Stream Habitat Features. Executive Summary

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1 EXECUTIVE SUMMARY: BROAD-SCALE ASSESSMENT OF AQUATIC SPECIES AND HABITATS The Broad-Scale Assessment of Aquatic Species and Habitats addresses the aquatic resources within the Interior Columbia Basin Ecosystem Management Project assessment area. It is directed along four primary themes: a broad characterization of the geophysical and biological settings that define the natural potential of the Basin to provide for aquatic resources; anthropogenic factors that affect aquatic habitats and species, with special emphasis on effects of Federal land management; a broad-scale assessment of the current condition of aquatic habitats and species, primarily fishes; and a synthesis of information in order to provide a regional context for Federal management strategies to protect and restore aquatic and riparian habitats. Geologic and geomorphic processes formed and continue to affect the Basin. These processes, in concert with the underlying physical environment, establish the template and constrain the successional pathways for aquatic habitats and their associated communities. Similarly, natural fluctuations in the marine environment due to variation in atmospheric and oceanic circulation patterns influence the productivity of anadromous fish stocks. They may temporarily mask changes in freshwater habitats. Human effects predated Euro-American settlement but increased dramatically with technological development. By the mid-8s, Euro-American settlers had begun to substantially alter the Basin's landscape and aquatic habitats. Large dam construction began about 9. The dams have greatly reduced the range of migrating fish. Fish spawning and rearing areas in the upper Columbia River Basin were isolated after the Grand Coulee (94) and Chief Joseph (955) dams were completed. Since 967, Hells Canyon Dam has blocked anadromous fish access to the Snake River and tributaries above the dam. A similar loss of most spawning and rearing habitats followed the construction of Cabinet Gorge Dam on the Clark Fork River above Lake Pend Oreille. Today there are at least,239 large dams in the assessment area, each with storage capacity in excess of 62, cubic meters. If small dams are included, the total storage capacity could be several times larger. There are thousands of small dams in the Basin, and most do not have fish passage facilities. The full extent to which these dams impede migration or affect spawning and rearing habitats of fishes has not been documented. Even though the rate of increase in storage volume has leveled since the mid-97s, the total number of dams continues to increase, suggesting that new construction is focused on smaller dams. Even with fish passage facilities, detrimental effects from dams occur. Direct mortality of juveniles continues in turbines and bypass systems. Indirect mortality is caused by physiological stress, increased susceptibility to predators, and the inability to find routes around dams and through slack water. According to U.S. Environmental Protection Agency estimations, overall water quality impairment within the Basin appears to be modest compared with total length of streams. Because these Executive Summary ; 63

2 estimates are based on existing and accessible data from locally specific State and Federal monitoring programs, they likely do not reflect the real extent and distribution of impairment. Many streams identified by the Forest Service as having elevated temperatures were not identified in Environmental Protection Agency assessment reports. In addition, water withdrawals for oftstream uses can reduce instream flows significantly. This can alter or eliminate habitat and affect water quality. Most streams in the region are now fully or overappropriated. Irrigation is the primary offstream use of water in the Basin. To look at changes in riparian vegetation we conducted a mid-scale, Basin-wide analysis. The analysis showed significant changes. There was a decline in shrublands in the riparian zones in more than half of the ERUs. Shrublands predominantly shifted to forests and herblands through succession or disturbance. Forests, woodlands, and herblands increased in area or stayed approximately the same. Cottonwood, aspen, and willow, typically riparian-associated species which are known to have significant declines, are included in the forest class. However, they are likely masked by the dominance of other species in this class. These cover types decreased in 6 of the 3 ERUs. Significant decreases occurred in the Snake Headwaters and Columbia Plateau. Significant increases in woodlands occurred in the Northern Great Basin, Blue Mountains, and Columbia Plateau. This increase is attributed to shrubland conversion to juniper stands. The integrity of riparian vegetation and its extent along rivers has been changed and fragmented throughout the Basin in response to forest conversion and streamside disturbance. Stream Habitat Features We used stream-inventory data and landscape information to detect and characterize land use effects on aquatic habitats. For decades various agencies have routinely inventoried streams within their jurisdictions in order to monitor key aspects of stream-channel conditions. These inventories provide a rich source of information for comparison across broad geophysical settings and management regimes. They also permit historical comparisons in some areas. Many historically surveyed streams were resurveyed recently throughout the Columbia River Basin. Changes in habitats were analyzed using die information from the resurveyed streams. Results of survey information and tests of relationships among habitat features, landscape features, and disturbance variables reinforce the evidence that streams within the assessment area have been significandy affected by human activities. Major decreases in pool habitat have been caused by two factors: the loss of riparian vegetation, and road and highway construction accompanying human activities (such as timber harvest, grazing, and farming). Most notably, pool frequency (large pools and all pools) is inversely correlated with road density and management intensity. The losses appear to have been the greatest in the lowergradient, biologically-productive areas of river basins most disturbed by humans. The magnitude of decreases in deep pools is substantial and extensive regardless of ERU. The unmanaged streams that were resurveyed generally are in steeper and more highly dissected landforms within the Columbia River Basin and therefore would have had fewer large or deep pools. Most unmanaged streams either have retained pools or have improved pool habitat during the last 55-6 years. A factor likely to be important in controlling pool frequency in the Columbia River basin is the abundance of in-stream wood. There is a correlation between wood frequency and pool frequency throughout the assessment area. This occurs most notably between large-wood and large-pool frequencies on low-gradient streams. Wood effectively stabilizes channels, influences sediment routing, provides a major component of the in-stream organic matter, provides cover for fish and habitat for invertebrates, and increases overall channel complexity. Protecting sources of in-stream wood for streams is important because: Executive Summary

3 wood is not readily available in many areas; it plays a critical role for pool formation and habitat conditions; and wood frequency is sensitive to management practices. The amount of fine sediment (sediment less than 6 mm) on channel beds is another important aspect of habitat quality that apparently is influenced by management. The results of our analysis indicate road density significantly affects surface fines and corroborates the link between forest management practices and channel sediment characteristics. The role that low-frequency events have in controlling channel morphology, is an aspect of channel conditions in the assessment area that has not been explicitly evaluated in this analysis. Events such as large floods, mass movements, and fire can profoundly affect stream channels by introducing and/or mobilizing large quantities of sediment, thereby altering bed structure and channel form in manners that can persist for decades to hundreds of years. Past human activities can strongly influence the timing and magnitude of natural events. Clearcutting and watershed disruption are linked to increased water yields, bedload movement, more frequent flooding and scour events, and channel instability. Long-term risk to fish and fish habitat on a regional scale is affected by potential long-lasting perturbations to channel conditions. Status and Distribution of Fishes A total of 42 fish taxa were reported within the Basin. We considered the fishes at three levels listed in order of increasing detail: ) fish species assemblages, 2) sensitive native species, and 3) key salmonids. We summarized the known occurrence of all native and introduced fish taxa, defined species assemblages, and calculated richness and diversity indices. We compiled information for 38 taxa considered sensitive, threatened, endangered, or of special concern. We then considered seven select salmonids in the greatest detail: bull, westslope cutthroat, Yellowstone cutthroat, and redband trout; steelhead; and ocean-type (age- migrant) and stream-type (age- migrant) chinook salmon. Our analysis was based on both a summary of known distributions and the prediction of distributions and status for select species throughout the entire assessment area. Classification of status for key species and distribution for all species, native and introduced, was supported by information collected through more than 4 biologists working throughout the region. We organized our conclusions along four major themes: ) composition, distribution, and status of fishes; 2) areas with strong populations; 3) system integrity; and 4) intensively managed areas. Composition, Distribution, and Status of Fishes The composition, distribution, and status of fishes within the Basin is very different than it was historically. The overall changes are dramatic and extensive, and in many cases irreversible. Some forms are extinct. Many others, especially anadromous fish, are extirpated from large portions of their historical range. Our clearest understanding offish status comes from the analysis of the seven key salmonids and is supported by our analysis of species assembages. Although several of the key salmonids remain distributed through much of their historical ranges (notably the cutthroat trouts and interior redband trout), declines in abundance, the loss of important life histories, local extinctions, and fragmentation and isolation of high-quality habitats are apparent. Wild chinook salmon and steelhead are approaching extinction in a major part of the remaining distribution. If current distributions of the key salmonids are good indicators of aquatic ecosystem health, many systems are only remnants of what were larger and more complex, diverse, and connected systems. Even with no further habitat loss the fragmentation and isolation may place remaining populations at risk. With the exception of the Central Idaho Mountains, Snake Headwaters, and perhaps the Northern Cascades, most of the important areas for the key salmonids exist as patches of scattered watersheds. Many are not well connected or are restricted to much smaller areas than historically. Executive Summary 65

4 Many of these important watersheds are associated with high-elevation, steep, and more erosive landscapes. These areas may have more extreme or variable environments contributing to higher variability in the associated populations and higher sensitivity to watershed disturbances. Risks could be aggravated by further development. The patchwork of important watersheds also suggests that remaining populations are not well distributed within the subbasins. Watersheds that were once likely to support a complex of lifehistory patterns and subpopulations within larger regional or metapopulations are now often fragmented. The loss of spatial diversity in population structure and of the full expression of life-history pattern may lead to a loss of productivity and stability important to long-term persistence. Although we know less about the rare and sensitive fish taxa than about the seven key salmonids, analyses of existing distribution and reviews of available literature provide important insights about common threats and appropriate management needs. Many of these taxa occur in isolated areas of the Columbia River basin, in isolated subbasins of the Great Basin, or are restricted to the Upper Klamath Basin. They typically occur in relatively depauperate subbasins, perhaps with only one or two native fish species present and in very restricted areas, often occupying one or two small habitat patches within subwatersheds (averaging 8, ha in size). Consequently, broad- or mid-scale assessments that focus on high native species diversity may not adequately describe their distributions. Areas with Strong Populations Though much of the native ecosystem has been altered, core areas remain for rebuilding and maintaining functional native aquatic systems. Even though they are reduced in numbers and distributions, native trout remain one of the most widely distributed taxa within the Basin. These indicators of environmental quality suggest that although we have serious problems, particularly in the larger rivers and in the low-elevation agricultural and range lands, the situation is somewhat better in the forested lands. Conditions remain the best in those areas that have experienced the least humancaused disturbance. We see a higher proportion of strong populations in higher-elevation forested lands than others, and the proportion declines with road density. Most of the areas exhibiting high aquatic integrity fall within forested areas, with the exception of areas inherently high in native species richness near the southern edge of the Basin. The largest areas of contiguous watersheds supporting strong populations of key salmonids are associated with the major river subbasins found in the Central Idaho Mountains, the Snake Headwaters, and the Northern Cascades ERUs. Important but more restricted areas are also found in the Blue Mountains, Upper Clark Fork, and the Northern Glaciated Mountains. Each of the key salmonids had some known or predicted strong populations. Strong areas for salmonids occurred in from less than percent of available subwatersheds for stream-type chinook salmon to 34 percent of available subwatersheds for Yellowstone cutthroat trout (table.5). There are few clusters of subwatersheds likely to provide highly productive habitat for multiple species, but collections of watersheds still exist within larger subbasins. However, the core for maintaining and restoring much of the biological diversity associated with fishes still exists. System Integrity Protection and maintenance of system integrity and functioning will require innovative approaches. Simple solutions such as setting aside small, scattered watersheds probably will not be adequate for the persistence of even current distributions and diversity. The problems are too complex and too pervasive. If maintenance or restoration of aquatic ecosystem integrity is an important goal, dramatic and decisive action is required to stop further alterations and restore areas that are degraded. Aquatic diversity and resilience are dependent on the maintenance of complex habitats and networks of those habitats at multiple scales. Executive Summary

5 Table.5 Current population status of seven key salmonids in the Basin and its relationship to lands administered by the Forest Service (FS) and Bureau of Land Management (BLM). Data are based on counts of subwatersheds. Species Percent of Percent of Occupied Percent of Percent of Percent of Sensitive to Historical Range Range Classed Strongholds in Strongholds Depressed on FS/BLM Occupied as Strong Wilderness on FS/BLM FS/BLM Land Uses Bulltrout Yes Westslope cutthroat Yes Yellowstone cutthroat Yes Redband Yes Steelhead Yes Stream-type Chinook 28 < Yes Ocean-type Chinook minor influence Conserving the remaining watersheds and habitats that have high intrinsic value or condition for aquatic species is the key to maintaining system integrity. Focus areas include diose areas supporting strongholds for one or multiple species, areas of high genetic integrity or fringe distributions, and areas that support narrowly distributed endemic or listed species. For example, many narrowly distributed endemic species are associated with small isolated systems of the interior Oregon Lakes and Klamath basins and illustrate the special significance of these areas. Reconnecting and expanding the mosaic of strongholds for widely distributed species such as the key salmonids would help improve system integrity. For wide-ranging fishes such as the salmon, steelhead, and other migratory trouts, this includes protection of water quality and passage in migratory corridors as well as protection of spawning and rearing areas. Conservation and restoration of important habitats for key salmonids could provide habitat for associated species and will sustain important processes that influence structure and function within these systems. Restoring or maintaining the integrity of migration corridors will be challenging. Restoration and management of watersheds on Federal lands only will not be sufficient. River corridors surrounded largely by private lands are a particularly important part offish habitat networks. The connections and habitat provided by larger river systems are critical to the maintenance of anadromous populations. The construction of dams and reservoirs and their complex effects on migration is viewed as the single greatest threat to the persistence of salmon and steelhead in the upper basins. Although much of the highest-quality habitat for these anadromous fish probably remains in the Central Idaho Mountains, no strong populations persist there due largely to passage mortality in migration corridors. These corridors provide a critical link diat maintains the complex life histories of other species as well. For example, there are non-anadromous species that retain migratory lifehistory patterns. Species such as bull, redband, Yellowstone cutthroat, and westslope cutthroat trout may move repeatedly between small rivers and headwater streams used for spawning and initial rearing and large rivers or lakes used for subadult rearing, overwintering, or seasonal foraging. Aquatic community composition has been influenced by the introduction of non-native species and hatchery-propagated native species. Non-native species containment would also increase system integrity. We found large numbers of introduced species throughout all major river systems. The changes are most severe in the Executive Summary 67

6 warmer mainstems, but higher-elevation tributaries are also affected. Land management agencies could cooperatively work with State fishery management agencies to reduce or eliminate stocking of nonnative and hatchery-reared fish in areas capable of supporting self-sustaining native species. Containing non-natives will provide benefits that go beyond system integrity. Intensively Managed Areas While watershed protection is an effective management approach, evidence suggests that system integrity can be maintained in some intensively managed areas. We found robust fish populations in areas with minimal disturbance. We also found that intensive land use did not necessarily eliminate all strong populations or areas with high integrity. We could not discern, however, whether intensively managed areas with high integrity are anomalies, regions where the effects on streams lag behind the changes on land, or are areas where intensive management and fish can coexist. A more careful examination of these areas may provide useful guidance for future management of disturbance in important watersheds. Ecosystem Management and Fishes Six major issues involved with ecosystem management and fishes were examined: ) catastrophic wildfire and active forest restoration; 2) the role of federal land management in managing for anadromous fishes; 3) the effect of roads on sedimentation and fishes; 4) the function of special emphasis watersheds relative to unroaded areas; 5) subbasin classification to provide a spatially explicit description of aquatic needs and opportunities; and 6) riparian habitat conservation area ecological requirements. Wildfire and Forest Restoration Refounding of populations through dispersal from local refuges and through complex life history and overlapping generations are two primary factors important in fish population recovery following a large wildfire. Spatially diverse and complex habitats are important to both types of population recovery. Complex landscapes not only produce a mosaic of burn effects, they also create a mosaic of pre-fire stream habitat conditions that provide important refuges within the burn perimeter. That same pattern of stream habitats, the size of the watersheds, and the connection of the watersheds to a larger river basin are likely important in the full expression of life history. Strong, well-distributed populations appear to have a high potential for recovery following intense wildfires. Depressed populations inhabiting marginal or degraded habitat may lack the resiliency to adequately deal with catastrophic disturbance. The use of intensive forest management to reestablish more natural landscape patterns and disturbance regimes has variable risks and benefits across the landscape. However, the consequences of large fires are dependent on habitat conditions and the inherent resiliency of local populations. Risks to aquatic ecosystems from fire may be most important where tliey have been seriously degraded and fragmented. Watersheds that support healthy populations may be at greater risk through disruption of watershed processes and degradation of habitats caused by intensive management than through the effects of fire. Role of Federal Land Management There is no question that Federal land management has an effect on anadromous salmonids; however, it is not known to what extent efforts to improve and/or protect habitat will aid in the recovery of depressed populations, given the other factors affecting these fishes. With current conditions in migrant survival, many stocks are at serious risk. Rehabilitation of depressed populations cannot rely on habitat improvement alone. It requires a concerted effort to address causes of mortality in all life stages. These include freshwater spawning and rearing, juvenile migration, ocean survival, and adult migration. Thus, to realize the benefits of improved migration and ocean survival, good-quality freshwater habitats and populations 68 Executive Summary

7 must be maintained, and the distribution of highquality spawning and early rearing habitats must increase. Improved federal land management is crucial to this task. Roads and Associated Activity Roads contribute to the disruption of hydrologic function and increase sediment delivery to streams. Roads also provide access, and the activities that accompany access magnify their negative effects on aquatic habitats. Activities associated with roads include fishing, recreation, timber harvest, livestock grazing, and agriculture. Roads also provide avenues for stocking non-native fishes. Unfortunately, we do not have adequate broad-scale information on many of these attendant effects to accurately identify their component contributions. Thus we are forced to use roads as a catch-all indicator of human disturbance. The discussion of the relationship of roads to fishes often centers around three themes: ) the belief that road-building practices have improved enough in the last decade that we should not worry about their effects on aquatic systems; 2) the legacy of past road building is so vast and road maintenance budgets so low that the problems will be with us for a long time; and 3) the belief that there is not a strong correlation between road density and fish habitat and population. From an intensive review of the literature, we conclude that increases in sedimentation are unavoidable even using the most cautious reading methods. Roads combined with wildfires accentuate the risk from sedimentation. The amount of sediment or hydrologic alteration from roads that streams can tolerate before there is a negative response is not well known. It is not fully known which causes greater risk to aquatic systems: building roads to reduce fire risk or realizing die potential risk of fire. More research is needed in this area. The ability of the Forest Service and Bureau of Land Management to conduct road maintenance has been sharply reduced because of declining budgets. This is resulting in progressive degradation of road drainage structures and a potential increase in erosion. Most problems are with older roads that are located in sensitive terrain and roads that have been essentially abandoned, but are not adequately configured for long-term drainage. Given the magnitude of the area of federal forests with moderate to high road densities, the job of road maintenance will be expensive. Most road networks have not been inventoried to determine influence on riparian or aquatic resource goals and objectives. We conducted two analyses examining the correlation of roads to habitat and fish population status. Each of these analyses support the general conclusion that increasing road density correlates with declining aquatic habitat conditions and aquatic integrity. Our results clearly show that increasing road densities (combined with the activities associated with roads) and their attendant effects are associated with declines in the status of four nonanadromous salmonid species. Those species are less likely to use moderate to highly roaded areas for spawning and rearing, and if found are less likely to be at strong population levels. There is a consistent and unmistakable pattern based on empirical analysis of thousands of combinations of known species status and subwatershed conditions. The analysis is limited primarily to forested lands managed by the Forest Service and Bureau of Land Management. Special Emphasis Watersheds We examined several efforts to identify special emphasis watersheds for conservation of aquatic resources and ecosystem function in the Basin in order to address whether habitat criteria or population presence and status are better indicators for such special fish emphasis watersheds. We used fish population strength to identify the best remaining habitats within the Basin by focusing on subwatersheds with designated strong populations of seven key salmonids. This approach has the distinct advantage of recognizing the biological building blocks necessary to maintain and rehabilitate fish Executive Summary S9-,.! "

8 populations in the Basin. The population status watershed approach incorporates excellent habitat, strong populations, and unroaded areas. Designated wilderness and potentially unroaded areas are important anchors for strongholds throughout the Basin. More than 8 million hectares (27%) of Forest Service and BLM lands in the Basin contain strongholds (4% of Forest Service and 4% of BLM). These stronghold subwatersheds contain large areas of unroaded land (about 4.7 million hectares), averaging 58 percent of the area of an individual subwatershed. Subbasin Classification We developed a simple classification of subbasins (approximate area of 28, hectares) throughout the Basin. The classification scheme provides a spatially explicit description of aquatic issues, needs, and opportunities that can be associated with similar descriptions for terrestrial ecosystems. We grouped the subbasins into three classes based on contiguous, well-connected subwatersheds with high aquatic integrity and strong populations. The categories range from the best connected to the most isolated and fragmented populations with few or no strongholds within a subbasin. RHCA Ecological Requirements We examined recent literature to look at the sufficiency of interim riparian habitat conservation areas (RHCAs) to maintain ecological functions and prevent cumulative effects. Forest plans and forest practice rules regulate two major features of RHCA: ) width; and 2) the type and amount of activities that can take place within them. By design, a RHCA is to be wide enough to maintain ecological function at the small watershed level and limit disturbance near streams. Interim RHCAs in the range of anadromous fishes and bull trout are prescribed at 9-meter minimum widths for fish-bearing streams in order to maintain stream function and prevent sediment inputs from non-channelized sources. A review of the literature indicates that this width is likely to be sufficient to provide for most riparian functions with a margin for error depending on the intensity and extent of activities within a RHCA. The likelihood of disturbance resulting in discernable in-stream effects increases as adjacent slopes become steeper. Thus, greater protective measures to protect or rehabilitate riparian function and structure on steeper slopes may be required to prevent or reduce in-stream effects. The specific width necessary to protect a given stream and riparian area structure and function can be determined based on watershed and site-specific analysis. Taken in aggregate, the standards for management of stream and riparian systems on forest lands are more restrictive and ecologically more effective than requirements for riparian areas where agriculture and urban or industrial land uses are dominant. No state within the Basin has enacted an agricultural practices act explicitly protecting riparian vegetation. Improved protection of riparian areas in agricultural lands is essential if salmon and many native fishes are to survive in the long term. Research Needs Our collective knowledge of status, distribution, and habitats for fishes is incomplete. The classifications of status were incomplete for 2 percent to 5 percent of the historic range for anadromous key salmonids, and 33 percent to 67 percent of the presumed range for non-anadromous key salmonids. Classification of status was most complete for chinook salmon and least complete for redband trout. Our knowledge reflects the historical focus offish-management and research agencies on production and yield, recreational fishing opportunity, and high-profile species rather than on biotic integrity or species conservation. Limited information is available for most fishes. Sampling methodologies are poorly developed, inventories are incomplete, and reference standards are virtually nonexistent. 7 Executive Summary

9 The development of consistent, reliable, large-scale species inventories and databases will be critical for long-term management and evaluation of aquatic ecosystems. Continued research to define critical habitat requirements and predict distributions at multiple scales will be a key element in understanding both current and potential distributions. Many of the 38 special concern taxa are poorly understood and in need of study and rigorous monitoring efforts. Habitat and population monitoring is essential if management is to respond to factors threatening the persistence of the narrowly distributed endemics. Evaluation of the roles of riparian buffer zones and corridors of variable structure, size, shape, and connectivity will improve integrated aquatic-land management. Field experiments can be developed to assess the potential role of riparian management areas in watershed management. These experiments may answer fundamental questions necessary for knowledgeable watershed management. They may provide information on the spatial dimensions (that is, width, length, depth, space, and continuity) necessary to achieve single and multiple ecological and/or social objectives and on how well these areas function through time. It is important to evaluate the role of hydrologic and geomorphic disturbance from extreme events on the biological structure and function of streams, lakes, and riparian management areas. Three types of studies can contribute to this evaluation. First, field surveys are needed to assess the effect of historical events such as fires and large floods. Second, intensive, opportunistic surveys could be undertaken during and following such rare events. Third, the resilience of riparian and aquatic ecosystems to changes in the magnitude and frequency of extreme events could be tested using human-caused events (such as regulating levels of dams and reservoirs). Executive Summary 7

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11 EXECUTIVE SUMMARY- TERRESTRIAL ECOLOGY OF THE BASIN A first-ever catalogue of biodiversity of the Basin revealed diverse communities of plants, invertebrates, and vertebrates. However, many species groups are largely unstudied. Over 43, species of macro-organisms are estimated to occur within the assessment area and 7,86 species are known to occur. Micro-organisms, critical to ecosystem health and function, probably tally at least several hundred thousand species. This biodiversity results from the wide variety of habitats, topographic conditions, and prehistoric events within the study area. For this assessment we evaluated 4,28 species of macro-organisms. We explicitly included,339 individual species and 43 species groups in a database on species-environment relations (SER). We also identified 296 species (excluding fish) that are of particular interest to American Indian tribes. Some 264 taxa (species, subspecies, or fish stocks) have Federal listing status (table.6). Among non-fish taxa, these include 84 Category 2 Candidate, 3 Category candidate, endangered, 6 threatened taxa, and taxon federally proposed as endangered. The Forest Service and Bureau of Land Management list 538 species (excluding fish) as sensitive. Some of the threatened and endangered species and many of the additional species of potential conservation concern are dependent on environmental or habitat components not evaluated at the broad scale. We do not project species' viability in this assessment. Rather, this assessment sets the stage and provides base information including species distribution, habitats and key environmental correlates, and management actions and effects, as a basis for subsequent viability evaluation. Species' viability under various planning alternatives is presented in another document. Our work provides an ecosystem context for managing and restoring habitats and environments for terrestrial species and communities. We provide a classification system for environmental correlates and for ecological functions of species and identify functional species groups based on their ecological roles. Although the FS and BLM are charged primarily with habitat management, knowledge of species' ecological roles and the dynamics of plant and animal communities provides a stronger knowledge base. It creates an ecological foundation for ecosystem management. We discuss selection of bioindicators for monitoring environmental changes and for assessing grassland deterioration problems. We examine possible actions for mitigation and restoration. Land managers will probably be most interested in the following products: (a) lists of habitats and associated species with the greatest declines in area or distribution since historic times; (b) Species- Environment Relations (SER) databases listing species by habitats and ecological functions. The databases are used to determine the potential effects of ecosystem management activities. They can be used to proactively craft activities which emphasize or restore specific habitats or functions; (c) over 52 species distribution GIS maps and additional maps showing areas of high biodiversity and species rarity and endemism; and (d) descriptions of how fungi, lichens, bryophytes, and invertebrates have key ecological roles in maintaining ecosystem health, long-term productivity, and sustainable resource use. Executive Summary 73

12 m x CD o i-t- <' CD c 33 Table.6 Numbers of taxa (species, subspecies, fish stocks) by Federal listing status, extirpated, and of special interest to American Indian tribes. Listing status classes: Cl = Category candidate ; C2 = Category 2 candidate; Forest Service sensitive (in at least one state within the assessment area); Bureau of Land Management sensitive (in at least one state within the assessment area); Joint FS/BLM sensitive = same species listed by both FS and BLM as sensitive; Tribal = species identified by the ICBEMP Science Integration Team as of particular interest to American Indian tribes. U. S. Fish and Wildlife Service Forest Service and Bureau of Land Management Class C C2 Threatened Endangered Federally proposed threatened Federally proposed endangered FS sensitive BLM sensitive Nonvascular Plants 3 Vascular Plants Invertebrates Fish Amphibians 6 Reptiles Birds Mammals 4 2 TOTAL Joint FS/BLM 45 Total FS/BLM Tribal 4 25 (...see Aquatic Species and Habitats chapter...)

13 Species at Risk The Assessment contains a complete catalogue of all federally listed threatened, endangered, and candidate species. The database also includes information on The Nature Conservancy and Heritage Program rare plant categories, and stateand agency-specific listing categories of all species. Summaries of conservation plans and useful management actions for federally listed species are provided. The assessment also identifies a number of additional taxa, especially plants and invertebrates, worthy of additional attention. These include: 394 fungi species; 4 functional groups of lichen species; sundry types of microbiotic crusts (not classified); at least 4 apparently regionally rare bryophyte species; 28 individual vascular plant species and 82 rare plant communities; 44 rare and endemic invertebrates (gastropods and insects); and various vertebrates. Among the vertebrates are the more aquatic-dwelling amphibians, reptiles susceptible to ground-disturbing management activities, and birds and mammals associated with habitats that are now scarce, declining, or increasingly fragmented. These include native grasslands, sagebrush, and old low- and midelevation forests. Basic inventories are needed for many of these species to determine their true rarity. We do not advocate a species-by-species approach to management of all such species at risk. Many of the species on these lists can be assessed in groups. Inventories, where desired, could aim at gathering information for many species simultaneously, and management guidelines could address their collective habitat and environmental requirements or locations of joint occurrence. Species Environment Relations Native grasslands (Fescue bunchgrass, Agropyron bunchgrass), shrublands (big sagebrush), and old single-story and multi-story stages of many forest types, especially lower montane forests, have declined in total area and shifted in distribution since historical times. Most declines have occurred on Federal lands, although non-federal lands have also experienced declines. Many species of plants and allies, invertebrates, and vertebrates are associated with these types. Vertebrate species associated with the decline of old-growth forests included primary cavity excavators arid species with large home ranges. Other vegetation types, including young successional stages of forests, coniferencroached sagebrush and disturbed riparian conditions, have increased in total area and distribution since historical times. Major ecological species functions are summarized from the SER databases. Understanding functions is critical to crafting appropriate ecosystem management guidelines; the fate of individual species is only one facet of terrestrial ecology conservation. The major ecological functions we addressed were: species contributing to major biomass; herbivory; nutrient cycling relations; interspecies relations; soil productivity; wood decomposition; and water quality. As a land management tool, Federal managers will probably find these ecological/ functional species groupings more useful than a list of individual keystone species. Probably no vertebrate became regionally extinct in historical times; information on other taxa is lacking. Small-bodied, less widely-vagile species may be at greater risk for declines or local extirpations. Range edges are important for species conservation. Using the SER model, we identified species closely associated with conditions affected by management including: forest canopy; mistletoe brooms; dead parts of live trees; trees with exfoliated bark; snags; down wood; litter and duff; fire processes and insect outbreaks; recreation; roads; and trails. This information may be useful for managers predicting potential activity effects. The information will help identify specific conditions for the conservation of species functional groups. Fungi Fungal flora and management activities, effects on fungi are poorly known. Some species are important to recreational and commercial gatherers. Many kinds of fungi occur, including species with narrow distributions, species that fruit after fire, species Executive Summary j.v^/gi

14 that fruit in dung, and species that are mychorrhizal and saprophytic and thus depend on host plants. Fungi conservation can include protection of type localities in small, site-specific mycological preserves and further study of species biology and ecology. Lichens Lichens play key ecological roles in ecosystems. These include contributing mass and nutrients to litter and duff, increasing canopy and soil moistureholding capacity, fixing atmospheric nitrogen, serving as food for animals, and acting as bioindicators for air quality. They may also have significance for some American Indian tribes. The 736 lichen species were divided into 4 functional groups based on ecological relationships. The groups occur on four main substrates: dead organic matter, corticate and decorticate wood, rock, and soil. Lichens are major components of native rangelands and provide critical soil functions. They have been threatened by exotic grasses, increased fire frequency, rangeland conversion, and livestock trampling. One lichen, Texosporium sancti-jacobi, is listed as a candidate (C2) species. Providing clumps of old trees and uneven-aged stands for their legacy of lichens can improve lichen conservation. Basic lichen surveys and studies of management effects are needed to supplement our poor knowledge base. Bryophytes Most bryophytes have wide Arctic-alpine and boreal distributions. Others are coastal and north Pacific or occur in arid environments as part of soil crusts. Four taxa are endemic to the assessment area. Eleven ecological groups of bryophytes were identified based on common use of substrates. Changes in water quality affect aquatic submerged and wet-rock species. Forest canopy openings often adversely affect mycorrhizal species associated with decaying wood and forest humus and duff. Commercial collection of bryophytes may affect some of the humus and duff species. Other species in bogs, fens, and other environments are poorly studied. Dry soil species are critical to soil protection. Many species, at least 4, may be regionally rare. An inventory would help determine status, especially bryophytes in arid habitats, peatlands, floodplains, geothermal areas, isolated canyons, on calcareous rocks, and mineralized deposits. Bryophyte conservation can include training for identification, adding bryophyte identification to field vegetation plot data, and inventorying bryophytes in protected areas. Vascular Plants Vascular plants in the assessment area number at least 8, species, which include at least 54 local or regional endemics. The diversity comes from complex biophysical environments along gradients of elevation, bedrock and soils, temperature, and moisture. Native plant communities have declined significantly in the assessment area, prompting concerns about future conservation of rare species and rare plant communities. Of particular concern are communities affected by grazing, exotic species introduction, and timber harvest. Examples include bunchgrass grasslands of the Palouse region and low elevation cedar/ hemlock old forests. The sustained harvestability of some 25 plant taxa are of concern to American Indians. Conservation measures can include monitoring rare species and plant communities; off-site collection of pollen, seeds, and rare plants; and protecting of key areas of high species rarity, endemism, and diversity. Invertebrates No terrestrial invertebrate species is listed as threatened, endangered, or Cl candidate (although five aquatic invertebrates are threatened or endangered). Thirty-eight terrestrial invertebrates are C2 candidate species. The FS does not list any as sensitive species and the BLM lists 25. Some 95 terrestrial mollusks would benefit from conservation attention singly or as groups; many of these are confined to calcareous substrates. Invertebrates are critical components of many ecosystem functions including detritivory and nutrient cycling. We identified 4 rare and endemic species that bear further watching. Functional roles of invertebrates include: detritivory and nutrient cycling; maintaining soil structure, chemistry, and productivity; Executive Summary

15 wood decomposition; herbivory, pathogenic effects on other organisms; and control of disease-causing organisms. Invertebrates can make excellent bioindicators of soil and vegetation health. Most arthropods are poorly known; many are unnamed. Arthropod predators may control other invertebrate populations including some defoliator pests. They require a mix of habitat types, down wood, and vegetation substrates. Invertebrate pollinators are critical to maintaining the flora. In grasslands and forests, species groups, particularly herbivores, are important links in food webs and affect vegetation succession. A few are agricultural or forestry pests. Fire and changes in soil chemistry directly affect invertebrates, especially in range and forest conditions altered from historic structures. Other concerns are mechanical and livestock compaction and soil mixing. Other activities potentially harmful to desirable invertebrates include overgrazing, some recreation, loss of sphagnum bogs, exotic plants or arthropods, and pesticide use. Providing a diversity of habitats, maintaining soil structure and soil chemistry, and preventing or eradicating exotic species could enhance conservation of invertebrate species. Vertebrates Amphibians require water or moist environments, are susceptible to exotic species, and are associated more with substrates such as down wood or talus than with vegetation types or stages. Amphibians transfer nutrients from aquatic to terrestrial environments, are prey for predators, and contribute major biomass in forest ecosystems. Studies are needed to determine the effects of water quality changes, canopy closure, pesticides, livestock grazing, eutrophication, and ultraviolet radiation on amphibians and on their dispersal and distribution. Reptile distribution is more closely associated with elevation, aspect, and substrate than with vegetation. Reptiles are susceptible to dams, off-road vehicle use, loss of wetlands, livestock grazing, and fire suppression. Better survey techniques for reptiles are needed. Birds are susceptible to managementinduced changes in vegetation, especially historic declines in old, single-story, interior ponderosa pine forests and grasslands dominated by Agropyron bunchgrass. In particular, impacts to grasslands have caused declines in Columbian sharp-tailed grouse numbers. Neotropical migrants would benefit from conservation and restoration of riparian, old forest, shrub-steppe, grassland, and juniper habitats. Mammalian population or habitat declines include some bat species and predators. Some 42 vertebrates are listed as endangered, threatened, or C2 candidate. Few locations still contain all top predators. Biogeography, Endemism, and Biodiversity Broad-scale biogeography of species is poorly studied in the assessment area. We identified some species closely associated with some of the nine landform classes. Distributions of local endemics can result from contracted ranges due to habitat loss or extirpations, overall scarcity of suitable environments, or other factors. Apparent peripheral, disjunct, and scattered distributions of some species may be an artifact of the location and size of the area of interest. Species such as boreal owl appear as disjunct populations because of breaks in distributions of suitable environments or incomplete sampling. Smaller and more isolated disjunct populations are likely to be more susceptible to local declines or extinctions. Locally endemic species or subspecies are highly habitat-specific, such as Coeur d'alene salamander. Most Ecological Reporting Units had at least some unique species, although many species overlapped several ERUs. Some species are closely associated with single biophysical factors, although many species are likely correlated with multiple factors. We mapped centers of concentration for () species rarity and endemism and (2) high biodiversity. Centers of concentration were mapped separately for plants and for animals. Locations with several centers of concentration for these two types defined smaller "hot spots" for plants and animals combined (map.9). We identified 2 hot spots of species rarity and endemism and seven hot spots of high biodiversity. Additional hot spots may be identified at finer levels of geographic resolution Executive Summary 77.