more participative ‘discussions’ that address a broad topic, and have a loose structure to help keep them moving are a very good way for all of us to brainstorm about common ideas and concepts and hopefully leave us with more ideas (and questions!) than we started with!

The question then is – how do we strike a good balance? On Wednesday, February 18th, we will have a round-table session on…round-tables(!) to get ideas and brainstorm and discuss this.

As very good food for thought in preparation, here are some tips from Chris Lortie on how to provoke thought and and manage discussions:


The secret lives of mountain lions in the Santa Cruz Mountains

As human developments continue to permeate previously open spaces, large carnivores are often the first species to feel the impact of these changes. The Santa Cruz Puma Project examined the behavioral responses of an apex predator, the mountain lion, to an increasingly human dominated landscape. During my presentation, I discussed our use of accelerometer technology as a new way to gain deeper insights into mountain lion behavior, movement and physiology, recent findings on mountain lion behavioral adaptations to living close to humans, and conservation outcomes that have resulted from our work.

I welcome comments with suggestions on how new technologies and behavioral ecology can help illuminate the conservation and management of large predators living close to humans. Please check out a recent video from NSF on our work with accelerometers!

What are the grand challenges for restoration ecology?

I want to become a restoration ecologist. Here is my post for the roundtable I did two weeks ago.



Here is the slide deck too:

Following the discussion, I came across several really useful papers on the topic.

These three in particular were really transformative.

Moore, K. D. and Moore, J. W. 2013. Ecological restoration and enabling behavior: a new metaphorical lens? — Conservation Letters 6: 1-5.

Hilderbrand, R. H. et al. 2005. The myths of restoration ecology. . — Ecology and Society 10: 19.
Temperton, V. M. 2007. The Recent Double Paradigm Shift in Restoration Ecology. — Restoration Ecology 15: 344-347.


General questions
1. How well does conservation biology and restoration ecology support and enable one another?
2. Does fundamental ecological theory significantly contribute to restoration ecology or does most restoration begin with a ‘problem’ that needs a solution?
3. Is most restoration ecology manipulative? How are mensurative experiments and observation leveraged in restoration ecology?
4. How inter-related are management and restoration in their alignment of needs and research agendas?
5. Are there syntheses of the local-versus-regional drivers that influence the outcome restoration efforts?
6. How commonly are the human factors included in restoration efforts or in experiments?
7. Does social science regularly contribute and support restoration efforts?
8. Does socioeconomic research support restoration? When it does, how it is used?
9. Is an effective restoration plan similar to a conservation blueprint?
10. What are main primary research topics that restoration ecologists examine?  Are there taxa and/or ecosystem specific biases and how general are the lessons?
11. What is the most common scale of restoration?
12. Are there themes that transcend restoration and speak to a wider audience?
13. Is restoration ecology increasing collaborative similar to other disciplines?
14. Are restoration ecology experiments often interdisciplinary?
15. What are the main challenges that most restoration ecologists would list in either doing research or in implementing a restoration effort?

Discussion: Obstacles faced by researchers who reuse, share and manage data, and strategies for overcoming them

Roundtable discussion for Wednesday, 17 Sept 2014
All too often it's an uphill battle for researchers who want to do the right thing. Photo Credit: Steve Garvie from Dunfermline, Fife, Scotland (Uphill struggle!) [CC-BY-SA-2.0], via Wikimedia Commons

Photo Credit: Steve Garvie from Dunfermline, Fife, Scotland (Uphill struggle!) [CC-BY-SA-2.0], via Wikimedia Commons

All too often it’s an uphill battle for researchers who want to do the right thing.




Why is it often harder than it should be to do the right thing when it comes to data management, sharing and reuse? I will introduce seven common sources of conflict that present obstacles to researchers who work with data. These seven sources of conflict were identified through qualitative analysis of transcripts for interviews and focus groups involving more than 35 researchers.


Following a brief introduction of these sources of conflict and resulting obstacles, we will discuss potential strategies for minimizing or overcoming these obstacles. Our conversation will focus around the following guiding questions:
  • For each source of conflict, what should be done to make it easier for researchers to do the right thing?
  • What can research centers like NCEAS do to prepare researchers and/or to improve the status quo?
  • What can I, as an individual researcher, do to avoid and/or prepare for potential obstacles, and to improve the status quo?

You may also be interested in checking out short stories based on some of the interviews:

I look forward to discussing ideas with you on Wednesday!