Influence of temperature on Chinook salmon survival and abundance across the species range.

Currently, I am comparing likely direct effects of future temperature patterns on Chinook salmon across their latitudinal range.  In collaboration with Mary Ruckelshaus and Tim Beechie of NOAA Fisheries and several others in a working group, I have developed a mechanistic lifecycle model predicting effects of peak temperatures on survival during Chinook egg, juvenile, and adult lifestages.  Collaborators  at the University of Washington Climate Impacts Group of and University of Montana NTSG provided a large scale hydrological model estimating historical and future river temperatures at the 1/16th degree resolution under two global climate model scenarios.

Focal watersheds were identified at  interior river basins in the Sacramento, upper Columbia, lower Thompson, and Yukon rivers  where adult escapement, harvest, age structure, and juvenile abundance data were available.  Traditional stock recruitment methods were used to estimate contemporary productivity rates.  Chinook salmon have optimized run timing to make use of freshwater habitats within their temperature limits. From the northern to southern edge of their distribution, we identified case studies reflecting recent impacts of high temperatures. This has  allowed us to synthesize species level functional relationships between temperature and survival, and to forecast survival and abundance patterns at local basins. With the hydrological model providing estimates of the historical/future temperature landscape, our assessment of current population dynamics allowed us to evaluate likely future effects of temperature on freshwater productivity rates, assuming community interactions and other factors remain constant.

Incubation temperatures during fall and winter may be a strong factor determining spawning habitat for some populations, resulting in optimal emergence timing for growth in the spring. Using Columbia river region hydrological data inputs, we are exploring seasonal thermal patterns in habitat preferred by early runs of Chinook salmon under a simple growth model, and are trying to identify the relative significance of  peak summer temperature restrictions  vs. selection for optimal emergence timing.


distribution map columbia

Sympatric speciation, and  population genetics of high dispersal species
    I conducted a phylogeographic study with widow, black and blue rockfish (Sebastes), with two years of adult and juvenile cohort samples in collaboration with Libby Gilbert, Carlos Garza, . In this effort, we attempted to resolve the significance of species-specific behaviors in determining mean lifetime alongshore dispersal among species sharing spawning season and adult habitat. Secondly, we addressed the importance of contrasting circulation patterns in central California vs. northern California and Oregon on rates of alongshore dispersal. Among all species, nearly panmictic levels of gene flow were observed over 850km distances.
   A surprising outcome of using high resolution nuclear genetic markers for this study (14-17 microsatellites)  was the observation of two morphologically-similar subspecies among the previously recognized single species of blue rockfish (Sebastes mystinus). The two groups of blue rockfish are reproductively isolated, and have developed a moderate level of  genetic differentiation equivalent to several other discrete, but closely related Sebastes species pairs.  The two species are sympatrically distributed over several hundred kilometers of overlapping range, and the low level of gene flow implies that behavior plays a major role in decreasing  hybridization and maintaining isolation.Sampling efforts are underway to learn the distribution, mechanism of reproductive isolation, ecological habitat associations, and length-at-age relationships of both species for stock assessment purposes.  

Cryptic Blue rockfish -  
    A new species discovery?  NOAA statisticians involved in stock assessments routinely interview fishers to verify and groundtruth collected data. One on our team  found that several boat operators in the area of Crescent City, CA ( Bruce Miller ) have long recognized two color morphs of blue rockfish with a list of correlated traits. While most  morphological types in nature result from simple color polymorphisms rather than reproductive isolation, the credit for species discovery probably should be credited to traditional knowledge of fishers of this highly abundant speices. In the field, it can be  challenging to identify these cryptic types.
blotched and solid blue

Ecological applications of physical ocean models

 With an applied fisheries perspective, I developed a Matlab toolbox for processing lagrangian floats data from a 3-D coastal ocean model (ROMS) in collaboration with Chris Edwards of UC Santa Cruz. In a central California implementation of this model, we measured the effect of coastline topographical features on mesoscale movement of drifters which could be assigned to display simple behaviors and seasonality.  Assessment of interannual variation and seasonality was conducted with COAMPS wind field forcing over 1999-2004.
     In collaboration with Steve Ralston, qualitative and statistical comparisons were made with a dataset of larval rockfish fish, krill and phytoplankton sampled interannually by NOAA Fisheries within the central and northern California region.
  Effect of cross-shelf position on retention, and expected distributions of alongshore dispersal outcomes was assessed for floats either fixed at several isobaric depths or permitted to move vertically. We have designed many aspects of this model to be relevant to evaluation of scale and seasonality of drift movement, connectivity between subregions,
the marine reserve performance monitoring that my collaborators are directly involved in Marine Protected Area (MPA) performance,

Destination after 30 days
(note - Quicktime required to view animation files)
This shows a series of ROMS (Regional ocean modeling system) simulations in central California, restarted one month apart during the year 2002, and each lasting for 30 days duration. Floats at 5m depth are color coded by their position after 30 days. This is done in order to show the start region of floats which are retained over the shelf, which could be considered analogous to successfully settling marine larvae. Yellow indicates floats further than 60km from shore, and red, green and blue are 0-20km, 20-40km, and 40-60km respectively. The running date is indicated in the title. The compass arrow shows the wind direction and magnitude at Monterey Bay buoy.

Exiting north/south/offshore border by 1 month

Here, simulations are each restarted one week apart during the year 2002, with each lasting for 30 days duration. Floats at 5m depth are color coded by the border they will hit by before one month (northern - blue, southern - red, offshore - green), or those retained within the model domain (black). Apologies - the fraction of floats in each exiting category is printed in the legend, however the text is difficult to read in this reduced size version-focusing on the colors will provide most of the experience.
central california roms field

           My doctoral work was carried out in the lab of Zack Powell. This entailed field sampling of range and abundance, phylogeographic and population analysis of two species of introduced and native estuary mud crabs. To explore the feasibility of nonanthropogenic coastal dispersal by invasive estuary organisms, I developed an oceanographic model of alongshore transport in the NE Pacific, with a statistical examination of factors contributing to asymmetrical directionality of larval dispersal as well as temporal patterns of episodes of long-distance dispersal.

In collaboration with Carol E. Lee, I carried out several physiological studies related to the repeated evolution of freshwater tolerance by the copepod Eurytemora affinis