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Fishery Bulletin 111(3) 
in Puget Sound is deep because of its glacial origin 
(Burns, 1985), compared with the much shallower es- 
tuarine systems on the East Coast of North America. 
Therefore, the shallow biogenetic habitats that have 
been altered by humans — a common occurrence in es- 
tuaries — encompass a relatively small fraction of the 
total available habitat. The local government is work- 
ing to assess the status of the Puget Sound ecosystem 
and to identify and implement measurable restoration 
goals. 3 However, this planning process is hindered by 
a paucity of long-term data on species and commu- 
nity trends. 4 Without such time series, it is difficult 
to assess the rate and extent of recovery that may be 
reached within planning timelines. 
Here we present our analysis of one of the longest 
continual and standardized surveys of the groundfish 
community in Puget Sound (surveys conducted by the 
University of Washington) to assess the nature and ex- 
tent of change that has accompanied significant resto- 
ration measures. Most significantly, the state of Wash- 
ington progressively prohibited commercial trawling 
by closing most waters of central and southern Puget 
Sound in 1989, and then closing all inland marine 
waters to nontribal bottom trawling in 2010. 2 There- 
fore, we hypothesized that these survey data — the 
collection of which began in 1991 — would provide an 
indication of rates of recovery of exploited fish stocks 
and community reorganization because not all species 
were exploited. Our time series is limited in spatial 
extent but provides a 20-year record of species com- 
position and abundance of the groundfish community 
and, therefore, may indicate the effect of commer- 
cial trawling and enable assessment of the status of 
recovery. 
This ecosystem affords a rare opportunity to track 
the recovery of groundfish populations and communi- 
ties in response to a commercial fishery closure. Typi- 
cally, information about fisheries effects has come from 
tracking changes in “no-take” marine reserves (Russ 
and Alcala, 1996; Babcock et al., 1999; Halpern, 2003). 
Although such spatial closures provide important in- 
formation for identifying restoration targets, no-take 
areas are often smaller in area than the range of popu- 
lations affected by fishing and, therefore, may not re- 
veal the full extent of fishing effects (Claudet et ah, 
2008). In contrast, the commercial trawl-fishing clo- 
sure in Puget Sound covered a large area that closely 
matches the distribution scales of resident populations. 
Moreover, because more than 2 decades have passed 
3 Puget Sound Partnership. 2009. Puget Sound Action 
Agenda : Protecting and restoring the Puget Sound ecosys- 
tem by 2020, 213 p. Pugest Sound Partnership, Olympia, 
WA. [Available from http://www.psp.wa.gov/downloads/ 
AA2009/Action_Agenda_FINAL_063009.pdf. 
4 Essington, T. E., T. Klinger, T. Conway-Cranos, J. Buchanan, 
A. James, J. Kerschner, I. Logan, and J. West. 2011. The bio- 
physical condition of Puget Sound. In Puget Sound Science 
Update, p. 205-423. Puget Sound Partnership, Tacoma, WA. 
[Available from http://www.psp.wa.gov/scienceupdate.php.] 
since the closure, we have the potential to describe not 
only the extent but also the trajectory of population 
recovery. Therefore, we can ask whether recovery was 
monotonic as predicted by simple population models or 
whether, instead, it was characterized by abrupt and 
sustained shifts in abundance and composition that 
would indicate either nonlinear population or commu- 
nity dynamics (Doak et al., 2008; McClanahan et ah, 
2011) or decadal-scale environmental drivers (Mantua 
et al., 1997; Anderson and Piatt, 1999). 
Our specific objectives were to determine 1) whether 
catch rates of resident Puget Sound groundfishes gen- 
erally increased through time following the closure of 
bottom trawl fisheries, 2) the extent to which shifts 
in this time series may represent population fluctua- 
tions or instead represent local effects that result from 
distribution shifts, 3) whether dynamics are best rep- 
resented by smooth trends through time or instead 
though more abrupt state-changes, and 4) whether ob- 
served trends in catch rates for resident Puget Sound 
groundfish populations may be linked to changes in 
environmental conditions reflected in oceanographic 
monitoring data. 
Materials and methods 
Study location and design 
Catch data were derived from bottom trawl surveys 
conducted in Port Madison, a large bay on the west 
side of central Puget Sound, north of Bainbridge Island 
(Fig. 1; see also Andrews and Quinn [2012] for specific 
sampling sites) as part of a Fisheries Ecology course 
of the University of Washington. The study area is lo- 
cated in the central basin of Puget Sound, the largest 
of the 4 main basins that compose the inland marine 
waters of Washington State. The area is not industri- 
alized, and the shoreline is primarily a natural bluff- 
beach formation typical of central Puget Sound with 
some armoring around private residences. All sampling 
was conducted on the third weekend in May, beginning 
in 1991 and continuing until 2012; sampling did not 
occur in 1992 and 1998. 
Bottom trawl surveys consisted of single tows of ~5 
min conducted at 4 fixed index sites at discrete depths 
(10, 25, 50 and 70 m) over 5 diel time periods: after- 
noon (-15:00-18:00 h), evening (-20:00-23:00 h), night 
(-01:00-04:00 h), morning (-06:00-09:00), and mid-day 
(-11:00-14:00 h). This survey design was intended to 
capture and account for diel shifts in onshore-offshore 
distribution of key species (Andrews and Quinn, 2012). 
Trawl paths did not overlap within sampling years but 
were staggered slightly. All sampling was conducted 
from RV Kittiwake. Each tow covered 0.37 km at 0.5 
m/s, with a standard Southern California Coastal Wa- 
ter Research Project bottom trawl that had a footrope 
