Electronic Supplementary Material S2. Summary of field-survey methods used to generate the distribution and abundance data of crabs, whelks, and oysters illustrated in Figure 1.
To quantify how the densities of whelks and the mortality of their oyster prey vary throughout the estuary, we conducted four annual intertidal surveys (2003-06) at 6 sites within the middle region of Tomales Bay (6-12 km from the ocean) and 3 sites within the inner bay (13-18 km from ocean) (Fig. 1). After selecting equal-sized sites (~300 m) with suitable oyster habitat (intertidal rocks within + 0.5 to –1.5 m MLLW), we divided each site into three –100 m sections perpendicular to the waterline. Each section was then bisected to create high and low intertidal oyster zones paralleling the waterline (six zones/site). In the center of each zone, a 15 m transect paralleling the waterline was established to measure oyster densities. To improve dispersion, each 15 m transect was divided into 7.5 m sub-transects along which we randomly selected three rocks to survey, yielding 6 rocks per transect (36 per site).
For each rock, we centered a 0.01 m2 quadrat on the top, bottom, and side surfaces and counted living and dead oysters. Using the three quadrats as sub-samples, we generated an average density of living and dead oysters for each rock. By converting a site’s mean density of living and dead oysters into proportional abundances, we normalized sites for differences in oyster density and recruitment. On the same randomly selected rocks, we quantified the abundance of native and invasive whelks within a 0.063 m2 quadrat, and these data were averaged to produce mean whelk densities for each site. Also at these same sites, we sampled crab densities (top predator) by deploying ~ten baited traps spaced at 10 m intervals. After 24 hours, we identified and counted crabs within each trap. For each site, we calculated a mean density of invasive and native crabs.
To illustrate striking differences of predator identity and oyster demography throughout the bay, we divided the estuary into two regions (i.e., inner and middle bay) and pooled each region’s data to show the mean (+SE) abundance for all three trophic levels: native and invasive crabs (Fig. 1a); native and invasive whelks (Fig. 1b); proportional abundance of oyster mortality (Fig. 1c); and mean abundance of living oysters (Fig. 1c).