As a whole-system example, consider seagrass habitat. When seagrass habitat is lost, it is not 
replaced with a lifeless void, but more typically with macroalgal or unvegetated habitats. 
Seagrass loss may cause populations of some valuable species to decrease, but populations of 
other valuable species in the estuary may simply move over, or may even increase. The total 
impacts of loss of a single habitat to aquatic populations within a lake or estuary must be 
assessed first, with consideration of those habitats that will replace the lost habitat; and second, 
with consideration of the entire suite of economically valuable fish, shellfish, and wildlife that 
will be affected. If only a small number of the important species are considered, 
"comprehensive" habitat alteration models will be driven by the initial selection of species, and 
may not reflect the true effects of habitat alteration. EPA ultimately wants to evaluate the 
societal impacts of habitat alteration. Though ambitious, it is therefore a priority (where 
possible) to develop truly comprehensive multi-species models that can examine habitat 
alteration and accurately predict a large majority of the impacts to economically valuable and 
charismatic species. 
These synthesis-oriented comprehensive models might also consider emergent properties that 
develop from combinations and arrangements of habitats within a shoreline, lake, or estuary. For 
example, a diversity of habitats arranged as a patchwork may or may not support more fish, 
shellfish, and wildlife than would uninterrupted expanses of the same habitats, or certain 
combinations of habitats, such as marsh and adjacent SAV, may be of particular value to fish, 
shellfish, and wildlife. These models might further consider how certain sentinel species are 
linked to the health of the ecosystems upon which they depend. Development of comprehensive 
multi-species models will require a synthesis phase (and iteration) to assemble the individual 
habitat alteration-population response relationships. The result will be validated comprehensive 
models, based on quantitative data, that can predict the total consequences of areal habitat loss to 
the great majority of economically valuable and charismatic populations. These comprehensive 
models also should be designed to place a quantitative fish/shellfish/wildlife resource value on 
shorelines, lakes, and estuaries, based on spatial habitat mapping. This resource value should 
reflect aquatic populations, and need not be tied to monetary standards. Multi-species models 
should predict quantitative changes in aquatic resource value that would result from habitat 
alteration to any mapped shoreline, lake, or estuary. This will allow better assessment and 
management of aquatic habitats and resources. 
Both the individual models and the comprehensive multi-species models should be designed 
around application to a risk-assessment framework. This will allow insertion of the habitat 
models into larger spatially explicit risk assessment models that can consider multiple stressors 
including habitat alteration, toxic chemicals, and others. 
4. Develop classification schemes within each identified habitat or system type where other 
important factors (salinity, geomorphology, and tidal energy) will affect the ability of habitats or 
systems to support priority populations. 
A classification scheme is necessary to allow appropriate application of the single-species and 
multi-species habitat alteration-population response models described above. For example, 
juvenile summer flounder settle in shallow sandy or muddy mesohaline and polyhaline estuarine 
habitats in the Mid-Atlantic, but do not utilize oligohaline areas (Rogers and Van Den Avyle 
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