Chapter 6 Biological Resources – Botanical and Wetlands This chapter describes the affected environment for botanical and jurisdictional wetland resources, as well as potential environmental consequences and associated mitigation measures, as they pertain to implementing the alternatives. The discussion focuses on the primary study area (area of project features, Temperance Flat Reservoir Area, and Millerton Lake downstream from RM 274). It also discusses the extended study area (San Joaquin River from Friant Dam to the Merced River, the San Joaquin River from the Merced River to the Delta, the Delta, and the CVP and SWP water service areas). Affected Environment Biological resources addressed in this section include terrestrial plant communities, special-status plants, designated critical habitat, special-status natural communities, and wetlands and other waters of the United States. Information in this section is based on descriptions of biological resource conditions documented during biological resources studies conducted in 2007, 2008, and 2010, as discussed below, and additional documents describing historical and potential conditions for biological resources in the primary and extended study areas. The following documents were reviewed in support of preparing this section: • Riparian Vegetation of the San Joaquin River (DWR 2002) • San Joaquin River Restoration Study Background Report (McBain & Trush 2002) • Temperance Flat Reservoir Alternatives Botanical Resources Baseline Report (Reclamation 2007) • Preliminary Delineation of Waters of the United States, Including Wetlands, for the Temperance Flat Reservoir (Reclamation 2008) Draft – August 2014 – 6-1 Upper San Joaquin River Basin Storage Investigation Environmental Impact Statement • Final Environmental Assessment/Initial Study: Water Year 2010 Interim Flows Project. San Joaquin River Restoration Program (Reclamation 2009) • Mapping Standard and Land Use Categories for the Central Valley Riparian Mapping Project (DWR 2009) • Supplemental Preliminary Delineation of Waters of the United States, Including Wetlands, for the Temperance Flat Reservoir Alternatives (Reclamation 2010) • SJRRP PEIS/R (SJRRP 2012) With the exception of the database searches, all the sources cited in the Affected Environment section of this chapter regarding the extended study area are sources cited in the SJRRP PEIS/R (SJRRP 2012). Vegetation Communities For purposes of this analysis, vegetation community nomenclature follows the Holland (1986) classification system. Some modifications were made to account for local variability and communities that are not specifically described in Holland, such as willow scrub and bush lupine scrub. California Wildlife Habitat Relationships (CWHR) nomenclature (Airola 1988, Mayer and Laudenslayer 1988) was used for unvegetated cover types, such as lacustrine and riverine areas that could not be classified using Holland’s terrestrial natural community types. A crosswalk analysis between the Holland vegetation community types, CWHR classification types, A Manual of California Vegetation Second Edition (Sawyer et al. 2009), and the plant community types for the action alternatives is provided in Table 6-1. Sensitive habitats include those that are of special concern to resource agencies or are afforded specific consideration through CEQA, Section 1602 of the California Fish and Game Code, Section 404 of the CWA, and the State’s Porter-Cologne Water Quality Control Act (Porter-Cologne Act), as discussed in Chapter 28, “Other NEPA and CEQA Considerations.” Sensitive habitats may be of special concern to these agencies and conservation organizations for a variety of reasons, including their locally or regionally declining status or because they provide important habitat to common and special- status species. Many of the vegetation communities and unvegetated habitat types in the primary and extended study areas qualify as waters of the United States subject to USACE jurisdiction under 6-2 – Draft – August 2014 Chapter 6 Biological Resources – Botanical and Wetlands Section 404 of the CWA and/or as waters of the State. In addition, riparian communities are generally subject to regulation under Section 1602 of the California Fish and Game Code. Vegetation communities that may be subject to regulation under Section 404 of the CWA or Section 1602 of the California Fish and Game Code are so noted in the community descriptions below. The CDFW maintains a list of terrestrial natural communities that are native to California. Within that list, CDFW identifies “special-status natural communities” (also known as sensitive natural communities), which it defines as “communities that are of limited distribution statewide or within a county or region and often vulnerable to environmental effects of projects” (CNDDB 2013a). These communities may not contain special-status species or their habitat. Special-status natural communities are tracked in the California Natural Diversity Database (CNDDB), a statewide inventory of the locations and conditions of the State’s rarest plant and animal taxa and vegetation types; however, no new special-status natural community data have been added to the CNDDB since 1990 when funding was cut for this portion of the program. Several vegetation communities that occur within the primary and extended study areas are designated as special-status natural communities, as noted in the community descriptions below. The following discussion describes the vegetation communities present in the primary study area, and in the San Joaquin River portion of the extended study area from Friant Dam downstream to the confluence with the Merced River (San Joaquin River Reaches 1–5). Greater detail is provided for these portions of the Study Area because the project would have more varied and substantially greater potential impacts on botanical and wetland resources within these areas than along the San Joaquin River from the Merced River downstream to the Delta, within the Delta, or within CVP and SWP water service areas. The extent to which the communities are present in the primary study area and the San Joaquin River between Friant Dam and Merced River portion of the extended study area is identified in Table 6-2. Their locations and extents in the primary study area are shown in Figure 6-1. Draft – August 2014 – 6-3 6 Environmental Impact State Upper - 4 Table 6-1. Crosswalk for Different Vegetation Community Nomenclatures Used in the Upper San Joaquin River Basin – Storage Investigation Draft San Joaquin River Basin Storage Investigation Wildlife Habitat – Upper San Joaquin August 2014 Relationships A Manual of California Vegetation Global and River Basin Storage Nomenclature (Airola Holland (1986) Nomenclature Nomenclature (Sawyer et al. 2009) State Rank Investigation 1988, Mayer and Nomenclature Laudenslayer 1988) Woodland Communities Quercus douglasii Alliance G4 S4 Blue Oak Woodland Blue Oak Woodland Blue Oak Woodland ment Quercus wislizeni-Quercus douglasii- Pinus G4 S4 Blue Oak Woodland Interior Live Oak Woodland Live Oak Woodland sabiniana Association Pinus sabiniana-grass Association G4 S4 Blue Oak-Foothill Pine Open Digger Pine Woodland Foothill Pine Woodland Pinus sabiniana-Quercus wislizeni/Ceanothus G4 S4 Blue Oak-Foothill Pine Digger Pine-Oak Woodland Foothill Pine Oak Woodland cuneatus Association Pinus sabiniana/Ceanothus cuneatus- Heteromeles arbutifolia Alliance Pinus sabiniana/Ceanothus cuneatus-Rhamnus Nonserpentine Digger Pine- Foothill Pine Chaparral G4 S4 Blue Oak-Foothill Pine ilicifolia Association Chaparral Woodland Woodland Pinus sabiniana-Quercus wislizeni/Ceanothus cuneatus Association Riparian Communities Alnus rhombifolia-Fraxinus latifolia Association G4 S4 Valley-Foothill Riparian White Alder Riparian Forest White Alder Riparian Valley-Foothill Riparian Great Valley Willow Scrub Fig-Willow Riparian Valley-Foothill Riparian — Fig Riparian Great Valley Mixed Riparian Sycamore Riparian Platanus racemosa Woodland Alliance G3 S3 Valley-Foothill Riparian Forest Woodland Populus fremontii-Acer negundo-Rubus armeniacus Association G2 S2 Valley-Foothill Riparian — Mixed Riparian Populus fremontii-Salix Association Great Valley Cottonwood Riparian Populus fremontii Alliance G2 S2 Valley-Foothill Riparian Cottonwood Riparian Forest Forest Great Valley Valley Oak Riparian Quercus lobata Alliance G3 S3 Valley-Foothill Riparian Valley Oak Riparian Forest Great Valley Mixed Riparian Salix laevigata-Salix lasiolepis Association G3 S3 Valley-Foothill Riparian Willow Riparian Forest Forest Salix exigua Shrubland Alliance G5 S4 Valley-Foothill Riparian Great Valley Willow Scrub Willow Scrub Salix laevigata/Salix lasiolepis/Artemisia G3 S3 douglasiana Association Valley-Foothill Riparian Great Valley Willow Scrub Riparian Scrub Rubus armeniacus Semi-Natural Stands — Table 6-1. Crosswalk for Different Vegetation Community Nomenclatures Used in the Upper San Joaquin River Basin Storage Investigation (contd.) Wildlife Habitat Upper San Joaquin Relationships A Manual of California Vegetation Global and River Basin Storage Nomenclature (Airola Holland (1986) Nomenclature Nomenclature (Sawyer et al. 2009) State Rank Investigation 1988, Mayer and Nomenclature Laudenslayer 1988) Riparian Communities (contd.) Cephalanthus occidentalis Association G5 S2 Valley-Foothill Riparian Buttonbush Scrub Buttonbush Scrub Broom Semi-Natural Shrubland Alliance — — Broom Scrub Spanish Broom Scrub Sambucus nigra Association G3 S3 — Elderberry Savanna Elderberry