March 15 – Non-climate processes and ‘species on the move’

Evidence from the past several decades shows that species distributions are shifting in response to climate change. However, even the most robust studies attribute less than half of observed changes in species distributions to local climate factors. Foundational ecology considers climate as just one of many drivers that determine species distributions. I will review five prevalent mechanisms that may explain some of the high variance around the relationship between species range shifts and climate velocity, and describe how they might affect a species’ climate tracking: (1) biogeographic boundaries, (2) habitat gaps and fragmentation, (3) biotic interactions such as competition, predation, and mutualism, (4) other abiotic constraints including light and trace elements, and (5) life history traits that determine dispersal capacity. This work supports conservation initiatives for threatened species by highlighting several processes that may limit their potential redistribution, and can inform analyses of observational data and species distribution models that seek to incorporate multiple processes rather than climate alone.

 

Alexa Fredston-Hermann
fredstonhermann@ucsb.edu

Alexa is a third-year PhD student at the Bren School of Environmental Science & Management at UCSB. Her research focuses on biogeographic processes that may prevent species from tracking climate change, particularly in the oceans. She has also studied human impacts to coastal marine ecosystems, and participated in the Ridges to Reef Fisheries SNAPP Working Group. Before entering graduate school, she worked for the Environmental Defense Fund on management of the West Coast groundfish fishery, and graduated from Princeton University in 2012 with a B.A. in Ecology and Evolutionary Biology.

March 8th – GRNmap and GRNsight: Open Source Software for Dynamical Systems Modeling and Visualization of Medium-Scale Gene Regulatory Networks

A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them that govern the level of expression of mRNA and proteins from those genes. Over a period of several years, our group has developed a MATLAB software package, called GRNmap, that uses ordinary differential equations to model the dynamics of medium-scale GRNs. The program uses a penalized least squares approach to estimate production rates, expression thresholds, and regulatory weights for each transcription factor in the network based on gene expression data, and then performs a forward simulation of the dynamics of the network using a sigmoidal or Michaelis-Menten production function. GRNsight is an open source web application for visualizing such models of gene regulatory networks. GRNsight accepts GRNmap- or user-generated Excel workbooks containing an adjacency matrix representation of the GRN, SIF, or GraphML files and automatically lays out the graph of the GRN model. GRNsight’s diagrams are based on D3.js’s force graph layout algorithm, which was then extensively customized. GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (activation or repression) and magnitude of the GRNmap weight parameter. Visualizations can be modified through manual node dragging and sliders that adjust the force graph parameters. In addition to discussing how these efforts have contributed to our understanding of the gene regulatory network controlling the response to the environmental stress of cold shock in budding yeast, Saccharomyces cerevisiae, I will put them in the context of an Open Science Ecosystem, in which the process and products of science are open and accesible to all. Together, the life cycle of these two programs illustrate the differences between the cultures of biology, mathematics, and computing, the challenges and benefits of bringing an existing code base up to open development standards (GRNmap), and the advantages of starting a project using best practices from the beginning (GRNsight). Our goal is to facilitate reproducible research.

Seaver College of Science and Engineering Faculty Staff Headshots

Dr. Kam Dahlquist is an Associate Professor of Biology and Affiliate Faculty of the Bioethics Institute at Loyola Marymount University. Dr. Dahlquist earned a B.A. in Biology from Pomona College and a Ph.D. in Molecular, Cellular, and Developmental Biology from the University of California, Santa Cruz. Dr. Dahlquist performed postdoctoral research at the Gladstone Institute of Cardiovascular Disease at the University of California, San Francisco, and taught for two years at Vassar College before joining the LMU faculty in 2005. In her research, Dr. Dahlquist follows an interdisciplinary approach to understanding gene regulatory networks that involves cutting-edge techniques in genomics, mathematical, and computational biology. This research crosses over into her teaching in such courses as Molecular Biology of the Genome, Biomathematical Modeling, Biological Databases, and Bioinformatics Laboratory. She believes that her research and teaching must be informed by and contribute to a broader social context. She has worked with various groups such as the UCSF Science and Health Education partnership and the Association for Women in Science (AWIS) to improve science education for all and to increase the numbers of women and minorities in science. She believes strongly in training her students to apply ethical standards to the conduct of scientific research. Finally, she promotes an Open Science Ecosystem in which the process and products of science are open and accessible to all.

kdahlquist@lmu.edu

Feb 22nd – Biocultural approaches to indicator development and use from local to global

Pacific Island communities are facing unprecedented challenges in conserving natural resources and maintaining human well-being. In these place-based communities, biocultural connections, or the integrated social, economic, cultural and environmental linkages between people and nature are widely believed to play a critical role in improving and maintaining the resilience of both human and ecological communities. However, indicators of human or ecological well-being rarely reflect the integrated nature of these systems.

We synthesized information from visioning exercises across multiple Pacific Island archipelagoes (Hawaiʻi, Fiji, Solomon Islands, Marshall Islands) to better understand the perspectives of Pacific Islanders on characteristics of vibrant biocultural landscapes and seascapes. Based on this and a review of the literature, we identified key elements that describe a resilient biocultural state for Pacific Island communities. We are using these elements to identify if and how international sustainability goals capture local perspectives and values. We are also using these key elements to develop a community self-assessment guide. Finally, we are in the process of comparing indicators of biocultural resilience and their drivers across the Pacific Islands. We expect the results of our work will guide practices on sustainability and well-being that better resonate with communities and better reflect important connections between people and nature.

Eleanor Sterling
Chief Conservation Scientist
Center for Biodiversity and Conservation
American Museum of Natural History
200 Central Park West
New York, NY 10024
http://cbc.amnh.org/
sterling@amnh.org

 

Stacy Jupiter
Wildlife Conservation Society
Associate Conservation Scientist
Fiji Country Program Director
sjupiter@wcs.org

 

Rachel Dacks
University of Hawaii
rdacks@hawaii.edu

Feb. 8 [Wed] – Obstacles to Groundwater Treatment at Santa Susana Field Laboratory: Assessing Water Management Options and Ecosystem Questions

The RocketOutfall team is working in collaboration with Boeing to advance the groundwater treatment process at the Santa Susana Field Laboratory. This project analyzes five methods Boeing could use to discharge this water, and investigates what impacts the most viable option (discharging treated water to a dry streambed) might have on the arid landscape. Boeing has previously pursued this option, but the CA Department of Fish and Wildlife (CDFW) has asked them to consider the impacts on the receiving creek’s vegetation before a final permit is granted. Boeing is partnering with the Bren School of Environmental Science and Management to answer CDFW’s questions, and consider alternative discharge options.

Presenters are members of the RocketOutfall team – a group of 4 graduate students from the Bren School of Environmental Science and Management specializing in Pollution Prevention and Remediation and Conservation Planning.

Feb 1, 2017 – Aligning coastal restoration with ecological and societal needs

Coastal habitats play critical ecological and societal roles in nearshore and estuarine systems.  Yet despite their importance, reefs, marshes and coastal forests around the world have been highly degraded and reduced to a small fraction of their historic extent.  In the United States and elsewhere, billions of dollars are being invested in coastal habitat restoration.  New policies emphasize planning processes that work across sectors and jurisdictions to fund projects that provide the greatest returns for people and nature.  As a result, state, county and local government agencies, non-governmental organizations and industry are facing hard questions about where to invest and how to set targets to meet these dual goals.  We have formed a multi-agency and NGO partner working group aimed at increasing understanding agency needs for decision-making, assessing past restoration projects, and developing achievable metrics and approaches for aligning ecological and social goals in future efforts.

Jonathan Grabowski, Ph.D.
J.Grabowski@northeastern.edu

Jon

 My research interests span issues in ecology, fisheries and conservation biology, social-ecological coupling, environmental policy, and ecological economics. I have used a variety of estuarine (oyster reef, seagrass, salt marsh, mud bottom) and marine (kelp bed, cobble-ledge) systems to examine how resource availability, habitat heterogeneity and predation risk affect population dynamics, community structure, and ecosystem functioning. Much of this work focuses on economically important species such as lobsters, cod, herring, monkfish, and oysters, and consequently is relevant for fisheries and ecosystem management. My lab also focuses on how habitat degradation and restoration influence benthic community structure, population structure, and the transfer of energy to higher trophic levels. In addition, we are interested in how fisheries management initiatives such as the design of closed areas, delineation of stock boundaries, fishing gear modifications, and quota setting impact fish population structure and fisheries productivity, essential fish habitat protection, community structure, and the social capital of stakeholders.

 

My lab’s research involves highly coupled social-ecological systems and integrates social and natural science approaches. For instance, we are examining the ecological consequences of shoreline hardening on ecosystem service provisioning while also investigating how the environmental connectedness of coastal residents influences their decision-making around this issue. We are also examining factors that influence coastal fishing communities’ perceptions of and trust in management to help improve their buy in and identify potential barriers. Finally, we are determining how factors such as urbanization and resource specialization influence the perceptions and values of coastal residents so that we can design more effective environmental policies around issues such as climate hazard preparedness and coastal habitat and resource management.

Wed. Jan. 11 – Alaska’s salmon and people in the (rapidly changing) 21st century

Elmendorf Salmon Viewing Platform

This talk is an informal sketch of the emergent State of Alaska’s Salmon and People (SASAP) initiative, jointly told by many of the project’s leads. In addition to providing listeners with an understanding of the SASAP process, we aim to provide insights into our own motivations for joining the work, sketches of work in our laboratories, and a general sense of the importance of salmon to the overall health of Alaska.

Presenters: Peter Westley, Jessica Black, Courtney Carothers, and Tobias Schwoerer

Peter Westley
Assistant Professor
College of Fisheries and Ocean Sciences
University of Alaska Fairbanks
Web: http://www.uaf.edu/sfos/people/faculty/detail/index.xml?id=76
Email: pwestley@alaska.edu

Using social media to advance your research career

Most of us use social media as an effective way to connect with
friends and family. For academics though, social media can be even
more effective at advancing professional goals. In this roundtable, I
will illustrate the many ways that roundtable participants can use
social media to powerfully further their career objectives. These
objectives include things like: keeping track of the latest
developments in the field, increasing awareness among colleagues of
your research, and furthering outreach goals. I will be focusing on
Twitter, though the principles are roughly the same across social
media platforms. At the end of the roundtable, my intention is that
participants will have gained actionable information about social
media that they can immediately put to work to further career goals.
This roundtable will involve some interactive activities, but
participants will not need to bring computers (or anything else) to
take part in these activities.

Jai Ranganathan

Center Associate
National Center for Ecological Analysis and Synthesis
jai.ranganathan@gmail.com

 

Plant Community Responses to Global Change Drivers

Global change will alter resources, which are predicted to change the composition and functioning of plant communities. Here, I present the results of several projects studying plant community changes in response to resource manipulations. First, I present data from an experiment at Konza Prairie Biological Station in Manhattan Kansas. In this experiment, nutrient additions (nitrogen and phosphorus) turned the tallgrass prairie from being dominate by C4 grasses to C3 forbs. Next, I detail plant community responses to resource manipulations across ~100 experiments world-wide. This data synthesis found that when 5 factors are simultaneously manipulated, there are drastic changes in the plant community. Additionally, the greater number of factors that are manipulated, the greater the change in productivity. Lastly, I review my current postdoctoral work, focused on developing new ways to study patterns of community change using rank abundance curves.

plants

Photo of the phosphorus plots experiment at Konza Prairie Biological Station. Photo Credit: Melinda Smith

The Day After: Bird Conservation in [Insert President-elect’s name]’s America! [Wed. Nov. 9th]

Come take your mind off the aftermath of the 2016 election by talking about birds, citizen science, and habitat restoration instead. I will present on the work done by the San Francisco Bay Bird Observatory (SFBBO), which is a nonprofit that works on bird conservation science and educational outreach projects. Although we work on many projects, I will primarily discuss our work with the South Bay Salt Pond Restoration Project, a new urban biodiversity project with Google, burrowing owls conservation, and our citizen science projects. SFBBO and many of its partners are always looking for collaborators and new projects so I look forward to any ideas for partnerships and gaps in knowledge.

 

I welcome discussion during roundtable and the following are some of my thoughts, although I welcome other ideas!
  • How to promote more linkages among academics and non-profits (i.e., applied ecology and conservation research!)
  • Working with citizen science derived data and how to get our data into the hands of more people
  • Ways to reach more diverse audiences with indoor and outdoor activities
  • Increasing corporate participation in urban ecology as well as the conservation value of urban greening and restoration

yiwei-o

Dr. Yiwei Wang
Executive Director
San Francisco Bay Bird Observatory
http://sfbbo.org/

 

Discussion on credit and collaboration in science today [Wed. Oct 5]

This week’s Roundtable will be a community discussion on credit and collaboration in science today, motivated by this recent article in The Chronicle of Higher Education: http://www.chronicle.com/article/The-Changing-Face-of/237451/

Here are a few questions we’ll use to structure the discussion:

Do you agree with the author’s assertion that the drive to apportion credit is hurting the spirit of collaboration in science?

Even if you disagree with the author’s argument, can you see any ways in which more precise accounting for credit in scientific collaboration might impact the spirit of collaboration?

What approaches could be used to help someone on the other side of this issue see and appreciate your point of view?

Please read the article and come to discuss evidence and experience you might have on this interesting and very relevant topic.  Hope you can join us!