There are many examples of birds with vestigial wings: ostriches and penguins use them for a different purpose, while kiwis' wings (see below) are stubby and basically useless. Other species have vestigial eyes that are malformed and covered by skin or scales, including the eastern Mediterranean blind mole rat and certain varieties of fish, salamanders and snakes. Why might this loss of function occur? Because both wings and eyes are costly to create and maintain. Notably, kiwis live in New Zealand, where a lack of large predators makes their inability to fly less of a disadvantage. And loss of eye function occurs only in species that live underground or in caves, and thus have little use for vision.
Cetaceans are some of the best cases of these phenomena. Whales have several vestiges, such as the pelvises embedded deep within their bodies. Embryology reveals yet more examples: hindlimb buds are initially visible but vanish after about seven weeks, a thin coat of hair is grown (and quickly lost), toothless baleen whales "develop embryonic teeth that disappear before birth." And remarkably, in rare cases whales are born with atavistic legs—sometimes even fully formed ones. These features point to their common ancestry with furry, four-legged, toothed land mammals.
Other examples of atavisms: Chicken embryos develop teeth if provided with a certain protein, revealing their reptilian ancestry. And splint bones in horses sometimes form into extra toes, showing how they "descend from smaller, five-toed ancestors."
Next up are genetic vestiges. 50 percent of the 800 olfactory receptor (OR) genes present in humans and other primates are inactivated, probably because we're so visually oriented that we don't need them. Dolphins—which "don't need to detect volatile odors in the air...and have a completely different set of genes for detecting waterborne chemicals"—still have OR genes, although 80 percent are inactivated. Genes for synthesizing vitamin C are also inactive in primates, fruit bats and guinea pigs. And genetic vestiges are sometimes directly connected to physical ones: for example, most mammals have a vestigial yolk sac, but mutations have inactivated the genes for producing the nutritious protein that once filled it.
The most amazing thing about these genetic vestiges is that "the sequences of the dead gene exactly mirror the pattern of resemblance predicted from the known ancestry of these species." That is, if a gene-inactivating mutation occurs, it generally occurs at the same place in all species, and the more closely related two species are, the more similar the genetic sequence will be. This phenomenon perfectly matches the hierarchical structure of the tree of life.
There's so much more I could cover from this chapter—at some point in the future I'll take an in-depth look at endogenous retroviruses and poor design—but I want to move on to some of the other completely different lines of evidence. Up next: biogeography.