Why should "closely allied" species inhabit neighboring patches of habitat? And why should similar habitat on different continents be occupied by species that aren't so closely allied? "We see in these facts some deep organic bond, prevailing throughout space and time," Darwin wrote. "This bond, on my theory, is simply inheritance." Similar species occur nearby in space because they have descended from common ancestors.
Paleontology reveals a similar clustering pattern in the dimension of time. The vertical column of geologic strata, laid down by sedimentary processes over the eons, lightly peppered with fossils, represents a tangible record showing which species lived when. Less ancient layers of rock lie atop more ancient ones (except where geologic forces have tipped or shuffled them), and likewise with the animal and plant fossils that the strata contain. What Darwin noticed about this record is that closely allied species tend to be found adjacent to one another in successive strata. One species endures for millions of years and then makes its last appearance in, say, the middle Eocene epoch; just above, a similar but not identical species replaces it. In North America, for example, a vaguely horselike creature known as Hyracotherium was succeeded by Orohippus, then Epihippus, then Mesohippus, which in turn were succeeded by a variety of horsey American critters. Some of them even galloped across the Bering land bridge into Asia, then onward to Europe and Africa. By five million years ago they had nearly all disappeared, leaving behind Dinohippus, which was succeeded by Equus, the modern genus of horse. Not all these fossil links had been unearthed in Darwin's day, but he captured the essence of the matter anyway. Again, were such sequences just coincidental? No, Darwin argued. Closely allied species succeed one another in time, as well as living nearby in space, because they're related through evolutionary descent.
Embryology too involved patterns that couldn't be explained by coincidence. Why does the embryo of a mammal pass through stages resembling stages of the embryo of a reptile? Why is one of the larval forms of a barnacle, before metamorphosis, so similar to the larval form of a shrimp? Why do the larvae of moths, flies, and beetles resemble one another more than any of them resemble their respective adults? Because, Darwin wrote, "the embryo is the animal in its less modified state" and that state "reveals the structure of its progenitor."
Morphology, his fourth category of evidence, was the "very soul" of natural history, according to Darwin. Even today it's on display in the layout and organization of any zoo. Here are the monkeys, there are the big cats, and in that building are the alligators and crocodiles. Birds in the aviary, fish in the aquarium. Living creatures can be easily sorted into a hierarchy of categories—not just species but genera, families, orders, whole kingdoms—based on which anatomical characters they share and which they don't.