Suisun Marsh Tidal Marsh and Aquatic Habitats Conceptual Model Chapter 4: Species FINAL REVIEW DRAFT 1 July 2010 Suisun Marsh Habitat Management, Restoration and Preservation Plan       Authors: Andrew Raabe, USFWS Rachael Wadsworth, NMFS Jini Scammell-Tinling, SRCD Steve Rodriguez, DFG Laura Cholodenko, DFG Carie Battistone, DFG Matthew Nobriga, DFG Cassandra Enos, DWR FINAL REVIEW DRAFT  Chapter 4: Species / Suisun Marsh Plan Tidal Marsh and Aquatic Habitats Conceptual Model    Table of Contents 4 SPECIES ........................................................................................................................................... 4-1 4.1 SPECIES OF CONCERN FOR SUISUN MARSH TIDAL MARSHES AND AQUATIC OPEN WATER ENVIRONMENTS 4-1 4.2 SENSITIVE SPECIES .......................................................................................................................... 4-6 4.2.1 California Clapper Rail (Rallus longirostris obsoletus) (FWS) ............................................... 4-6 4.2.2 California Black Rail (Laterallus jamaicensis coturniculus) (DFG) ........................................ 4-8 4.2.3 Suisun Song Sparrow (Melospiza melodia maxillaris) (DFG) .............................................. 4-10 4.2.4 Salt Marsh Common Yellowthroat (Geothylpis trichas sinuosa) (FWS) .............................. 4-12 4.2.5 Salt Marsh Harvest Mouse (Reithrodontomys raviventris) (FWS) ....................................... 4-13 4.2.6 Suisun Shrew (Sorex ornatus sinuosus) (DFG) .................................................................. 4-14 4.2.7 Delta Smelt (Hypomesus transpacificus) (DFG) ................................................................. 4-18 4.2.8 Longfin Smelt (Spirinchus thaleichthys) (DFG) ................................................................... 4-19 4.2.9 Sacramento Splittail (Pogonichthys macrolepidotus) (DFG) ............................................... 4-21 4.2.10 Chinook Salmon (Oncorhynchus tshawytscha) (NMFS) ................................................. 4-23 4.2.11 Steelhead (Oncorhynchus mykiss) (NMFS) .................................................................... 4-25 4.2.12 Green Sturgeon (Acipenser medirostris) (NMFS) ........................................................... 4-28 4.2.13 Soft bird’s beak (Cordylanthus mollis ssp. mollis) (FWS) ............................................... 4-30 4.2.14 Delta tule pea (Lathyrus jepsonii var. jepsonii) (FWS) .................................................... 4-32 4.2.15 Suisun thistle (Cirsium hydrophilum var. hydrophilum) (FWS) ........................................ 4-32 4.3 SUISUN MARSH SPECIES AND GUILDS OF MANAGEMENT INTEREST .................................................... 4-33 4.3.1 Waterfowl (SRCD) .............................................................................................................. 4-33 4.3.2 Shorebirds (SRCD) ............................................................................................................. 4-44 4.3.3 Sportfish and Native Fish .................................................................................................... 4-59 4.3.4 Mammals (DFG) ................................................................................................................. 4-66 Ch4_Species_Suisun TMAq CM_Final Draft_2010-0630sws.doc 4-i FINAL REVIEW DRAFT  Chapter 4: Species / Suisun Marsh Plan Tidal Marsh and Aquatic Habitats Conceptual Model    List of Tables (in text) TABLE 4-1. CONSERVATION STATUS AND HABITAT FUNCTIONS, SUISUN MARSH SPECIES ................................... 4-2 List of Figures (follows text) Figure 4-1. California Clapper Rail Conceptual Model Figure 4-2. Black Rail Conceptual Model Figure 4-3. Suisun Song Sparrow Conceptual Model Figure 4-4. Salt Marsh Common Yellowthroat Conceptual Model Figure 4-5. Salt Marsh Harvest Mouse Conceptual Model Figure 4-6. Suisun Shrew Conceptual Model Figure 4-7. Delta Smelt Conceptual Model Figure 4-8. Longfin Smelt Conceptual Model Figure 4-9. Sacramento Splittail Conceptual Model Figure 4-10. Chinook Salmon Rearing Conceptual Model Figure 4-11. Chinook Salmon Migration Conceptual Model Figure 4-12. Central Valley Steelhead Rearing Conceptual Model Figure 4-13. Central Coast Steelhead Rearing Conceptual Model Figure 4-14. Central Valley Steelhead Migration Conceptual Model Figure 4-15. Central Coast Steelhead Migration Conceptual Model Figure 4-16. Green Sturgeon Rearing Conceptual Model Figure 4-17. Green Sturgeon Migration Conceptual Model Figure 4-18. Rare Plants Conceptual Model Figure 4-19. Diving Benthivores Conceptual Model Figure 4-20. Diving Piscivores Conceptual Model Figure 4-21. Dabbling Omnivores Conceptual Model Figure 4-22. Dabbling Herbivores Conceptual Model Figure 4-23. Shorebirds Conceptual Model Figure 4-24. Striped Bass Conceptual Model Figure 4-25. White Sturgeon Rearing Conceptual Model Figure 4-26. White Sturgeon Migration Conceptual Model Figure 4-27. Prickly Sculpin Conceptual Model Figure 4-28. Tule Perch Conceptual Model Figure 4-29. Three Spine Stickleback Conceptual Model     List of Appendices (follows figures) Appendix 4-A: Wildlife of Suisun Marsh (DFG) Ch4_Species_Suisun TMAq CM_Final Draft_2010-0630sws.doc 4-ii FINAL REVIEW DRAFT  Chapter 4: Species / Suisun Marsh Plan Tidal Marsh and Aquatic Habitats Conceptual Model    4 Species This chapter presents a series of brief conceptual models for several target species and guilds of tidal marsh and aquatic open water habitats in Suisun Marsh. Species selected for these conceptual models are those identified as species of concern or of management interest. This chapter describes how the key physical and ecological processes discussed in the previous chapters influence each species at one or more points in their life histories. It describes the ecological functions that tidal marsh restoration provides at each stage along the evolutionary trajectory from when restoration begins to years in the future; for many species, those functions change with stage of development. This model makes the assumption that a geographic matrix of multiple restoration areas implemented at different times and each evolving at different rates according largely to their location will result over the longer term in the broadest number of species supported, each at relatively high population abundances. 4.1 Species of Concern for Suisun Marsh Tidal Marshes and Aquatic Open Water Environments Table 4-1 below lists all species of concern for tidal marshes and open water environments to be restored within Suisun Marsh. Ch4_Species_Suisun TMAq CM_Final Draft_2010-0630sws.doc 4-1 Table 4-1. Conservation Status and Habitat Functions, Suisun Marsh Species Species Listing Status Tidal Aquatic Tidal Marsh Sloughs Conc Montezuma and Minor w/in Tidal Low Low Mid High Upland Common Name Species Name Model Federal State Bays Suisun Sloughs Sloughs Marsh Intertidal Marsh Marsh Marsh Transition INVERTEBRATES Corophium Amphipods Corophium spp. RFB RFB RFB RFB Asian Clam* Corbicula fluminea RFB California Bay Shrimp Crangon franciscorum RFB RFB RFB RFB Dungeness Crab Cancer magister J/F J/F Oposum Shrimp Neomysis mercedis RFB RFB RFB RFB Oriental Shrimp* Palaemon macrodactylus RFB Overbite Clam* Corbula amurensis RFB RFB FISH Central Valley steelhead Oncorhynchus mykiss Y T A/M, A/F, A/M, A/F, J/M, J/M, J/F, J/F, J/R J/F, J/R J/F, J/F, J/F, J/M, J/F J/F J/R J/R J/R J/R Central California Coast Oncorhynchus mykiss T A/M, A/F, A/M, A/F, J/M, J/M, J/F, J/F, J/R J/F, J/R J/F, J/F, J/F, steelhead J/M, J/F J/F J/R J/R J/R J/R Salmonids Central Valley spring-run Oncorhynchus tshawytscha Y T, X T A/M, J/M, A/M, J/M, J/F J/M, J/F J/F J/F J/F J/F J/F chinook salmon J/F Winter-run chinook Oncorhynchus tshawytscha Y E, X E A/M, J/M, A/M, J/M, J/F J/M, J/F J/F J/F J/F J/F J/F salmon, Sacramento J/F River Central Valley fall/late fallOncorhynchus tshawytscha Y C SC A/M, J/M, A/M, J/M, J/F J/M, J/F J/F J/F J/F J/F J/F run chinook salmon J/F Delta Smelt Hypomesus transpacificus Y T, X A/F, J/F, A/F, A/B, J/F, A/F, A/B, A/B , L, E L L, E J/F, L, E Longfin Smelt Spirinchus thaleichthys Y P A/F, J/F, A/F, A/B, J/F, A/F, A/B, A/B, E, L L L, E J/F, L, E Northern Anchovy Engraulis mordax A/F, J/F, A/F, J/F A/F, J/F A/F, J/F J/R Splittail Pogonichthys Y A/F, J/F A/B, A/F, J/F, A/B, A/F, A/B, A/F, Pelagic macrolepidotus L, E J/F, L, E J/F, L, E Striped Bass* Morone saxatilis Y A/M, A/F, A/M, A/F, J/F, A/F, J/F , J/F, L, E L, E L Tule Perch Hysterocarpus traski A/B, A/F, J/F A/B, A/F, A/B, A/F, J/F J/F Sacramento splittail Pogonichthys SC macrolepidotus Prickly Sculpin Cottus asper L A/F, J/F, L, E A/B, A/F, A/B, A/F, J/F, L, E J/F, L, E Starry Flounder Platichthys stellatus A/F, J/F, A/F, J/F A/F, J/F A/F, J/F A/F, J/F A/F, A/F, A/F, J/R J/F J/F J/F Green sturgeon Acipenser medirostris Y T, PX A/M, A/F, A/M, A/F, J/M, A/F, J/M, J/F, J/R J/F, J/R J/F, J/F, J/F, J/M, J/F, J/F, J/R J/F, J/R J/R J/R J/R Benthic J/R Yellowfin Goby* Acanthogobius flavimanus A/F, J/F, A/F, J/F, L A/F, J/F, L A/F, J/F, L L Ch4_Table4-1_SMP_tidal-aquatic conc model_species list table_2009-0824dfg_2010-0630sws.xls 4-2 7/1/2010 Table 4-1. Conservation Status and Habitat Functions, Suisun Marsh Species Species Listing Status Tidal Aquatic Tidal Marsh Sloughs Conc Montezuma and Minor w/in Tidal Low Low Mid High Upland Common Name Species Name Model Federal State Bays Suisun Sloughs Sloughs Marsh Intertidal Marsh Marsh Marsh Transition White Sturgeon Acipenser transmontanus Y A/M, A/F, A/M, A/F, J/M, A/F, J/M, J/F, J/R J/F, J/R J/F, J/F, J/F, J/M, J/F, J/F, J/R J/F, J/R J/R J/R J/R J/R BIRDS Bufflehead Bucephala albeola F F F Common Goldeneye Bucephala clangula F F Barrow's Goldeneye Bucephala islandica SC F F Canvasback Aythya valisineria SC F F F Ring-Necked duck Aythya collaris F F Greater Scaup Aythya marila F F Lesser Scaup Aythya affinis F F Redhead Aythya americana SC F F Ruddy Duck Oxyura jamaicensis F F Surf Scoter Melanitta perspicillata F F Double-Crested Phalacrocorax auritus WL F F Diving Cormorant Ducks and Eared Grebe Podiceps nigricollois F F F F F F F Allies Pied-Billed Grebe Podilymbus podiceps F F F F F F F Western Grebe Aechmophorus occidentalis F F Clark's Grebe Aechmophorus clarkii F F Common Merganser Mergus merganser F F Red-breasted Merganser Mergus serrator F F Common Loon Gavia immer SC F F American Coot Fulica americana F F F F California brown pelican Pelecanus occidentalis E E F F californicus American white pelican Pelecanus erythrorhynchos SC F F Mallard Anas platyrhynchos F F F F F F F, B American Wigeon Anas americana F F F F F F F Dabbling Green-winged Teal Anas crecca F F F F F F F Ducks and Northern Pintail Anas acuta F F F F F F Allies Northern Shoveler Anas clypeata F F F F F F Tule Greater White- Anser albifrons elgasi SSC F F F F F F F F Fronted Goose Great Blue Heron Ardea herodias S F F F F F F F Black-crowned Night Nycticorax nycticorax S F F F F F F Herons, Heron Egrets, and Snowy Egret Egretta thula F F F F F F Bitterns Great Egret Ardea alba S F F F F F F Least Bittern Ixobrychus exilis SC F F F F F California Gull Larus californicus F, Lo F, Lo Gulls and Ring-Billed Gull Larus delawarensis F, Lo F, Lo Terns Elegant Tern Sterna elegans SC F F California Least Tern Sterna antillarum browni E E A/F,J/F A/F,J/F A/F,J/F R R Ch4_Table4-1_SMP_tidal-aquatic conc model_species list table_2009-0824dfg_2010-0630sws.xls 4-3 7/1/2010 Table 4-1. Conservation Status and Habitat Functions, Suisun Marsh Species Species Listing Status Tidal Aquatic Tidal Marsh Sloughs Conc Montezuma and Minor w/in Tidal Low Low Mid High Upland Common Name Species Name Model Federal State Bays Suisun Sloughs Sloughs Marsh Intertidal Marsh Marsh Marsh Transition Salt Marsh Common Geothlypis trichas sinuosa Y SC A/F,J/F A/F,J/F A/F,J/F A/F,J/F Yellowthroat Passerines Suisun Song Sparrow Melospiza melodia Y SC A/F,J/F A/F,J/F A/F,J/F A/F,J/F maxillaries , R , R Tricolored blackbird Agelaius tricolor SC Bald Eagle Haliaeetus leucocephalus E, S, F F FP White-tailed Kite Elanus leucurus FP F F Osprey Pandion haliaetus S F F Northern Harrier Circus cyaneus SC F F F Raptors Swainson's Hawk Buteo swainsoni T F F American Peregrine Falco peregrinus anatum E, S, F F Falcon FP Burrowing Owl Athene cunicularia SC F, B Short-eared Owl Asio flammeus SC F F F California black rail Laterallus jamaicensis Y SC T A/F,J/F A/F,J/F A/F,J/F A/F,J/F A/F,J/F,R coturniculus , , R Rails California clapper rail Rallus longirostris obsoletus Y E E A/F,J/F A/F,J/F A/F,J/F A/F,J/F A/F,J/F Long-billed Curlew Numenius americanus WL F F F F F F Lo Lo Western Sandpiper Calidris mauri F F F F F Lo Lo Least Sandpiper Calidris minutilla F F F F F Lo Lo Long-Billed Dowitcher Limnodromus scolopaceus F F F F F F Lo Lo Shorebirds Short-Billed Dowitcher Limnodromus griseus F F F F F F Lo Lo Marbled Godwit Limosa fedoa F F F F F Lo Lo Willet Tringa (= Catoptrophorus) F F F F F Lo Lo semipalmata MAMMALS American beaver Castor canadensis F F F California sea lion Zalophus californianus F F Harbor seal Phoca vitulina F F Muskrat Ondatra zibethicus F F F North American river Lutra canadensis F F F otter Salt marsh harvest Reithrodontomys raviventris Y E E A/F,J/F A/F,J/F A/F,J/F mouse , R , R Suisun shrew Sorex ornatus sinuosus Y SC A/F,J/F A/F,J/F , R , R Tule Elk Cervus elaphus nannodes A/F,J/F, R REPTILES and AMPHIBIANS Northwestern pond turtleClemmys marmorata SC A/F,J/F, R A/F,J/F, R R,B marmorata PLANTS Soft bird's-beak Cordylanthus mollis ssp. E, X R mollis Suisun thistle Cirsium hydrophilum var. E, X hydrophilum Ch4_Table4-1_SMP_tidal-aquatic conc model_species list table_2009-0824dfg_2010-0630sws.xls 4-4 7/1/2010 Table 4-1. Conservation Status and Habitat Functions, Suisun Marsh Species Species Listing Status Tidal Aquatic Tidal Marsh Sloughs Conc Montezuma and Minor w/in Tidal Low Low Mid High Upland Common Name Species Name Model Federal State Bays Suisun Sloughs Sloughs Marsh Intertidal Marsh Marsh Marsh Transition Suisun Marsh aster Aster lentus SC Delta tule pea Lathryus jepsonii ssp. SC jepsonii Mason’s lilaeopsis Lilaeopsis masonii R (DFG 2005, Goals Project 1999, K. Hieb DFG pers.comm. 2006, Liguori 1995, M. Nobriga DWR Pers. Comm. 2006, Moyle et al. In Review, Orsi 1999, Stevens 1977, SEW 2001, and USFWS 1996) Life Stage: (A) = Adult, (J) = Juvenile, (L) = Larval, (E) = Egg Habitat Function: (B) = Breeding, (R) = Rearing, (F) = Foraging, (M) = Migrating, (Lo) = Loafing Listing Status (P) = Species proposed, (PX) = Species listed, critical habitat proposed, (X) = Critical habitat listed, (E) = Listed as Endangered under Endangered Species Act, (Rare) = Limited in distribution, declining throughout their range, or with vulnerable life history stage, (SC) = Species of Special Concern, (T) = Listed as Threatened under Endangered Species Act, (S) = Sensitive(CDFGandUSBLM),(WL)=WatchList(CDFG),(FP)=FullyProtected(CDFG) * = Non-native species Ch4_Table4-1_SMP_tidal-aquatic conc model_species list table_2009-0824dfg_2010-0630sws.xls 4-5 7/1/2010 FINAL REVIEW DRAFT  Chapter 4: Species / Suisun Marsh Plan Tidal Marsh and Aquatic Habitats Conceptual Model    4.2 Sensitive Species An enormous, diverse assemblage of fish, amphibians, reptiles, birds, and mammals uses the habitats within Suisun Marsh at one or more points during their various life stages. Many of these species are listed sensitive and/or special-status species. This section contains brief conceptual models of habitat usage for 15 of these sensitive species, representing multiple guilds and types of habitat dependencies. Appendix 4- A contains a complete list of all species that use Suisun Marsh, and the general habitats in which they are found. 4.2.1 California Clapper Rail (Rallus longirostris obsoletus) (FWS) Species Description The California clapper rail is a secretive, hen-like waterbird, indigenous to estuarine marshlands in the San Francisco Bay (Goals Project 2000). California clapper rails occur almost exclusively in tidal salt and brackish marshes with unrestricted daily tidal flows, adequate invertebrate prey food supply, well developed tidal channel networks, and suitable nesting and escape cover during extreme high tides. They once occupied coastal California tidal marshes from Humboldt Bay southward to Morrow Bay, and estuarine marshes of San Francisco Bay and San Pablo Bay to the Carquinez Strait (SEW 2000). Resident populations are currently limited to San Francisco Bay, San Pablo Bay, Suisun Bay, and associated tidal marshes. Conceptual Model of California Clapper Rail Use of Tidal Marshes in Suisun Marsh The conceptual model for California clapper rail is displayed in Figure 4-1. Primary drivers for the California clapper rail are the inundation regime, the invertebrate community, access to high ground refugia and channels (marsh geomorphology), salinity, and the marsh plain vegetation communities. Size of the marsh, location relative to other marshes and buffer areas between the marsh and upland should be considered when selecting sites for California clapper rail habitat restoration. Habitat that has direct tidal circulation is preferred and is characterized by predominant coverage by pickleweed (Salicornia virginica) with extensive stands of Pacific cordgrass (Spartina foliosa), and, in the North Bay, Scirpus robustus, abundant high marsh cover, and an intricate network of tidal sloughs which provide abundant invertebrate populations (Grinnell et al. 1918, DeGroot 1927, Harvey 1988, Collins et al. 1994) as well as escape routes from predators (Zembal and Massey 1983, Foerster et al. 1990). Research suggests that rail density is positively correlated to channel density. Local populations of breeding California clapper rails are most dense where patches of historical and youthful marshlands are together in at least 100 ha in size. Such patches typically comprise some historical and youthful marshlands together (Collins and Evens 1992, Collins et al. 1994). The primary diet of clapper rails consists of various invertebrate species, including mussels, clams, crabs, snails, amphipods, worms, spiders, insects, and fish (Williams 1929, Applegarth 1938, Moffitt 1941). Most Ch4_Species_Suisun TMAq CM_Final Draft_2010-0630sws.doc 4-6 FINAL REVIEW DRAFT  Chapter 4: Species / Suisun Marsh Plan Tidal Marsh and Aquatic Habitats Conceptual Model    foraging occurs when food is more available during low tide when mudflats and tidal sloughs are exposed (Applegarth 1938, Foerster and Takekawa 1991). Non-native mammalian predators represent the most severe short- and long-term threat to the species. Non-native species, such as the red fox (Vulpes fulva) and feral cats (Felis domestica), pose a serious threat to adult clapper rails (USFWS and USN 1990, Foerster et al. 1990, Foerster and Takekawa 1991, Zembal 1992, Albertson 1995). Norway rats (Rattus norvegicus) and raccoons (Procyon lotor) also pose serious threats to clapper rail eggs (DeGroot 1927, Applegarth 1938, Harvey 1988, Foerster et al. 1990). No studies have been conducted to confirm these threats in Suisun Marsh. Lack of extensive blocks of tidal marsh with suitable structure is the ultimate limiting factor for the species’ recovery; vulnerability to predation is exacerbated by reduction of clapper rail habitat to narrow and fragmented patches close to urban edge areas that diminish habitat quality. Dikes provide artificial access to terrestrial predators, and displace optimal cover by high marsh vegetation. Non-native plant species management is also essential to protect from invasives such as smooth cordgrass (Spartina alternaflora) and pepperweed (Lepidium spp.). The rapid invasion of San Francisco Bay by exotic Spartina alterniflora (smooth cordgrass) also threatens to cause major long-term structural changes in tidal salt marsh creek beds and banks, creek density, and marsh plains, and could impair future habitat for California clapper rails. Contaminants, particularly mercury, selenium, and polychlorinated biphenyls (PCBs) are significant factors affecting viability of California clapper rail eggs (Schwarzbach et al. 2001, 2002, 2006, Novak et al. 2005). Restoration in heavily subsided areas could benefit from the addition of dredge material, but this could potentially introduce contaminants (Foin et al. 1997). Restoration of the high marsh should include a buffer zone between the high marsh and the upland ecotone. There is some evidence that rails will abandon their habitat if frequently disturbed, so the buffer zone should have limited access. The creation of channels would also provide secure escape routes for rail movement back and forth with the tides (Foin et al. 1997). Expected Restoration Effects at Each Trajectory Stage California clapper rails utilize the low intertidal, low marsh, mid marsh, high marsh, and upland transitional zones. Rail foraging and refugia habitat encompasses the lower, middle, and high marsh zones, as well as the adjacent transitional zone. Lower and middle marsh zones provide foraging habitat at low tide. Higher marsh areas (high marsh and transitional zones) with dense vegetation are used for high-tide refugia (DeGroot 1927; Harvey 1988; Foerster et al. 1990; Evens and Collins 1992; Collins et al. 1994). California clapper rails typically nest in the upper-middle tidal marsh plain or high tidal marsh zones, not upland habitat transition zones bordering tidal marsh. Ch4_Species_Suisun TMAq CM_Final Draft_2010-0630sws.doc 4-7