Update: here are two new videos (2015) that help explain the ideas below and on this website. Thanks to the Yamhill Watershed Stewardship Council!
Short answer: The landscapes that existed before extensive alteration by Europeans are generally considered to be intact, well-functioning ecosystems. Whether they were managed by Indians (and many were extensively managed for millenia) or whether they were relatively untouched by humans, the advance of Europeans so drastically altered the landscape, that it began to lose species at an alarming rate. Therefore the reference used is often what was here when Europeans arrived. This is not to say things were perfect prior to European settlement. There is a whole body of literature on use and occupation of the Americas before contact that is still being researched.
At the time of European settlement, oak savannas and woodlands interspersed with wet and dry prairies dominated the valley floor, and conifers grew in thick stands only at higher elevations around the perimeters. (See historic WV veg)
The Willamette Valley prairies, oak savannas and woodlands that existed at the time of European settlement in the mid 1800’s were diverse, species-rich and productive. They are now largely converted to agriculture or development. The portions remaining are in need of protection and management to prevent the invasion by either non-native species that degrade the whole system, or by thick stands of Douglas firs and shrubs. These native species will encroach on natural prairie, savannas and woodlands in the absence of fire. Fire as a management tool is what kept these areas so productive, and the lack of management is causing the loss of many species that depend on this habitat.
Now, whether the (formerly) warm, dry climate encouraged more frequent fires and therefore maintained a more open fire-resistant landscape of grassland, large oaks and scattered large Douglas firs, or whether Indians exerted a greater influence on the landscape is a subject of current research. Likely there were parts of the Willamette Valley that were more intensively managed than others (see recent research by Megan Walsh and others).
Both influences contributed to the look of the landscape. However, the decimation of the Indian population by disease before the first pioneers arrived, also was a major factor. There are still many unanswered questions about details, but the existence of these open landscapes has been well documented.
A lively topic of debate in recent years has been the idea of “restoring” an ecosystem. As people acquired more experience with the actual practice of ecological tinkering, things turned out to be more complicated than just putting all the species back where they were (this is actually impossible).
Although ecologists use historical reconstructions to find clues to a “reference”ecosystem, one cannot return to a single point in the past, because like all life, ecosystems are on a continuum of development and change. Mostly people try to get the system back on a healthy trajectory.
The web of interactions of all life in a habitat is vastly complex; there is no managing it for a particular state, all we can hope for is to replace as many parts as possible, get rid of most of the invasive species, so the engine can crank up and run, providing the ecosystem services we need to survive.
There are several problems with this approach, even though it is a pretty good one. Many people have assumed that nature was somehow pristine and untouched before Europeans started messing things up on a grand scale. This is a misconception that a lot of recent research has debunked. Two good books that elucidate these issues are 1491: New Revelations of the Americas Before Columbus by Charles C. Mann, and Tending the Wild by M. Kat Anderson. [See my post on Dr. Anderson’s book]
Essentially, both North and South America were, at various times, heavily populated, managed landscapes for millenia before Europeans stumbled onto the scene. Many of the scenes so lovingly described by John Muir as untouched nature, were so productive and lovely precisely because they were managed by Indians.
So, restoration is a complicated business, and the landscape we strive for is not one that existed necessarily. But it may be an approximation of one that functioned well in the past, and we hope it works better after we make alterations. It is still difficult to determine what these alterations should be. The effects of climate change will complicate the picture even more. In the past, species could move across the landscape (change their range) in response to a change in climate, and this is amply documented in paleoecological studies of vegetation changes over time (see especially Cathy Whitlock’s work on vegetation history in the west). The problem in the present is that change may happen too quickly for plants and animals to adapt; even if they could change quickly enough, they cannot move freely through a populated landscape without corridors of natural areas. Even hedgerows in agricultural land are helpful for the dispersal of species. Some people are suggesting using “assisted migration” – intentionally moving species so they can colonize different territory.