Biodiversity Indicators of the Sierra Nevada

Tree Microhabitats

Pileated Woodpecker Holes

(Above: Freshly excavated pileated woodpecker holes, Eldorado National Forest)

Structure is an important aspect of biological diversity and is derived from both living and non-living forms. Examples of these types of structures include snags (dead trees that become wildlife habitat), large downed logs, rock outcrops, pockets of poor soils that support unique plant assemblages, mistletoe "brooms" atop oaks and conifers, and many other attributes of natural forest ecosystems. The multi-layers of a natural forest with its many different age classes is also a type of structure that disappears when forests are managed intensively for lumber outputs. Abiotic features are those that are non-biological and include soils, minerals, topography, fire and other disturbance regimes, and climate. All of these factors interact with the living organisms of the forest and the processes of evolution to create stable, resilient ecosystems that support high levels of biodiversity.  

In forest management, some biological structures that are essential to provide breeding, feeding, and shelter for multiple organisms have not been addressed well -- or at all -- in environmental planning. Recently, researchers examined tree microhabitat structures as indicators of biodiversity in Douglas-fir forests of the Pacific Northwest. When they compared the frequency and abundance of tree microhabitat structures in natural stands and in stands of varying active management histories, they found  that stands that had been subjected to overstory reduction had 85 percent less microhabitat structures as did natural stands.

Tree microhabitats include such features as broken tops, cracks or scars, hollow chambers, stem cavities, bark bowls and pockets, and burls. Many of these structures are the result of various stages of decay within or on the tree. They are not only correlated with abundance of forest species (biodiversity), but they also happen to be indicators of naturally mature or old-growth stands. American marten and Pacific fisher also utilize these important structures
At least 85 different species of North American birds require tree cavities for nesting structures. Woodpeckers, owls, titmice, chickadees, flycatchers, nuthatches, and bluebirds are among the many cavity nesting birds. Bark pockets are used for roosting by several species of bats in the Sierra Nevada.  Brown creepers also use them for nesting sites. Pockets, cavities and bowls contain decayed residue that provide food and habitat for invertebrates and small mammals, as well as substrate for fungi that are eaten by a variety of mammals. Mistletoe brooms create misshapen dense clusters of branches that provide excellent concealment for denning sites, nests, and to protect young.

The authors concluded that where the goal is to increase biodiversity and stand complexity, along with "longterm social, economic, and ecological benefits," it is crucial to adopt silvicultural practices that preserve tree microhabitats while also preserving all the remaining natural stands in the Pacific Northwest. These recommendations can and should be applied to the Sierra Nevada, where the development of legacy structures is even more critical due to the longer time it takes to grow trees in the relatively drier climate in this region.  

Download this paper, and read more about how individual legacy trees influence vertebrate diversity, under Resources at the bottom of this page.

Dead Wood

Laudenslayer Jr., William F.; Shea, Patrick J.; Valentine, Bradley E.; Weatherspoon, C. Phillip; Lisle, Thomas E.  2002.  Proceedings of the Symposium on the Ecology and Management of Dead Wood in Western Forests  Reno, NV. Gen. Tech. Rep. PSW-GTR-181. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station; 949 p.

How Dead Trees Sustain Live Organisms in Western Forests from the Proceedings of the Symposium on the Ecology and Management of Dead Wood in Western Forests is an exhaustive literature review of the science of dead wood in forest ecology. Standing snags are one type of dead wood that contribute to biological diversity in the forests of the Sierra Nevada, but down wood -- logs on the ground in various stages of decomposition -- also provide habitat, substrate, shelter and cover and are essential to all of the processes that cycle throughout the forest ecosystem. According to the data collected, more biodiversity is associated with dead wood than any other habitat element. At the same time, under industrial forest management regimes, or business as usual in California's private timber lands, after multiple rotations less than 1 percent of deadwood remains.

Trees die from many natural causes throughout the forest, but in the Sierra Nevada, regular fire has historically been the major source of disturbance resulting in killed and injured trees. Because of the importance of dead wood to biological diversity, fire is necessary in the Sierra Nevada to maintain high levels of diverse dead and dying tree structures. This poses a management challenge, especially in areas where human populations have encroached upon the forest borders, and where it has become a necessity to extinguish fires in order to protect life and property. Smoke and health concerns are another issue that prevents the use of wildland fire to accomplish ecological and restoration objectives. Sierra Forest Legacy's community forestry work today is focused on finding restoration solutions to these kinds of issues in order to sustain wildlife and critical habitats and achieving resilient, fire-adapted landscapes.

Some of the highlights of the report include:

  • Hundreds of species depend on dying and dead logs and trees
  • 57 percent of listed vertebrate species are reliant upon or strongly associated with dead wood. Many more cryptogams, fungi, and invertebrates are dependent upon dead wood
  • Dead wood comprised 30-40 percent of the total wood volume in unmanaged stands and declined to about 20 percent after one rotation and to about 1 percent after several rotations of
    intensive fiber extraction (industrial forestry)
  • 15 bird species occurred more frequently in burns than any other cover type, including four cavity nesters: hairy, three-toed, and black-backed woodpeckers, and the mountain bluebird.
  • The black-backed woodpecker specializes on the larvae of beetles which bore into the sapwood of fire- or beetle-killed trees
  • Beetle-infested stands provide the ideal (and possibly only productive) habitat for some woodpecker species
  • Salvage logging and fire suppression are especially detrimental to the black-backed woodpecker
  • Three species of bats -- the California myotis, fringed myotis, and pallid bat -- only use dead trees for roosting
  • Terrestrial-breeding salamanders are especially dependent upon down dead wood

Dead wood on the ground influences vertebrate abundance and richness by providing:

  • Necessary substrate, energy, and nutrients for many invertebrates and fungi upon which a wide range of amphibian, reptile, bird, and small mammal
  • Sheltered areas for reproduction in a range of vertebrates from salamanders to black bears, and cover from aerial predators
  • A modified microclimate (cooler, moister, more stable temperature than surrounding habitat) that is essential to species that cannot tolerate extremes in temperature or humidity (several amphibians).
  • Runways for small mammals and display or lookout posts for birds
  • Increased habitat diversity and aeration in water by forming riffles, small waterfalls, and pools, thereby creating habitat for amphibians and fish which are in turn fed on by other vertebrates.
    • Structures exploited by near-aquatic vertebrates as cover, foraging sites, or
    basking (e.g., river otter [Lontra Canadensis], mink, painted turtles [Chrysemys picta]
    • Access routes for predators, especially under snow cover (e.g., weasels, marten)

Examples of tree microhabitats

Old-growth cedar with stem chamberOak snag with cavities











Above: (L) Old-growth cedar with hollow chamber and bark pockets (Lassen National Forest); (R) oak snag with woodpecker excavated cavities ( Kanaka Valley, El Dorado County)

Osprey nest in top of snagOld black oak with hollow chamber











Above: (L) Osprey nest atop broken snag (Digger Creek, Shasta County); (R) old black oak with hollow chamber (Battle Creek watershed, Tehama County)

Lightning scar in old growth ponderosa pineDecaying tree

Above: (L) Lightning strike in this old-growth ponderosa pine provides habitat for nesting, denning, and concealment (Eldorado National Forest); (R) This decaying log is providing habitat for wildlife while building forest soil (Plumas National Forest)

Snag with pileated woodpecker holes












Above: These snags -- standing dead trees -- exhibit extensive woodpecker excavations that provide habitat for a variety of forest animals. Note the mistletoe "broom" atop the tree on the right. Mistletoe provides good support for raptor nest building. The berries are also an important food source for a variety of animals. Photos by Eric Knapp.

Below: More examples of cavities excavated by woodpeckers. The spike-like plant in the foreground, right, is a saprophytic species, Pinedrops, or Pterospora andromedea. It has no green leaves, and survives by sharing energy derived from underground mushroom hosts, which themselves live symbiotically with the roots of associated living trees. Saprophytic plants and mushrooms both play an important role in recycling nutrients and enriching the soil.

biodiversity microhabitatsPinedrops with  old growth













Fire scarred giant sequoia

Ancient Giant Sequoias like the one on the right frequently have spacious cavities and chambers hollowed out by fires over centuries of time. These provide high quality denning, resting, and shelter sites for a variety of mammals, including the rare Pacific fisher.




Help us document tree microhabitats and their role in biodiversity. You can help us in our efforts to preserve these important components of wildlife habitat by sending us your high quality photos of tree cavities, snags, chambered tree stems, bark pockets, down logs, broken tops, etc. Send photos to: admin[AT]


Bunnell, F.L., I. Houde, B. Johnston, E. Winde. 2002. How dead trees sustain live organisms in western forests. USDA Forest Service Gen. Tech. Report PSW-GTR-181. (319 KB PDF)

Mazurek, M.J. and W. J. Zielinkski. 2004. Individual legacy trees influence vertebrate wildlife diversity
in commercial forests. Forest Ecology and Management 193: 321–334
(179 KB PDF)

Michel, A.K. and S. Winter. 2009. Tree microhabitat structures as indicators of biodiversity in Douglas-fir forests of different stand ages and management histories in the Pacific Northwest, U.S.A. Forest Ecology and Management 257:1453-1464 (820KB PDF)


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