Over the last several decades, human alterations have greatly changed the face of the California coastal zone, including the widespread loss of estuaries. The California halibut, Paralichthys californicus, is an ecologically and economically important finfish, and is known to depend upon inshore waters for nursery grounds. However, it remains poorly understood as to which specific habitat types (open coast, enclosed bays and estuaries, small lagoons) are most important as productive nursery grounds. In light of continued coastal change, information is needed on the relative importance of nursery habitat types for the proper implementation of marine reserves designed to protect the halibut.

The contribution of nursery habitat types will be determined using trace element analysis of California halibut otoliths (ear bones). These elements can be viewed as signatures that serve as a record of the environmental conditions experienced by fish over time and which differ across habitat types. Also, statistical analysis of long term CalCOFI data will be analyzed to examine how changes of coastal habitat types over time have affected the larval abundances and distributions of the halibut. To determine the level of connectivity between halibut populations, stable isotope analysis of otolith material (which varies with temperature and indicates latitudinal position over time) will be employed as well as molecular tools. A matrix model, that includes life-history information on halibut from specific habitats, will be created. With sensitivity analysis, this model will describe how halibut standing stocks are affected by coastal habitat alteration. Additionally, a patch isolation model will be employed to examine the effects of disturbance on halibut metapopulations (why connectivity data is needed).

This study will identify key nursery habitat for juvenile California halibut and reveal the sensitivity of halibut standing stocks to perturbations of coastal habitat types. Also, this study will be one of few to incorporate microconstituent analysis, molecular tools, and modeling in order to more fully understand population structure and dynamics within a species.

In coastal wetlands, invasive plants often act as ecosystem engineers altering flow, light and sediments which, in turn, can affect benthic animal communities. However, the degree of influence of the engineer will vary significantly as it grows, matures and senesces, and surprisingly little is known about how the influence of an ecosystem engineer varies with ontogeny. We address this issue on the tidal flats of San Francisco Bay where hybrid Spartina (foliosa x alterniflora) invaded 30 years ago. The invasion has altered the physico-chemical properties of the sediment habitat, which we predicted should cause changes in macrofaunal community structure and function. Through mensurative and manipulative approaches we investigated the influence of different growth stages of hybrid Spartina on macrobenthos and the underlying mechanisms. Cross-elevation sampling transects were established covering 5 zones (or stages) of the invasion, running from the tidal flat (pre-invasion) to an unvegetated dieback zone. Additionally, we experimentally removed aboveground plant structure in the mature (inner) marsh to mimic the 'unvegetated areas'. Our results revealed four distinct faunal assemblages, which reflected Spartina-induced changes in the corresponding habitat properties along an elevation gradient: a pre-invaded tidal flat, a leading edge of immature invasion, a center of mature invasion, and a senescing dieback area. These stages of hybrid Spartina invasion were accompanied by a substantial reduction in macrofaunal species richness and an increase in dominance, as well as a strong shift in feeding modes, from surface microalgal feeders to subsurface detritus/Spartina feeders (mainly tubificid oligochaetes and capitellid polychaetes). Knowledge of the varying influence of plant invaders on the sediment ecosystem during different phases of invasion is critical for management of coastal wetlands.