Ecology, Evolution and Conservation

California is one of 25 global hotspots of biodiversity that encompass 1.4% of the Earth’s surface but account for 60% of the world’s species. BML researchers study the area from San Francisco to Point Arena, a stretch of coastline known for the complexity of its marine and terrestrial environments and the global prototype of coastal upwelling areas. Local habitats at the Laboratory are particularly diverse. Researchers study seagrass beds, mudflats, coastal prairie, dunes, sandy beaches, subtidal and rocky intertidal communities. Researchers explore these habitats to tease apart the complex relationships among terrestrial and marine organisms – from the neural pathways of behavior to community structure shaped by predator and prey.

Invasive species are a leading cause of declines in biodiversity and the productivity of ecosystems worldwide. BML is a primary field site for invasive species research at UC Davis, a leading institution for invasion biology in the United States. BML scientists find novel and effective approaches for the control of invasive species through better understanding of community interactions and ecological theory. The Laboratory supports access to two of the best-studied marine environments for invasive species in the world, Bodega Harbor and San Francisco Bay. Further, BML researchers are at the forefront of using oceanographic data to better understand and quantify the dispersal of larvae in coastal upwelling ecosystems. In particular, hourly maps of surface currents obtained from an array of HF radar stations have proved invaluable in the assessment of connectivity between nearshore adult habitats. Oceanographers and ecologists at BML work closely to develop an integrated view of larval ecology.

Much of the ecological research at BML has a clear link to conservation biology. In addition to these links, research programs at BML include direct restoration efforts focusing on endangered salmonids and abalone.

Biodiversity and Community Ecology

biodiversityBiodiversity is, simply, the variety of life on Earth, and can be characterized at various levels from genes, to species and ecosystems. Understanding the causes of patterns of the diversity of life on Earth and the functional consequences of natural and human-caused variation in that diversity are fundamental goals of ecology and a focus of active research at BML. These studies are all the more pressing given the impact that human activities have on biodiversity.

The close proximity of a range of habitat types to BML facilitates comparative research on the effects of biodiversity in different ecosystems from kelp forests to mudflats and rocky shores to seagrass beds. The overarching finding from this research is that maintaining the diversity of coastal ecosystems increases the productivity, stability and resilience of these ecosystems in the face of human-caused and natural change. This often works much as diversity buffers financial portfolios from unpredictable market conditions: different stocks (or species in this case) differ in how they respond to variation in the environment, either in space or among locations, such that diversity ensures sustained production.

Specific research from the Stachowicz lab indicates that these effects of biodiversity are strong across very different ecosystems. Experimental work in kelp forest mesocosms highlight how foraging strategies of different predatory invertebrates combine to ensure that herbivores are kept in check and prevented from overgrazing kelp forests. Across a range of kelp forest sites, those that have a diverse predator community have fewer herbivores and as a result maintain a lush growth of kelp.

Just in front of BML, a nearly decade long experiment manipulating diversity of seaweed by the Stachowicz lab has showed that the effects of biodiversity on ecosystem stability and productivity increase over time. These effects occur because seaweeds use the topographically complex rock in different ways such that no one species can make use of all the space available. Importantly, multi-factor experiments have shown that diversity’s effects are strong—just as important as factors such as grazing that have long been appreciated to play a critical role in intertidal ecology. This work also shows that diversity at the base of the food web can influence the diversity and abundance of animals that use seaweeds for food and habitat.

eelgrass

Finally, “hidden” diversity in the form of genetic diversity within species plays an analogous role in communities dominated by a single important species, such as the eelgrass beds found in Bodega Harbor. These productive ecosystems not only provide habitat for commercially and recreationally fished species but also reduce erosion. Yet they are dominated by a single species of seagrass, the eelgrass Zostera marina. A series of experimental and observational studies conducted in Bodega and Tomales Bays by the Stachowicz lab in collaboration with the Williams lab showed that planting seagrass beds with high levels of genetic diversity enhances the success of those beds, leading to greater production and resilience to overgrazing by migratory geese. Individual genotypes differ in their properties to a sufficiently large degree that they are complementary to one another in their use of resources. At larger scales BML scientists have helped develop a global network of scientists studying the role of biodiversity at the genetic and species level on the health of seagrass ecosystems. This network (Zostera Experimental Network, or ZEN) was just funded by the National Science Foundation to expand to over 30 sites worldwide across Asia, North America and Europe and will offer research classes to undergraduates at UC Davis to allow them to participate in research activities at partner sites across the globe.

The Williams laboratory tackles many environmental issues in nearshore seagrass and seaweed communities, which are important for producing food and habitat for for other species, many of which are commercially valuable (Dungeness crabs, rockfish) or even endangered. The lab has two major goals. One is to understand how these marine plant communities function. For example, how fast do they photosynthesis and acquire nitrogen to build protein or recycle nutrients and what does the functioning tell us about the plant’s ability to withstand or recover from pollution or invasive species.  The second goal is to apply the research to the management of these important communities, which in the case of seagrasses are in global decline. Physiology is the major research approach and the lab has many different instruments and supports the research of many other researchers and their students.

The Don Strong laboratory addresses the trophic ecology of herbivore plant interactions. They have studied the decomposition of lupine wood by isopods and fungi at the Bodega Marine Reserve (Bastow et al 2008). They have also studied the decomposition of the invasive grass Holcus lanatus on the BMR (Bastow et al 2008b). The studies of the trophic structure in the soil at BMR discovered that dispersal of entomopathogenic nematodes overrides their local dynamics in the rhizospheres of lupine (Ram et al 2008 a & b). Strong’s lab has also studied the interspecific competition of these nematodes at the BMR (Gruner et al 2008). As well they wrote a review of invasive plants for a University of California Press Encyclopedia of invasive species (Evans and Strong 2011).

don strongAnother area of research in the Strong lab concerns invasive Spartina species in estuaries. They have been particularly active with the invasion of San Francisco Bay by hybrid cordgrass, Spartina alterniflora x S. foliosa. The Strong laboratory discovered these hybrids during the 1990s and has informed the $21 million eradication hybrid eradication campaign conducted by the California Coastal Conservancy, Invasive Spartina project. Pertinent to this work are publications on the evolution of self-fertility in these plants and their ongoing hybridization in San Francisco Bay (Ayres et al. 2008 a & b, Sloop et al. 2009, Sloop et al. 2010) and in Spain (Castillo et al. 2010). Their research on the Spartina alterniflora invasion of Willapa Bay, WA has also informed the massive control effort there, and they analyzed the spread of these invaders by means of a stochastic model of remotely sensed spatial data (Dennis et al 2011). The Strong lab has published two reviews of the global invasion of Spartina species and their hybrids (Strong and Ayres 2009 and Strong and Ayres 2013).

Terrestrial Ecology

wooly bearMany workers define ecology as the science that explains the abundance and distribution of species. Despite a century of work on questions surrounding this, the field has only a rudimentary grasp on the factors that are important. Rick Karban (Dept. Entomology) has been censusing populations of wooly bear caterpillars in the Bodega Bay area for 25 years however, there is relatively little in the way of understanding the factors that produce patterns in abundance and distribution. The ‘usual suspects’ all have relatively little explanatory power: weather, food limitation, and parasitoids all fail to provide much insight. Indeed, caterpillars often recover from the attacks of their tachinid parasitoids and alter their diets when parasitized to increase their chances of surviving. Including a more complete food web in our analysis does not appear to provide more resolution although ants may be unappreciated as predators and food quality may also be important. Karban is collaborating with Perry de Valpine to attempt to develop new analytical techniques that will account for more of the variance in abundance data. He is also collaborating with Marcel Holyoak to examine spatial patterns of abundance.

Sharon Strauss (Ecology and Evolution) has a long-term focus on the inextricable interrelationship between ecology and evolution, and its effect on the functioning of natural systems. Her lab’s research focuses on how organisms are influenced both ecologically and evolutionarily by the complex communities in which they are embedded. The ecology of organisms reflects their long-term evolutionary history, with all its contingencies. The extent to which related species share and diverge in ecologically important traits, and how this shared ancestry affects community assembly, is a growing area within ecology. In addition, ecological dynamics and community assembly are influenced by micro-evolutionary change. Ecological communities and abiotic environments exert selection on organisms; evolution in response to such selection, under the constraints of long-term evolutionary history, often results in populations that differ in traits from the parental generation. These different trait values, in turn, can feed back to affect the ecology of a system.

trifoliumThe Strauss lab has asked how does relatedness interact with mechanisms of community assembly in a native plant community? With Jean Burns and Brian Anacker, Strauss has studied plant community assemblages at the UC Bodega Marine Reserve. They use experimental approaches, planting individuals into the niches of more and less closely related species, to understand niche conservatism and coexistence among species. They are also measuring many traits and environmental attributes across their site to understand the major contributors to coexistence in this diverse community

Another project on the Bodega Marine Reserve is understanding the role of rhizobia and soil communities in coexistence of diverse Trifolium species assemblages. There are 9 native species of Trifolium, and many introduced ones. In collaboration with Maren Friesen at MSU, Strauss will be starting a large project in which they use transcriptomics of Trifolium species planted across soil niches, in the presence and absence of the local competitor, as well as rhizobial sequencing and rhizobia-species affinity/interactions to understand competitive/mutualistic interactions and N-fixation efficiency.

Ecomechanics

Research conducted in Brian Gaylord’s laboratory explores how organisms interface with physical attributes of their environments, and how such interactions influence population pattern.

Effects of turbulence on larval settlement

Gaylord Lab

The Gaylord lab and colleagues recently discovered that intense fluid turbulence sparks a previously unknown response in larval sea urchins. It causes larvae to abruptly transition to a physiological state where chemical cues induce settlement. This response could improve the chances that larvae end up in suitable habitat, since strong turbulence arises primarily only on wave-swept shores preferred by adults. Work on this topic has led to publications in the Proceedings of the National Academy of Sciences, and Biological Bulletin.

Ecology of biomaterials

The structural properties of the tissues that make up the body parts of organisms can play important roles in dictating how plants and animals interface with their environments. Work by the group has explored how bottom-dwelling invertebrates filter tiny food particles from the water column – in particular how they overcome limitations on the stiffness of the fingerlike projections they use as capture devices. We also developed new techniques for measuring the strength of microscopic shells of larval mussels, through which the Gaylord lab showed that ongoing changes in ocean chemistry decrease the forces needed to break them. Findings from these research efforts have appeared in the Journal of Experimental Biology, including a contribution designated as a ‘Highlights 2011’ article.

Physical stress and the mechanics of disturbance

dispersalThe dynamics of populations often track chronic or episodic agents of mortality, many of which are abiotic. Members of the ecomechanics lab have been working to understand how mussel beds reduce during low tides the thermal and desiccation stresses encountered by invertebrates that reside within the matrix of the bed. In somewhat contrasting efforts undertaken during periods of high tide, they also quantified wave forces acting on seaweeds of a range of sizes and morphologies; such forces often dislodge appreciable numbers of these organisms during storms.

Dispersal processes and their population consequences

A longstanding problem in marine ecology is determining patterns of population connectivity ensuing from the dispersal of planktonic larvae. The Gaylord lab has worked to clarify the role of ocean currents in contributing to the establishment of geographic range limits in species with such larvae; resultant insights appear in a recent, highly regarded textbook, Marine Macroecology. They have also studied dispersal of algal spores, as well as transport of nutrients and their uptake by kelp forests. Laboratory members have furthermore quantified properties of the very nearshore currents that likely dominate the dispersal process in many coastal species. These lines of research have produced publications in the Annual Review of Marine Science, Journal of Experimental Biology, Limnology and Oceanography, and Marine Ecology Progress Series. In a project newly funded by the National Science Foundation, Gaylord and colleagues are also exploiting a large-scale die-off of sea urchins to test ideas about recovery dynamics and the degree and character of stochasticity in larval delivery.

Invasive Species

zebrafishMarine invasive species are species introduced by human activities to new habitats where the species are not native. Marine invasive species are causing more and more costly economic problems, such as fouling the hulls of boats, which slows the vessels and increases the fuel costs. BML researchers continue to be among the top in the field of marine invasive species. In the past five years, they determined that ocean warming is leading to an increase in invasive species, a result that attracted the attention of naval architects who want to keep ahead of the curve in designing hulls of ships to resist fouling. In another project, BML scientists led a team of UCD students and collaborators from the Smithsonian Institution and Portland State University to conduct a study for the State of California comparing the various vectors that deliver invasive species to the State’s waters, including ballast water, ships hulls, aquaculture, the aquarium trade. The vector comparison study was the first of its kind and was published in the high impact general journal BioScience. These studies garnered much media attention. During the past five years, BML scientists were invited to speak on marine invasive species and their management before the American Association for the Advancement of Sciences and the National Council on Science and the Environment.

Climate Change and Biological Invasions

Increasingly, Ted Grosholz’s research is addressing the interaction between climate change and biological invasions. As the result of participation in an NCEAS (National Center for Ecological Analysis and Synthesis) working group on climate change and invasive species, he has continued his collaborative work on synthetic analyses of climate change impacts on the invasion process that began with participation in an NCEAS working group on climate change and invasive species. One project included a comprehensive study of field and lab experiments that varied climate change variables and assessed the impacts simultaneously on native and non-native species. The results of these analyses demonstrated that in terrestrial systems, native and non-native species responded similarly to experimentally manipulated climate change variables. However, in aquatic systems (freshwater and marine), increased temperature and CO2 more strongly impacted native species relative to introduced species. Overall, Grosholz has found that with respect to future climate change projections, aquatic systems may be particularly at risk from invasions. This may help managers determine which systems should be the priority for reducing stressors that can be managed in order to lessen risks due to changing climates. In a second project, he brought together the few dozen studies that have documented the effects of extreme climatic events on biological invasions. As trends in temperature, pH, sea level rise and other markers of change increase, so does the magnitude and frequency of extreme events. Most of the evidence suggests that these events selectively facilitate successful growth and spread of existing invaders.

This work is significant in bringing attention to two key issues. The first is the focus on extreme climate events, which are likely to have the greatest influence on ecosystem function in the future. The second issue is the effects on these rare events on invasions, since most other studies to date have only addressed the effects of mean values of climate variables on invader success. The Grosholz lab has developed a set of analytical tools for distributional and demographic data from invasive species to assess invasion potential at different invasion stages. They have used data from three case studies (a vine, a marine mussel and a freshwater crayfish) using current and projected climatic conditions to generate three examples of this integrated assessment approach. Their results show that the particular climatic variables can have contrasting effects or operate at different intensities across habitat types that can be invasion stage specific. They found that projected climate trends may increase the likelihood of invasion in some habitats and decrease it in others. This approach is likely to provide information that can inform management decisions and help to optimize invasion phase-specific management efforts for a wide range of invasions.

NSF Supported Non-Indigenous/Invasive Species and Pathogen Facilities

The new non-indigenous/pathogen facility and effluent treatment system being established at BML (2014) will support non-indigenous and invasive species research. When complete, the facility will enable visiting scientists and graduate and undergraduate students the ability to investigate introduced/invasive species as well as pathogens (see above) that are the basis for emerging diseases, and changing biodiversity.

Conservation

Salmonids

BML has had a long history of salmonid research, with a major project on enhancing the endangered winter run Chinook salmon in the 1990s, followed by research on fish health in local endangered Coho salmon in the 2000s. The unique salmonid facility at UCD has large tanks with seawater and freshwater sources for holding broodstock under environmental conditions, a hatchery, and a grow-out facility with fish pathogen capabilities.

Abalone

abaloneAfter severe depletion by over-fishing, the white abalone, Haliotis sorenseni, was the first marine invertebrate species to be listed as endangered. Currently, wild populations are composed of large, old individuals that are reproductively isolated form one another. Models estimate that the population will continue to shrink to fewer than 1,000 individuals in the next 10-15 years, with aging animals reaching their maximum life span of ~30 years. BML (G.N. Cherr, PI) has achieved the first successful captive spawning of white abalone in nearly a decade, in 2012 and 2013 with funding from NOAA. The addition of these animals almost triples the total number of captive white abalone in the broodstock program in the highly specialized culture facilities at BML. Broodstock conditioning and continued spawning of captive animals will enable outplanting of juveniles to optimal habitat in California with the hope of restoring this species.

Populations densities of white abalone are exceedingly low after extensive fishing in the 1970s. Today populations are composed of large, old adults that are declining at an alarming rate of 14% per year. The Bodega Marine Lab is the center of the captive breeding program for white abalone. The work in the Laura Rogers-Bennett laboratory at BML, seeks to gather critical population density information to see where these species are thriving and in what areas they are declining. They have found that in the southern portion of the range sea surface temperatures have increased over the past 30 years and populations have of both of these abalones have declined.

Marine Invertebrate Fisheries and Conservation

wacResearch in the Marine Invertebrate Fisheries and Conservation Lab (resident scientist Laura Rogers-Bennett, Center for Wildlife Health and CDFW) focuses on examining processes which impact marine invertebrate populations and communities then applying these findings to fisheries management and marine conservation issues. Marine invertebrates have become the most important fisheries in California in terms of both volume and value. In 2012, four of the top five fisheries were marine invertebrates. Unfortunately, an understanding of the life histories, biology and population dynamics of many of California marine invertebrate fisheries lags behind. The Rogers-Bennett lab’s research focuses on gathering data to inform the life history information and fisheries management of marine invertebrates. Their work is centered in nearshore kelp beds in northern California home to two important marine invertebrates that support fisheries.

Red abalone, Haliotis rufescens, are the foundation for an important recreational fishery north of San Francisco. More than 38,000 divers and rock pickers take, on average, 260,000 abalone per year. Researchers on the Rogers-Bennett lab are quantifying the growth and reproduction rates for red abalone in northern California. They use these data to develop matrix population modeling tools to ask questions about the efficacy of the existing size limits and Marine Protected Areas (MPAs). They also work to determine the relationship between abalone density and aggregation characteristics. Recently, the Rogers-Bennett lab has been working to determine the cause of a large-scale red abalone die off in Sonoma County which occurred in Aug. 2011 coincident with a Harmful Algal Bloom.

rogers-bennet lab

The second fishery that the Rogers-Bennett lab tracks and studies is the commercially exploited red sea urchin, Strongylocentrotus franciscanus, fishery. This is a dive fishery and is frequently one of the top five fisheries in the state. This fishery is based on the gonad of both sexes and gonad quality is a major determinant of this fishery. They have been working to track not only red sea urchin density (Fig. 1) but also gonad quality inside and outside MPAs.

A network of MPAs has been established in California. The Rogers-Bennett lab is working inside and outside MPAs in the North Central and North coast regions to examine the impact of no fishing on both the red abalone and red sea urchin fisheries. This is accomplished by using dive surveys which were started in 1999.

The Dungeness crab (Metacarcinus magister) fishery in 2012 was the second most valuable fishery in California. These crabs are notorious for large population fluctuations from year to year and the mechanisms driving these swings are poorly understood. The last three years have been very good years for the fishery with record breaking landings. Since 2007, the Rogers-Bennett lab has been sampling the recruitment of larval crab megalopae at key bays in northern California. By quantifying the scale of recruitment they are working with our partner in Oregon to develop an indicator of the strength of the fishery. There are findings that oceanographic conditions during the year are impacting the scale of recruitment at this early life history stage.

Restoration: Native Olympia Oysters Under Climate Change

Ted GrosholzAn important focus of Ted Grosholz’s research involves the ecology and potential for restoration of native Olympia oysters Ostreola conchaphila (previously Ostrea lurida) in western estuaries. Estuaries in California have been heavily impacted by human activities which have resulted in declines in ecosystem function. One important approach to restoring these functions is the restoration of native oysters, which historically provided many of the same ecosystem services as oysters in the eastern U.S. including the provision of habitat for native invertebrates and fishes and improving local water quality. Now many local, state, and federal agencies and natural resource managers are interested in improving the health of California estuaries by restoring native oyster populations. To this end, the Grosholz lab’s research program addresses climate change in the context of both limiting populations of native Olympia oysters Ostrea lurida as well as efforts to restore their populations. With funding from the NOAA/NERR Science Collaborative, and in collaboration with partners from San Francisco Bay NERR (Matt Ferner), Elkhorn Slough NERR (Kerstin Wasson) and UCD/SERC (Chela Zabin), they are investigating the effects of climate change variables on the future of restoration of this important foundation and fishery species in San Francisco Bay and Elkhorn Slough, CA. The Grosholz lab are explicitly testing the influence of multiple climate change variables including sea surface and air temperatures, dissolved oxygen (hypoxia), and salinity on native Olympia oysters in both the lab and field settings. A second project involves large scale restoration of native oyster and eelgrass habitat simultaneously. This project is funded by the California Coastal Conservancy and involves partnerships with San Francisco State University (Kathy Boyer),UCD/SERC (Chela Zabin), USGS (Susan de la Cruz), PWA (Jeremy Long), Environcorp (Bud Abbott), and CA Coastal Conservancy (Marilyn Latta). The Grosholz lab are conducting restoration in plots distributed across several acres at two sites in SF Bay, an East Bay site at Eden Landing and a Marin County site on TNC lands. These focus of this work is to explicitly test the effectiveness of different restoration methods and to understand the potential impacts and synergies of restoring these two habitats concurrently. An additional goal is to also understand the potential for the oyster recruitment structures to reduce wave energy and protect shorelines from erosion.

For more information, see the following websites:

Restoration: Salt Marsh Restoration following Eradication of an Ecosystem Engineer

shore birdMuch of the Grosholz lab’s recent work over the last several years has involved measuring the community and ecosystem impacts of the invasive salt marsh cordgrass Spartina on a broad range of organisms from primary producers to shorebirds in San Francisco Bay. This has been a collaborative project funded by the National Science Foundation (CNH Coupled Natural and Human Systems). Our currently funded project through the NSF CNH Program focuses on the recovery and restoration of the salt marsh ecosystem following eradication of invasive hybrid Spartina. This work is a collaborative project with other UC Davis faculty including both scientists (Alan Hastings) and social scientists (Jim Sanchirico, Mark Lubell) to understand where, when and why this system may recover to its prior state. Following eradication of the invasive Spartina the system may recover either a marine mudflat or a habitat vegetated with native plants depending on tidal elevation. The Grosholz lab are using a variety of experimental approaches involving habitat manipulations to accelerate or retard recovery, isotopic tracer studies to follow changes in food webs, long-term field surveys conducted both before and after eradication, and active restoration of native vegetation, in partnership with the SF Invasive Spartina Project to quantitatively assess the restoration process under a variety of conditions. With the social science collaborators, They are developing a bioeconomic model of the tradeoffs among eradication and restoration programs under different scenarios of agency participation that attempts to balance the invasive species eradication with the recovery of endangered California Clapper Rails.

For more information about invasive Spartina, see the following websites: