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While they are the most diverse marine mammal group today, numbering over eighty species, the fossil record documents over six hundred whale species that no longer exist.

      The first phase of whale evolution is fundamentally about transformation: the tinkering and repurposing of structures from an ancestral state (originally for use on land) to a new one, in aquatic life. Transformation requires an initial state, and some starting points in evolution can be difficult to discern. For example, hearing, sight, smell, and taste are all senses that evolved for nearly 300 million years on land before the first ancestors of whales took to the sea. While it’s convenient to think of the reshaping of hands into flippers in whales as an undoing, that’s a mistake: whales didn’t undo 300 million years of terrestrial modifications. They did not, for example, recover gills. Instead, the story is far more interesting. Whales worked with what their ancestors had as land animals, modifying many anatomical and physiological structures for a new use rather than some phantasmagoric evolutionary reversal.

      The second phase, after whales got back in the water, encompasses any whale lineage obliged to spend its life exclusively in the water; this phase also spans all of the consequences that arise from that constraint. You can think of evolutionary innovation as a hack on constraint. In other words, novelty in evolution is the appearance of a totally new structure, such as baleen, that confers not just a slight advantage to those who possess and inherit it but shifts their descendants into a completely new dimension of adaptation. The second phase of whale evolution, when innovations such as filter feeding and echolocation appear and fuel the diversification of today’s whales, stretches in time from the first aquatic whales, about forty million years ago, to the present day, including all living cetaceans, along with hundreds of extinct forms in between.

      In the past 250 million years, many backboned animals converted from living in terrestrial ecosystems to living in oceanic ones. The first wave happened throughout the time of the dinosaurs, when many different reptile lineages invaded ocean ecosystems from 250 million to 66 million years ago. Since the mass extinction at the end of the Cretaceous, the ecologically dominant ocean invaders have been mammals—including everything from whales to sea otters—although penguins and Galápagos marine iguanas are also more recent reentrants. All of today’s marine mammal lineages are distantly related to one another, whether it’s a whale, a sea otter, a seal, a sea cow, or a polar bear (yes, technically polar bears too, which eat seals and hop across ice-covered seas).

      What makes early whale evolution so important is that the completeness of the fossil record from the early stages—Pakicetus, Ambulocetus, Maiacetus, and all others like them during that first phase—is unmatched by any other group in the fossil record. We simply don’t have the range of fossils showing the specific anatomical transformations from land to sea for any other mammal or reptile the way we do with whale origins.

      Even so, the evidence for whale origins has only recently been uncovered. Until about forty years ago, we had no idea what the hind limbs of the earliest whales in the first evolutionary phase really looked like. The discovery of Pakicetus in 1981 gave us mostly bones from the neck up—paleontologists discovered a small W-shaped braincase exhibiting, among other features, an involucrum, but it otherwise looked like any other land mammal’s. They found the skull—pinched and delicate, like a handheld vase—in river deposits, and concluded that the earliest whales lived some part of their life on land. Without more of a skeleton, at the time they could only speculate about what these whales looked like from the neck down.

      In 1994 the discovery of Ambulocetus clarified this picture, showing that the earliest whales had weight-bearing fore and hind limbs, with separate phalanges perhaps connected in life by webbing. Relatively large feet in Ambulocetus were a clue about its swimming style, which likely involved flexing its spinal column along with its broad feet, in one motion. Mechanically this style is somewhere between paddling with hands and feet (using drag for forward motion) and employing a hydrofoil, as modern whales do with their tail fluke (using lift, instead of drag). Our pelvis is rigidly connected to our backbone, whereas in Maiacetus, the pelvis was only partially connected to the backbone, permitting a lot of flexibility for the whole spinal column to undulate up and down. The shape of a few tail vertebrae can reveal a lot about locomotion—in Ambulocetus the fact that the tail vertebrae are longer than they are tall tells us that these early whales had long, thickened tails, although we still don’t have enough bones to know what direction these powerful tails might have moved.

      Ambulocetus still didn’t provide enough evidence to help answer the big questions about whale origins: Where did they fit into the mammalian family tree? Who are their closest relatives? By the 1990s, DNA studies had shown that hippos are the closest living relatives to whales. Hippos and other even-toed hoofed mammals, such as cows, deer, and pigs, are seemingly unlikely relatives, until you look at their stomachs. Even anatomists in the nineteenth century knew that living whales had multichambered stomachs like these ungulates, pointing to a possible evolutionary relationship. Paleontologists, however, had other extinct fossil mammals in the running for whale’s closest relatives: mesonychids, which had strikingly similar teeth and were wholly carnivorous, as whales are today, but left no descendants. Without more skeletal material from four-legged whales, especially from their limbs, there was no way to parse the stories of DNA versus fossils for the deepest origins of whales.

      Then, in 2001, two competing groups of paleontologists reported the same pivotal piece of evidence from different species of early whales: they each had discovered that the anklebone of ancient land-dwelling whales was exactly like those of living even-toed ungulates. This bone, called the astragalus, looks like two 35 millimeter film canisters taped together like a raft; in your hand it feels like some kind of board-game piece. Cows, goats, and camels all have it. Living whales don’t because they have no feet, and the only traces of hind limbs are reduced to nubbins of bone next to free-floating pieces of their pelvis, wrapped deeply in their body walls—making fossil hind limbs in early whales the only source for this information. Mesonychids didn’t have these double-pulley anklebones, which meant their tooth similarities with early whales were the result of convergent evolution—something that has happened frequently in mammal evolutionary history. The discovery that early whales had a so-called double-pulley astragalus confirmed the DNA findings: whales were just highly modified even-toed hoofed mammals, minus the hooves.

      Since finding Pakicetus, paleontologists working in remote parts of Egypt, Pakistan, and India have discovered a rich variety of early land-dwelling whales that lived about fifty million to forty million years ago, toward the end of a geologic epoch called the Eocene. These early whales seem to have been experimenting with ecological modes that have parts both familiar and strange: Ambulocetus looked crocodile-like; Maiacetus more like a sea lion, which had not yet evolved; still other strange early whales such as Remingtonocetus were an amalgam of zoological categories, something like a long-snouted otter; and Makaracetus, named after a mythological South Asian creature that is half fish, half mammal, had a downturned snout, perhaps for eating clams. All of these early whales belonged to extinct branches at the base of the whale family tree; our expectation about what makes a whale is hindsight biased, based on how we see them today—a great challenge paleontologists face when trying to understand the biology of these extinct whale relatives.

      Knowing how whales turned out makes our retelling of their evolutionary pathway a tidy, preordained story. It’s easy to imagine Pakicetus, looking something like a lost dog dipping its toes in the water, followed then by intermediate stages of creatures each spending more time in the water: Ambulocetus, which could hear underwater and lunge at prey with its

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