Q. Should the names of birds be capitalized? For example, is it “little blue heron” or “Little Blue Heron” (a problem since “little” and “blue” can sound like descriptors and not part of a creature’s formal name)? Or “heron” generally and “Little Blue Heron” specifically?
A. In Chicago style, common names for birds are usually lowercased, whether you’re referring to a little blue heron or a blue-footed booby, and except for any proper noun or adjective (American crow). If you’re worried that it won’t be clear that you’re referring to a specific type of heron rather than to a heron of a particular size and color, revise your text accordingly (e.g., a bird known as the little blue heron).
It should be noted that organizations dedicated to animals tend to use initial capitals for common names (as on this page from the Cornell Lab of Ornithology), an approach that solves the problem of ambiguity. But in most types of prose, lowercase is the rule for such names. See also CMOS 8.129 and 8.130; for names like Egretta caerulea (the scientific name for the little blue heron), see 8.121.