Few technical writing errors drive editors to distraction like superfluous capitalization does. This eruption of capitalitis (a pathogen otherwise known as Uppercasis ludicrosii) is most often seen in references to plants and animals.
Words that comprise the names of plant species are generally lowercase: “Lumber from the live oak is rarely used for furniture.” Exceptions occur when one or more of the words is named after a person or a geographical location, as in the name of the California poppy. (The flowering plant bougainvillea is named after French explorer Louis Antoine de Bougainville, but plant names so inspired are still lowercase.)
An exception is also made for references to types of fruits and vegetables, such as Red Delicious apples or Early Girl tomatoes. Then there are names of cultivars, or cultivated varieties, of plants, such as that of a kind of broccoli, Brassica oleracea ‘Calabrese’.
The convention in botany is to enclose the name of the cultivar in single quotation marks. Note also the exception to the rule about placing closing punctuation within quotation marks; this format, also employed in linguistics and philosophy, reflects the intention to clarify the precise terminology in question.
Notice the italicized name mentioned just above, and the jocular one in the first paragraph: Those are examples, respectively authentic and artificial, of binomial nomenclature, the system of Latin-inspired scientific names for life-forms. The first element, the genus name, is capitalized; the second element, the species name, is not (even if it derives from a place name, as in Artemisia californica, the name of a plant found in California). Such terms, as shown here, are generally italicized.
Binomial nomenclature is, of course, also used for animals, including the singularly curious one designated as Homo sapiens. However, as in the case of plant names, animal names are not capitalized (“I spotted a red-tailed hawk,” not “I spotted a Red-Tailed Hawk”), except when an element of the name is a proper noun, as in “Steller’s jay” and “Siberian tiger.”
Animal breeds, unlike types of produce and plant cultivars, are given no special treatment: Your cocker spaniel is special, of course, but its breed name merits no capitalization. However, many names of breeds of dogs and cats are exceptions, such as those of the German shepherd, the Siamese cat, and the Thoroughbred horse. The preponderance of such examples may be the cause of confusion about capitalization of animal names.
The rules are complicated, but it’s a simple enough matter to get a ruling: Check the dictionary.