American Fisheries Society Symposium 39:111–123, 2004 © Copyright by the American Fisheries Society 2004 Ecological Patterns of Early Life Stages of Fishes in a Large River-Floodplain of the San Francisco Estuary TED R. SOMMER*, WILLIAM C. HARRELL, RYON KURTH, FREDERICK FEYRER, STEVEN C. ZEUG, AND GAVIN O’LEARY Aquatic Ecology Section, California Department of Water Resources 3251 S Street, Sacramento, California 95816, USA Abstract.—We examined assemblage patterns of early life stages of fishes for two major tributaries of the upper San Francisco Estuary: (1) Sacramento River channel, and (2) Yolo Bypass, the river’s seasonal floodplain. Over four hydrologically diverse years (1999–2002), we collected 15 species in Yolo Bypass egg and larval samples, 18 species in Yolo Bypass rotary screw trap samples, and 10 species in Sacramento River egg and larval samples. Fishes captured included federally listed species (delta smelt Hypomesus transpacificus and splittail Pogonichthys macrolepidotus) and several game species (Ameri- can shad Alosa sapidissima, striped bass Morone saxatilis, crappie Pomoxis spp., and Chi- nook salmon Oncorhynchus tshawytscha). As in other regions of the estuary, alien fish comprised a large portion of the individuals collected in Yolo Bypass (40–93% for egg and larval net samples; 84–98% for rotary screw trap samples) and Sacramento River (80–99% for egg and larval net samples). Overall ranks of species abundances were significantly correlated for Yolo Bypass and Sacramento River, suggesting that each assemblage was controlled by similar major environmental factors. However, species diversity and richness were higher in Yolo Bypass, likely because of a wider variety of habitat types and greater hydrologic variation in the floodplain. In both landscapes, we found evidence that timing of occurrence of native fishes was earlier than aliens, consis- tent with their life history and our data on adult migration patterns. We hypothesize that Yolo Bypass favors native fishes because the inundation of seasonal floodplain typically occurs early in the calendar year, providing access to vast areas of spawning and rearing habitat with an enhanced food web. Conclusions from this analysis have implications for the management of aquatic biodiversity of tributaries to the San Fran- cisco Estuary and perhaps to other lowland rivers. Introduction creased habitat area and diversity (Junk et al. 1989), terrestrial carbon subsidies to food webs Data from relatively undisturbed large rivers (Thorpe et al. 1998), and decreased predation indicate that the structure and function of dif- or competition (Corti et al. 1997). For fishes, ferent trophic levels are determined by inter- floodplain may function as spawning habitat actions between the river channel and its flood- (Penaz et al. 1992; Killgore and Baker 1996), plain (Junk et al. 1989). Floodplains can as rearing habitat (Sabo and Kelso 1991; provide higher biotic diversity and increased Gehrke 1992; Turner et al. 1994), and as mi- production of fish (Bayley 1991; Gutreuter et gration corridors (authors’ unpublished data). al. 2000) and invertebrates (Gladden and Unfortunately, there is relatively little infor- Smock 1990; Sommer et al. 2001a). Potential mation from large, regulated rivers, particu- mechanisms for floodplain effects include in- larly in temperate areas, where floodplain con- nectivity has typically been compromised by river channelization and the construction of * Corresponding author: [email protected] dams and levees (Michener and Haeuber 1998). 111 112 SOMMER ET AL. In this study, we examined assemblage water spills into Yolo Bypass over Fremont trends in the early life stages of fishes in two Weir, inundating the floodplain to a mean major tributaries of the San Francisco Estu- depth of generally less than 2 m. In low-flow ary: (1) Sacramento River channel, and (2) Yolo periods, water is confined to a tidal perennial Bypass, the river’s seasonal floodplain (Fig- channel along the eastern edge of the flood- ure 1). Several attributes of this system made plain. Although agriculture has been one of the it attractive for study. The floodplain is mostly primary land uses in the floodplain for the past separated from the adjacent river channel by three decades, the majority of the floodplain is a levee, allowing us to differentiate between presently (or soon to be) managed for wildlife fish assemblage responses in each landscape. in “natural” habitats, including riparian and Like most other regions in North America, upland areas, emergent marsh, and permanent much of the historical floodplain habitat of ponds. The reach of the Sacramento River ad- large rivers in California has been lost due to jacent to Yolo Bypass is a deep (>5 m) channel channelization and levee and dam construc- with minimal emergent vegetation and has tion (Rasmussen 1996). However, the fact that steep, rock-covered banks with a narrow ripar- Yolo Bypass is one of the largest contiguous ian corridor; the lower half of this reach is a areas of floodplain habitat on the West Coast tidal freshwater channel. Outflow from Sacra- of the United States may greatly enhance its mento River and Yolo Bypass rejoin near Rio biological significance. In addition, the region Vista, where the combined discharge enters the is the focus of a major habitat restoration ef- brackish regions of the estuary. fort (CALFED 2000). Landscape scale data on In addition to changes in physical habi- trends in assemblages of early life stages of tat, the biota of the estuary has been altered by fishes in river and floodplain habitat could be a large number of species introductions relevant for resource management in the San (Cohen and Carlton 1998). Phytoplankton, Francisco Estuary and perhaps other regions. zooplankton, and macroinvertebrates have Our study was designed to address the fol- declined substantially following the introduc- lowing specific questions for early life stages tion of the alien bivalve Potamocorbula amu- of fishes: (1) does species composition and rensis (Kimmerer and Orsi 1996; Orsi and diversity differ for the two landscapes? and Mecum 1996; Jassby and Cloern 2000). Native (2) what are the temporal dynamics of the as- fishes have shown population decreases due semblages in each landscape? to multiple factors (Bennett and Moyle 1996), leading to the listing under the Federal En- Study Area dangered Species Act of two races of Chinook salmon Oncorhynchus tshawytscha, steelhead The San Francisco Estuary is one of the larg- Oncorhynchus mykiss, delta smelt Hypomesus est estuaries on the West Coast (Figure 1). The transpacificus, and splittail Pogonichthys system includes extensive downstream bays macrolepidotus. (Suisun, San Pablo, and San Francisco) and a delta, a network of tidal channels that receive Methods inflow from the Sacramento and San Joaquin rivers. The delta drains about 40% of Califor- Our overall approach was to collect compara- nia (Atwater et al. 1979). The estuary has been tive physical and biological data in the Sacra- substantially altered by a variety of anthropo- mento River channel and adjacent Yolo By- genic factors, including levees, dams, land pass floodplain. Field data were collected reclamation activities, water diversions, and during winter through early summer for 4 contaminants. The primary floodplain of the years (1999–2002). Flow in Yolo Bypass and Sacramento River is the Yolo Bypass, a 24,000- the adjacent stretch of Sacramento River dur- ha, partially leveed basin (Sommer et al. ing 1999–2002 was recorded at gauges oper- 2001a). The 61-km floodplain floods in winter ated by U.S. Geological Survey. Daily water and spring in about 60% of years, typically temperatures for each site were obtained from when Sacramento basin flows exceed approxi- temperature recorders (Onset Corp.) installed mately 2,000 m3/s. During these flood events, in tidal channels of Yolo Bypass and Sacra- ECOLOGICAL PATTERNS OF EARLY LIFE STAGES OF FISHES IN A LARGE RIVER-FLOODPLAIN 113 FIGURE 1. Location of Yolo Bypass and sampling stations identified with solid circles. 114 SOMMER ET AL. mento River (Figure 1). We sampled early life were used for analysis. The degree to which stages of age-0 fishes during winter and species assemblages differed between the two spring of 1999–2002 by egg and larval nets habitats was examined in three ways. First, and rotary screw trap. species ranks were compared between Sacra- The egg and larval net sampling was de- mento River and Yolo Bypass by calculating a signed to examine the general composition Spearman coefficient of rank correlation for and timing of fish assemblages in each habi- the combined data for 1999, 2001, and 2002. tat, not to identify fine scale spatial variation. Second, species richness was calculated based Sampling was generally conducted weekly on the combined data for all 3 years. In addi- during flood periods and monthly during low tion, Shannon indices (H’) were calculated for flow periods. Paired samples were usually each location based on the sum of the species collected at each location, except in 1999, collected over the same time period. The Sh- when an extra 11 samples were collected in annon indices were then compared between Yolo Bypass, and in 2000, when very few Yolo Bypass and Sacramento River using a t- samples were collected in either Sacramento test designed especially for the comparison of River (N = 1) or Yolo Bypass (N = 4). We used two diversity indices (Zar 1999). fixed sampling sites (Figure 1) located away For rotary screw trap data, we summa- from overhanging vegetation and bank eddies, rized the number of fishes, less than or equal in water velocities of approximately 15–60 to 40 mm fork length (FL), that were clearly cm/s, depending on flow. The 500-µm-mesh age-0 based on inspection of length-frequency net was 4 m in length with a 0.65-m-diameter data. Although this size range was somewhat mouth. The net was fished passively in cur- arbitrary, initial data review suggested that the rent near the surface for approximately 10 min rotary screw trap adequately sampled early during mid-morning (0900–1100 hours).