**T1Q3 Is the conceptual model used to transform these measurements into
an indicator widely accepted as a scientifically sound representation of
the phenomenon it indicates?**

Two analytical approaches were used for these data. Both approaches are
frequently used by federal agencies, states and research organizations
to assess benthic macroinvertebrate communities. One relates to the
overall benthic condition and the other gives information on the
presence of expected taxa. For this analysis, the 48 conterminous states
are divided into nine broad ecoregions, which are based on groupings of
EPA Level III ecoregions (see
<http://www.epa.gov/wed/pages/ecoregions/level_iii.htm>).

The first approach, an Index of Biological Integrity (IBI), was
developed on an ecoregional scale. The IBI reduces complex information
about community structure into a simple numerical value based on metrics
that reflect several different aspects of community structure and
function. The measures integrated in this index include taxonomic
richness (number of taxa); taxonomic composition (e.g., insects vs.
non-insects); taxonomic diversity; feeding groups (e.g., shredders,
scrapers or predators); habits (e.g., burrowing, clinging or climbing
taxa); and tolerance. Separate metrics are used for each of these
categories in different regions of the U.S., based on their ability to
best discriminate among streams. Each metric is scaled against the
5th-95th percentiles for the streams in each region to create an overall
IBI, whose value ranges from 0 to 100. For this indicator, a reference
distribution was developed by comparing the IBI scores for the
least-disturbed sites in each region to the stressors present at these
sites, using Principal Components Analysis (PCA). All sampled sites were
then classified based on thresholds set at the 5th and 25th percentiles
of the reference distribution. The method used to develop the IBI was
also used in the EMAP West Report (Stoddard et al., 2005).

The second approach was a predictive Observed/Expected (O/E) model,
which compares the actual number of taxa observed at each WSA site (O)
with the number expected (E) to be found at a site that is in minimally
disturbed condition (Armitage, 1987). First, reference sites were
divided into several groups based on the observed benthic assemblages.
Within each group of reference sites, the probability of observing each
taxon was determined. Next, a multivariate model was developed to
characterize each group of reference sites in terms of shared physical
characteristics (variables that are largely invariant to human
influence, such as soil type, elevation, and latitude). This predictive
model was then applied to each of the test sites to determine which
group(s) of reference sites they should be compared with, based on
shared physical characteristics. For each test site, the "expected"
probability of observing each taxon was calculated as a weighted average
based on (a) the probability of observing that taxon in a particular
group of reference sites and (b) the probability that the test site is
part of that particular group of sites, based on the predictive model.
For example, if the physical characteristics of a site suggest that it
has a 50 percent chance of belonging to group A and a 50 percent chance
of belonging to group B, the "expected" probability of finding taxon X
at the site will be (0.5)(probability of finding X in group A reference
sites) + (0.5)(probability of finding taxon X in group B reference
sites). Once the probability of observing each taxon was determined,
these probabilities were added to generate a total "E" for the site. For
example, if there were 4 taxa, each with an "expected" probability of
0.6, the total "E" would be (0.6 + 0.6 + 0.6 + 0.6) = 2.4. The actual
number of taxa collected at the site (O) was then divided by "E" to
arrive at an O/E ratio (Hawkins et al., 2000; Hawkins and Carlisle,
2001). An O/E of 1.0 means the site's taxa richness is equal to the
average for the reference sites. Each tenth of a point below 1 suggests
a 10 percent loss of taxa. This O/E approach is well established and is
documented in several sources, including Hawkins et al., 2000, and
Hawkins and Carlisle, 2001.

For this indicator, the O/E ratio is based only on taxa with at least 50
percent probability of being observed in the reference sites---i.e., the
most common taxa.

Further information on both methods can be found in:

Barbour, M.T., J.B. Stribling, and J.R. Karr. 1995. Multimetric approach
for establishing biocriteria and measuring biological condition. In:
Biological assessment and criteria: tools for water resource planning
and decision making. Lewis Publishers, pp. 63-77.

Hawkins, C.P., and D.M. Carlisle. 2001. Use of Predictive Models for
Assessing the biological Integrity of Wetlands and Other aquatic
habitats. In: Bioassessment and Management of North American Freshwater
Wetlands. John Wiley and Sons, pp. 59-84.

Hawkins, C.P., R.H. Norris, J.N. Hogue, and J.W.
Feminella. 2000. Development and evaluation of predictive models for
measuring the biological integrity of streams. Ecological Applications
10: 1456-1477.

Karr, J.R., K.D. Fausch, P.L. Angermeier, P.R. Yant, and I.J. Schlosser.
1986. Assessing biological Integrity in running waters: A method and its
rationale. Special publication 5. Illinois Natural History Survey.

Stevenson, R.J., R.C. Bailey, M.C. Harrass, C.P. Hawkins, J.
Alba-Tercedor, C. Couch, S. Dyer, F.A. Fulk, J.M. Harrington, C.T.
Hunsaker, R.K. Johnson. 2004. Interpreting results of ecological
assessments. Pages 85-111 in M. T. Barbour, S. B. Norton, H. R. Preston,
and K. W. Thornton (eds), Ecological Assessment of Aquatic Resources:
Linking Science to Decision-Making. Pensacola, FL: Society of
Environmental Toxicology and Chemistry.

Stoddard, J.L., D.V. Peck, S.G. Paulsen, J. Van Sickle, C.P. Hawkins,
A.T. Herlihy, R.M. Hughes, P.R. Kaufmann, D.P. Larsen, G. Lomnicky, A.R.
Olsen, S.A. Peterson, P.L. Ringold, and T.R. Whittier. 2005. An
Ecological Assessment of Western Streams and Rivers. EPA 620/R-05/005.
Washington, DC: U.S. Environmental Protection Agency.

U.S. EPA. 1996. Biological Criteria: Technical Guidance for Streams and
Small Rivers. EPA 822-B-96-001. Washington, DC: U.S. Environmental
Protection Agency.

Van Sickle, J., C.P. Hawkins, D.P. Larsen, and A.T. Herlihy. 2005. A
null model for the expected macroinvertebrate assemblage in
streams. Journal of the North American Benthological Society 24(1):
178-191.

Wright, J.F., M.T. Furse, and P.D. Armitage. 1993. RIVPACS: a Technique
for evaluating the biological quality of rivers in the UK. European
Water Pollution Control 3(4): 15-25.

Yoder, C.O., and E.T. Rankin. 1995. Biological response signatures and
the area of degradation value: new tools for interpreting multimetric
data. In: Biological assessment and criteria: tools for water resource
planning and decision making. Lewis Publishers, pp. 263-286.