We ran into the capitalization problem on our project, in
which we had bird, plant, herp, and mammal names, plus
the formal names of vegetation zones (e.g., the Ponderosa Pine
zone). The bird names were capitalized by convention, and
the zones were capitalized, but then it looked weird to
see:

"The Ponderosa Pine zone is characterized by dominance of
ponderosa pine in most stands. In cooler parts of the zone,
Douglas-fir (or is it douglas-fir?) and lodgepole pine may
be common. Typical bird species are White-headed Woodpeckers...
Typical mammals are the yellow pine chipmunk...."

We finally decided to cap ALL species names. It looks okay
for, e.g., Red-tailed Chipmunk, but it takes a little mental adjustment
to write the following without flinching:

"Most investigated Wolf sightings in the Okanogan Highlands were most
likely to have been misidentified Coyotes or Dogs."

I prefer the capitalization, for all the reasons others have
mentioned, plus you don't waste time puzzling species names that
have a work that could be capitalized in some contexts and
not in others. (Rocky Mountain juniper or rocky mountain juniper?).

Kelly Cassidy