Sierra Nevada Bio-region
Chapter 1: Ecological Integrity of Ecosystems

Current Condition


As the Pacific Southwest Region embarks upon Forest Plan Revision, it is important to consider the broader context in which individual national forests occur. This is particularly important for ecosystems and ecological integrity. Many plants and animals know no boundaries. Fires cross where they will. Species migrate over time. Although the Sierra Nevada mountain range is a distinct geological entity, there is no demarcation in vegetation types and cover where the southern Cascades begin. Because of these interconnected species, ecosystems and landscapes, this bio-regional topic paper, that provides the broader context for Forest Plan revisions, encompasses the Modoc National Forest south to the Sequoia National Forest (Map of the assessment area). This was the same area selected and included in the 1996 Report to Congress, Status of the Sierra Nevada, Sierra Nevada Ecosystem Project (SNEP). The same area was also encompassed by the 2001 and 2004 Sierra Nevada Forest Plan Amendment (Framework).

Forest Specific Ecological Integrity

This chapter is organized in a hierarchical manner. There are some subsections and indicators that are covered and discussed for the entire bio-region. The primary means is to break the bio-region into meaningful subregions as described in the introduction. The subregion is where the bulk of analytical information is found, using much of the same data that is available at the forest scale (such as forest inventory and vegetation mapping data). Since each of the three forests with forest plan revision in progress, the Inyo, Sequoia, and Sierra National Forests, have slightly different schedules for completing their plan revisions, there may be different approaches utilized by each forest to tier to the bio-regional topics.

Introduction and Background

Ecological integrity of ecosystems is a broad term. In the simplest explanation, ecology encompasses living things (i.e. plants, animals and other critters), their environment (i.e. air, soil, water), and how they interact or relate to each other. Ecosystems are defined by the different living and non-living things that occur together in any area. General examples include aquatic ecosystems (lake, stream and river), terrestrial ecosystems (forest, woodland, shrubfields or chaparral, rock outcrops, grasslands, alpine scree), and riparian ecosystems (stream or lakeside plants and animals).

Aquatic ecosystem – water based

Riparian ecosystem – interface between water and land

Terrestrial ecosystem – land-based

Ecological integrity is a harder to define concept. It has been characterized in various ways. According to the planning rule (36 CFR 219.19) it is defined as:

“The quality or condition of an ecosystem when its dominant ecological characteristics (for example, composition, structure, function, connectivity, and species composition and diversity) occur within the natural range of variation and can withstand and recover from most perturbations imposed by natural environmental dynamics or human influence.”

One way to address ecological integrity is through measure of key ecological functions or services (i.e. providing clean water or forests resilient to fire) or indirectly through comparison with the “natural range of variability”. There are pros and cons and uncertainty in utilizing either of these approaches. For example, with aquatic ecosystems in the bio-region, they have been heavily modified by water developments such as dams and diversions. Given the dependence of much of the state (and country and more) on the agricultural industry this water supports, power and municipal water supply, it is unlikely that a comparison with the historic range of variability will be as useful as what are the key ecological services and how are they affected by climate change and management actions to improve fire resilience and aquatic system restoration? For terrestrial ecosystems, the natural range of variability may be more relevant but there may be a high level of uncertainty around key elements such as the historic distribution and habitat uses by the California spotted owl or the Pacific Fisher. For vegetation composition and structure and the historic role of fire as a process, the natural range of variability approach may be more useful. In this assessment, we are utilizing a combination of approaches: both the natural range of variability and ecosystem service.

Vegetation composition and structure at the community, landscape and bio-regional scale will be addressed by considering the natural range of variability. Currently, detailed literature reviews and assessments are in progress by the US Forest Service Region 5 Ecology Program lead by Dr. Hugh Safford. Most other components or indicators of ecological integrity are being addressed in terms of current function and condition, lacking a good means to assess the natural range of variability for them.

Some of the most proximate measures for monitoring ecological integrity are indices of biological diversity (Lindenmayer et al. 2000). Typically it is very difficult to assess population parameters for very many species simultaneously, however birds are one group of species for which it is possibly and cost-effective to monitor many species with minimally invasive field survey techniques. Birds are ideal organisms for monitoring ecological integrity and being part of adaptive management process (Rich et al. 2004) for the following reasons:
1) They segregate at the micro-habitat level and have habitat relationships that are well known.
2) Most species are diurnal and sing repeatedly, they are exceptionally cost effective to monitor, quantify, and show to partners; typically a dozen or more species can be detected by a single method on a single visit.
3) Highly standardized data gathering protocols have been established for birds, and they are used throughout the continent.
4) Numerous long-term databases on birds and habitat currently exist and are cooperatively stored, managed and easily accessible through the Avian Knowledge Network.
5) Birds are perhaps the best group of species to compare across multiple geographic scales (project-level, state, regional, and continental).
6) Coexisting suites of bird species can include both ‘indicator’ and ‘umbrella’ species that are known to represent habitat conditions, ecosystem functions and other difficult to monitor species.

PRBO Conservation Science has an ongoing monitoring program, associated data base, and interactive web-based tool for over 100 bird species in and around all nine forest of the Sierra Nevada bioregion ( that can assist current planning efforts and assess management actions on ecosystem integrity in the future.

Connectivity and structure of vegetation are being assessed in terms of function for wildlife habitat and floristic diversity. Fire was and is a key ecological process that shaped functional terrestrial and riparian ecosystems in the bio-region (van Wagtendonk and Fites-Kaufman 2006). It affected biological composition, structure, nutrient cycling, hydrologic regulation, and energy flow. Therefore, it is being used as an indicator for these other ecosystem processes that are more difficult to directly measure.

Selection of indicators and measures was based on a conceptual model framework as recommended by Noon (2003). In this approach, the interactions of processes and components of an ecosystem are considered and used as a basis for selecting those components or processes that are most important in the functioning and resilience of that ecosystem. Predators are often key components. As mentioned previously, fire is typically a key process in the western United States. Separate conceptual frameworks were constructed for aquatic, riparian, and terrestrial ecosystems. They are works in progress and we are working on scientific, interagency, and public collaboration to improve them. In general, we are utilizing a dynamic systems approach.

Coarse and Fine Filter Approaches for Monitoring Biodiversity
One of the fundamental and ongoing debates in forest management is centered on the scales and intensity of monitoring wildlife species to assess responses to changes in the environment. In a recent publication in the Journal of Wildlife Management (Schultz et al. 2013) several experts in wildlife conservation planning express concern of the Forest Service’s historic reliance on what is termed “coarse filter” approaches to monitoring wildlife species. The authors state, “Research indicates that the coarse-filter approach is unlikely to provide a reliable basis for multi-species conservation planning, (Cushman 2008), only limited testing of the approaches validity has occurred (Noon et al. 2009), and the monitoring of a select group of species using a fine-filter approach is necessary to determine the efficacy of coarse-filter approaches (Committee of Scientists 1999, Flather et al. 2009). A recent review of the degree to which coarse-filter models can be used to infer animal occurrence concluded that ‘..the observed error rates were high enough to call into question any management decisions based on these models’ (Schlossberg and King 2009).” The authors go on to state that the basic assumption that habitat is a valid proxy for species health is at best a risky stretch and at worst a weak and incomplete picture of the health, functioning and diversity of a particular ecosystem.

Another monitoring approach, also largely driven by expediency, postulates that species surrogates (indicator species) are adequate proxies for suites of species associated with various vegetation types across a landscape. In recent research (Cushman et al. 2010) examined 72,495 bird observations of 55 species across 1046 plots across 30 sub-basins and found “few significant indicator species relationships at either scale” where there was a presumed association.

In PSW-GTR-237, Managing Sierra Nevada Forests (2012) authors Malcolm North and Patricia Manley suggest that “coarse filter” approaches such as the California Wildlife-Habitat Relations model “generally fail to account for the different spatial and temporal scales at which species may respond to forest conditions or assess habitat features other than large trees and canopy cover.”

The Sierra Nevada Framework Environmental Impact Statement (2001) habitat projections for old forest attributes are an example of the coarse filter approach. Old forest habitat--large trees greater than 50 inches in diameter and large snags--were projected to increase significantly over a 140-year time scale. Oaks modeled to 60 years showed similar results. Yet, species monitoring has demonstrated that the California spotted owl, one of the key sensitive species of management concern closely tied to these habitat values, is currently experiencing a declining population trend (Keane 2013). The information regarding declining spotted owl trend was the result of fine-filter monitoring via a long-term spotted owl research project. If managers (and conservation advocates) were to rely simply upon the optimistic habitat projections in the 2001 Framework Plan and EIS (which the conservation community actively supported) we would be flying blind in what looks like an increasing grave situation for the owl’s survival.

Fine-filter monitoring approaches are less likely to oversimplify how animals use habitat and are more likely to capture effects of fine scale habitat fragmentation, predator-prey relations, behavioral responses to changed conditions, the value of understory diversity and snags and downed wood, landscape scale relationships or connectivity and spatial and temporal patterns of detection and non-detection.

In the new Forest Service Draft Directives, FSH 1909.12, Chapter 30 Monitoring, Section 32.12 “Selecting Monitoring Indicators,” stresses the financial feasibility, practicality, measurability and relevance to key monitoring questions. Section 32.13 establish eight monitoring indicators for tracking ecological conditions and progress toward desired conditions, plan objectives and important trends. Included in the directives are indicators to assess ecological conditions and status of focal species that are tied to ecological conditions.

These are generally coarse filter metrics that will be further defined in the specific revision of forest plans, including the Inyo, Sierra and Sequoia National Forest early adopter forests in California. Chapter 20 of the new Directives address the need for specific fine-filter standards when more general ecosystem indicators are not specific enough to address at-risk species needs such as nest tree protection or culverts allowing proper fish passage.

The National Forest Management Act requires the Forest Service to provide for a diversity of plant and animal species and not simply a range of ecological conditions that may or may not support diversity. The new Forest Service Planning Rule and its Directives system must ensure diversity of plant and wildlife species is maintained. The Forest Service’s obligation cannot devolve into a suite of invalid assumptions, ruled by efficiency which ultimately fail to meet the intent of the NMFA and the public’s expectation that Forest Service land managers will examine closely and rigorously the effects of management and changing conditions on the land.

At this time, we are not attempting to integrate condition of different indicators into a single combined evaluation of ecological integrity. However, it is likely that in the next phase, several options for doing this will be included. An example of this approach that is being considered includes the BLM Rapid Ecological Assessments (especially the Mojave Basin in progress).

In order to achieve valid measures of ecological integrity, the assessment will provide data on the quality and composition of non-conifer composition elements that are essential habitat features. These are so-called fine filter elements, but the proper way to think about them is that--as part of an ecological process--biological diversity emerges from niche partitioning. If there is not enough habitat in the different niches, species cannot find the resources they need, and there will be declines, particularly among those that are habitat specialists because there are fewer of them.T his is not just an either/or, fine grain versus coarse grain issue: it is essential to understanding ecological integrity for a biological assessment of this type.

Also, it is proper to use species that are rare or are thought to be in decline as priority “components” or indicators for the fine filter approach. In fact the FS is obligated to do so, under ESA and NEPA requirements to prevent species from becoming threatened with extinction. For example, if owl, fisher and marten and some subset of rare plants are focus species, then the discussion will need to be broad enough to capture the elements/components/indicators/ that are associated with these species. These will include the prey species, and the status of their food sources as well. Ecology requires a look up and down the food chain (as was done in the PNW spotted owl research), in order to understand the real capability of any given habitat or vegetation community.

Returning to a coarse filter approach in our example, several or more of the individual indicators deemed most important for ecological function are each rated with index values associated with sustainable, transitioning, and degraded conditions and then the values are combined. The combination of values can be a simple addition or an average. In this particular BLM example, the individual indicators combined were: landscape condition model index, landscape connectivity index, invasive plants index, fire regime departure, and change in extent. A similar approach is being examined for this assessment. Here, it may be most useful to combine different measures of biodiversity condition to generate a single rating that would be useful in ecosystem service evaluations.

The index or scorecard approach can also be approached with weighting different individual indicators, depending upon their perceived importance (to services or regulations) or vulnerability to stressors. Tools, such as the Vensim dynamic feedback model (http:/, allow “what if” evaluations of different weights for different indicators. This makes it possible to generate a range of condition ratings depending upon the valuation of different users. We are exploring this approach as one means of integration of ecological, social, and economic conditions and values. These models are displayed visually, have feedbacks between different elements or indicators, and the inputs can be qualitative or quantitative, simple or complex. It is an approach that is readily transparent and facilitates dialogue and testing of different assumptions and viewpoints. An example that is also shown in Chapter 3, to illustrate the feedbacks between drivers and stressors, and ecological, social, and economic conditions is shown below.
Comment: This graphic seems to illustrate that everything is related to everything else (which is what ecology tells us, essentially), but we cannot be sure of its meaning otherwise. In a biological assessment, social considerations are only relevant as anthropogenic change, or changes to ecosystems that result from human activities. Anthropogenic impacts then are the spectrum of changes that have acted upon the ecosystem since approx. 1850 (or, going back further in time, highlight the beneficial impacts of Native American land management practices, and then discuss the impact that the departure of their influence has had on fire regimes). All of these can be enumerated and will be overlapping and will be cumulative.

In this assessment, the emphasis is on a limited set of meaningful, measurable indicators that vary with major ecosystem type (aquatic, riparian, and terrestrial). Wherever possible, indicators that have been identified in previous or on-going scientific studies or reviews have been included. The intent is to consider all sources of information and at this time to gather additional information that we may not have known about or thought to consider. Geographic data was prioritized.

There is a huge need for the Social Ecological Integration to apply environmental concerns and knowledge in positive way that helps all existing forms of recreation and land use to continue and flourish. A new way of thinking is needed based on dispersing use to reduce environmental impacts. Finding ways to keep existing routes and areas open to the public while addressing reasonable environmental issues. To address increased use by encouraging building new routes and allowing additional access to disperse and reduce impacts. This new way of thinking would benefit the public and the environment, rather than the current trend of using environmental issues as a club to further restrict land uses and thereby concentrating land use and needlessly harming the environment. (Road and Trail Change In Use Evaluation-California State Parks PEIR 2012 & USDA Forest Service 1996-National Off-Highway Vehicle Activity Review)

Incorporating future conditions into ecological integrity

To evaluate whether the "dominant ecological conditions" of an ecosystem can "withstand and recover from most perturbations" (quotes refer to planning rule definition of ecological integrity) it will be necessary to evaluate whether future conditions are likely to be different from the current and past and incorporate this potential for change (even if it lies outside the range of natural variability) into management planning. Climate change is and will continue to be a pervasive influence the function of ecosystems, and the Forest Service. Many tools are available for assessing such changes, including the California LCC Environmental Change Network ( where maps can be generated to evaluate the distribution of current vs. future habitats, and the locations of areas which are likely to contain highest densities of priority conservation species targets (Figure XX). Specifically, it may be appropriate to recognize that certain vegetation types are likely to shift distributions 'upslope' to higher elevations where current and past climate conditions may be more similar in the future. This re-shuffling of the geography of habitats will create both a new landscape spatially, and new organization of important processes that shape the ecosystem (fire patters, precipitation patterns, timing of seasonal changes, species distributions, etc.).

Figure XX. Maps of current vs. projected future habitat type distributions and zonation analysis of priority avian conservation species targets. Maps were taken from the California LCC Environmental Change Network (

current future veg.jpg

ecn zonation.jpg

Literature cited:
Lindenmayer, D. B., Margules, C. R. and Botkin, D. B. (2000), Indicators of Biodiversity for Ecologically Sustainable Forest Management. Conservation Biology, 14: 941–950.

Rich, T. D., C. J. Beardmore, H. Berlanga, ... (2004). Partners in Flight North American Landbird Conservation Plan. Cornell Lab of Ornithology. Ithaca, NY.

Ecological/Geographic Variation and Assessment Stratification

Ecosystems and uses are not uniform across the bio-region. They vary from north to south, from east to west, with soil productivity, aspect, topographic position and climate that vary with elevation. For example, the southern Sierra Nevada reaches higher elevations and is drier (Figure x. Map of precipitation). Going north, precipitation increases to the west, but areas to the east become more prevalent on Forest Service units. There are also changes with increasing elevation that correspond with colder temperatures and shorter growing seasons. These are reflected in shifts in dominant and characteristic, plant, animal and other living things as well as characteristic fire patterns (fire regimes).

Figure x. Ecoregions, large landscapes with similar vegetation, soils, geology, climate, and topography. From Baileys xxxx.
M261G-Modoc Plateau Section
M261D-Southern Cascades Section

M261F-Sierra Nevada Foothills Section
M261E-Sierra Nevada Section

341D-Mono Section
322A-Mojave Desert Section
*Also add 341F- nyo Mountains Section to Bailey's (above).
Broad zones that roughly correspond to elevational changes in climate and ecosystem composition (dominant plants and animals) were developed based upon the literature (i.e. Franklin and Fites-Kaufman 1996, Terrestrial Vegetation of California (Barbour et al. 2007). These include: foothill, lower montane and mid-montane, upper montane, subalpine and alpine zones. On the lee slope of the Sierra Nevada, the elevations tend to be higher because it is drier and colder.

FoothillEcological ZoneandTransitiontoMixed Conifer

Mosaic of Chaparral, Gray pine and grassland
Ponderosa pine/black oak

WestsideMontaneEcological zone

Giant Sequoia
Ponderosa pine-mixed conifer
Douglas-fir mixed conifer

Upper MontaneEcological Zone

Red fir
Jeffrey pine
Subalpine/AlpineEcological Zone


Eastside Ecological Zones

Yellow Pine
*In table above, list Eastside Ecological Zones in a similar way to westside, vs. lumping all as one
The framework for characterizing this ecological and geographic variation includes nested categories (Table x. )
Bio-Regional Assessment Subarea
Ecological Section (Bailey)
Dominant Vegetation Types/Zones
Azonal Types (with geo-graphic variation)
Administrative Unit
Modoc Plateau (M261G)
sage, pinyon-juniper, yellow pine, upper montane
Riparian, including meadows, and aspen (riparian and other)
Sierra Nevada Foothills (M261F)
Southern Cascades (M261D)
sage, foothill woodland, hardwood, yellow pine, mixed conifer, upper montane, plantation
Lassen NF
Sierra Nevada (M261E)
foothill woodland, hardwood, yellow pine, mixed conifer, upper montane, subalpine, plantation
Yellow pine, mixed conifer, upper montane, subalpine/alpine
Lake Tahoe Management Unit
foothill woodland, hardwood, yellow pine, mixed conifer, upper montane, subalpine/alpine, plantation
Great Basin ?
Sage, pinyon-juniper, yellow pine, upper montane, subalpine/alpine, plantation
In addition, a new ecological category will be addressed, the "conifer plantation" type which cannot be ignored from a scientific and ecological basis. The conifer plantation has not been described in any of the existing ecological frameworks and must be included as agriculture, or removed from the database for "mixed conifer." This is an important metric to understand, particularly as it relates to cumulative impacts on private lands, fire behavior, biological diversity and rare species habitat, and other effects/impacts.

Ecological-Cultural Relationships and Patterns

Native Americans have lived throughout the bio-region for thousands of years (see Chapter x). The people of various tribes have and now are tied to different ecosystems across the bio-region that basic life needs of food, shelter, and culture. It is not surprising that patterns of tribal distribution are concordant with different ecosystems in the bio-region. The map of tribal territories in the SNEP assessment shows that many of the larger areas representing tribal territories correspond with ecological subregions identified in the previous section. Tribes such as the Miwok and Maidu, that were and are distributed in the northern and central Sierra Nevada along the western slopes, coincide with dominantly mixed hardwood and conifer systems, where acorns are prevalent. The Mono and Washoe tribe lands coincide with the eastside ecosystems and subregions described here.
Map of Tribal territories of the Sierra Nevada ca. A.D. 1800

There was and to a lesser degree currently is an interaction between Native American land uses and management and ecosystem condition and function. Native Americans often used fire or other means to tend basketry or food materials (Figure x), to improve habitat conditions for game species such as deer, and maintain meadow ecosystems. The Native American influence in the Sierra Nevada has been well documented by all relevant research and is not limited to riparian areas (Anderson and Moratto 1996).

See: Anderson, M.K.; Moratto, M.J. 1996. Native American land use practices and ecological impacts. In: Sierra Nevada ecosystem project: final report to congress, vol. II, assessments and scientific basis for management options, Ch. 9. Davis, CA: University of California, Centers for Water and Wildlands Resources: 1-20.

In riparian areas, a high proportion of plants that are important for basket weaving occur. These plants, such as willow, dogwood, or big-leaf maple, sprout following top removal. The stems grow straighter, with fewer insect nests, when they have been burned or cut. Although fire naturally occurred in riparian areas at different intervals throughout the bio-region, it is well documented that Native Americans supplemented lightning ignitions with targeted burning. Other species that require regular burning to maintain their viability and quality as weaving materials include beargrass (Xerophyllum tenax), deer grass (Muhlenbergia rigens), redbud, Ceanothus species, giant chain fern (Woodwardia spp.), and white root (Carex barbarae). There are other examples as well. Management for biodiversity, particularly through the use of beneficial fire, will help to maintain viable populations of the diverse plants and animals that are necessary for NA traditionalists to continue their cultural practices.

Figure x. Photos compiled by Dr. Frank Kanawha Lake, researcher at the US Forest Service Pacific Southwest Research Station and member of the Karuk tribe of northwestern California. Lower photos are from his doctoral research on traditional ecological management of riparian willows using burning for basketry materials. Upper photos are of Native American basket weaver and baskets. [Comment: need to add photos from Sierran tribes].



Other Information Sources

Sequoia-Kings Canyon National Parks Natural Resource Condition Assessment

The Sequoia-Kings Canyon National Parks have completed an assessment on natural resource conditions within the two parks. The final report is currently being published. The NPS has provides the DRAFT report, but due to it's large size, it has been split into five parts.
Part 1 (Cover - 53; 12MB)

Part 2 (pages 54-143; 12MB)

Part 3 (pages 144-193; 7MB)

Part 4 (pages 194-269; 8MB)

Part 5 (pages 270-309; 3MB)

Conceptual Models for Key Ecological Integrity Indicators/Measures

A conceptual model of how key components and processes of terrestrial ecosystems interact was utilized to frame which indicators were important to assess. This is an approach recommended by Noon (2003) to develop ecosystem monitoring indicators. In adaptive management, there is a continual iteration of assessment, monitoring, and planning. It makes sense to apply the same conceptual model to the assessment as the monitoring phase. The intent was to develop a framework that is concise, and not overly complex, which highlights the most important conditions and processes that influence ecosystem function and services. Numerous conceptual models could be derived, and this one is meant to be simple, doable and based upon the history of management issues and concerns in the bio-region.

Conceptual models were developed for each of the major ecosystem types: aquatic, terrestrial, and riparian.

Due to the scope and extent of the ecological integrity of aquatic, terrestrial and riparian ecosystems, these subtopics were placed in separate sub-chapters on the WIKI.

[snapshot: 4/9/2013 @0931]