I prefer to capitalize the common names of all species, regardless of
class, although I'll admit that Domestic Dog and Coyote look strange with
caps while Gray Wolf looks okay. What I don't like is seeing bird species
in caps and mammals not in caps in the same sentence.

For the original poster who is having the disagreement with the editor,
you might want to point out the other major inconsistency in
capitalization that most newspapers follow, which is capitalization of
Realtor while other professions (many that require MUCH more education!)
are always in small letters (doctor, lawyer, etc.).

Kelly Cassidy
Pullman, WA