Animal diversity II: vertebrates and human evolution

Vertebrates are a small fraction of animal species, about 70,000, but they include the largest animals that have ever lived and the animals most familiar to us, including ourselves. This lesson traces vertebrate evolution through a series of innovations: the notochord and backbone, jaws, limbs, the amniotic egg and the features of mammals. It ends with the evolution of humans, one of the best documented and most intensively studied stories in biology.

Chordates

Vertebrates belong to the phylum Chordata, deuterostomes that share four features at some stage of life: a notochord, a flexible rod that supports the body; a dorsal hollow nerve cord, which becomes the brain and spinal cord; pharyngeal slits or pouches behind the mouth; and a muscular tail extending beyond the anus. Humans show all four as embryos: the notochord survives as the soft centers of the discs between vertebrae, the pharyngeal pouches become parts of the ear, tonsils and glands, and the embryonic tail is reabsorbed to form the coccyx.

Two groups of invertebrate chordates help reveal the ancestral body plan. Lancelets are small, fish-shaped filter feeders that keep all four features throughout life. Tunicates, or sea squirts, have a tadpole-like larva with all four features, but adults settle down as sac-like filter feeders. Genomic studies suggest tunicates are the closest living relatives of vertebrates.

The vertebrate tree

Vertebrates are chordates with a backbone of vertebrae around the nerve cord, a skull protecting a well-developed brain, and, in most, an internal skeleton of bone. Their evolution can be read as a nested series of innovations, each defining a clade.

Jaws, bone and fins

The first vertebrates, about 530 million years ago, were jawless. Jaws evolved about 440 million years ago from the skeletal supports of the front pharyngeal slits, an elegant example of evolution modifying existing structures. Jaws turned vertebrates into effective predators and set off a radiation of jawed fishes. Ray-finned fishes are now the largest vertebrate group, about half of all vertebrate species. Many have a swim bladder, a gas-filled sac that adjusts buoyancy and that evolved from the lungs of early bony fishes, not the other way around.

Onto land: tetrapods

Tetrapods, the four-limbed vertebrates, evolved from lobe-finned fishes. Fossils from about 385 to 360 million years ago document the transition in remarkable detail: Eusthenopteron, a fish with limb bones in its fins; Tiktaalik, with a neck, sturdy shoulders and wrist-like joints (lesson 1); and Acanthostega and Ichthyostega, with true limbs bearing seven or eight digits, which still lived mostly in water. Limbs seem to have evolved first for moving through shallow, weedy water, and were later used on land.

Amphibians were the first tetrapods to exploit land widely, but most still need water to reproduce: they lay shell-less eggs in water, and many have aquatic larvae, such as tadpoles, that metamorphose into adults. Their thin, moist skin is used for breathing, which makes them sensitive to pollution and drying, and many species are declining because of habitat loss and the chytrid fungus (lesson 8).

The amniotic egg and reptiles

About 320 million years ago, a group of tetrapods evolved the amniotic egg: an egg with a shell and internal membranes that hold water, store food, exchange gases and handle waste. It let vertebrates reproduce on dry land, away from water. The amniotes soon split into two lineages: one led to mammals, the other to reptiles. Living reptiles include turtles, lizards and snakes, the tuatara of New Zealand, crocodilians and birds.

Birds are reptiles: specifically, they are living dinosaurs. Fossils such as Archaeopteryx, from about 150 million years ago in Germany, and many feathered dinosaurs found in China since the 1990s show that feathers evolved in theropod dinosaurs before flight, probably first for insulation and display. Birds and crocodilians are each other's closest living relatives. Alberta's badlands have produced some of the best-preserved feathered dinosaur and early bird-relative fossils, and in 2016 a small feathered dinosaur tail preserved in amber from Myanmar was described, showing the structure of the feathers in three dimensions.

Mammals

Mammals are amniotes with hair, mammary glands that produce milk, three middle ear bones (two of which evolved from jaw bones of their reptile-like ancestors, a transition well documented in fossils) and, in most, a diaphragm and teeth of different shapes. They are endothermic, generating body heat internally. Mammals originated about 200 million years ago and remained mostly small during the age of dinosaurs, radiating spectacularly after the end-Cretaceous extinction.

Body size shapes almost everything about how animals live. Larger animals have lower metabolic rates per kilogram, live longer and reproduce more slowly. In 1932, Max Kleiber showed that across mammals, whole-body metabolic rate scales roughly with body mass to the three-quarters power: \(B \propto M^{0.75}\). Per kilogram, then, metabolism falls as \(M^{-0.25}\).

# Kleiber's law: basal metabolic rate B = 3.4 * M^0.75 watts (M in kg; constant approximate)
animals = {"deer mouse": 0.02, "red squirrel": 0.2, "beaver": 20, "human": 70,
           "moose": 450, "blue whale": 100_000}
for name, m in animals.items():
    b = 3.4 * m ** 0.75
    print(f"{name:<12} {m:>9,.2f} kg: {b:>9,.1f} W total, {b/m:6.2f} W per kg")

deer mouse        0.02 kg:       0.2 W total,   9.04 W per kg
red squirrel      0.20 kg:       1.0 W total,   5.08 W per kg
beaver           20.00 kg:      32.2 W total,   1.61 W per kg
human            70.00 kg:      82.3 W total,   1.18 W per kg
moose           450.00 kg:     332.2 W total,   0.74 W per kg
blue whale   100,000.00 kg:  19,119.6 W total,   0.19 W per kg

Per kilogram, a deer mouse burns energy roughly 12 times faster than a moose, and a moose about four times faster than a blue whale. That is why small mammals must eat almost constantly, why shrews and mice can starve within hours, and why small mammals in Canada's winters hibernate or shelter beneath the snow, while large mammals such as moose and bison endure the cold in the open.

Primates and human origins

Primates are mammals adapted, in their ancestry, to life in trees: grasping hands and feet with nails, forward-facing eyes with depth perception, and large brains relative to body size. Apes, including gibbons, orangutans, gorillas, chimpanzees, bonobos and humans, lack tails. As lesson 6 showed, genetic evidence places chimpanzees and bonobos as our closest living relatives, sharing a common ancestor with us roughly 6 to 7 million years ago.

Hominins are the species on the human side of that split. The fossil record now includes about two dozen named hominin species, and it shows that human evolution was not a single march but a branching bush, with several species often alive at once. Bipedalism, walking upright on two legs, came first, millions of years before large brains or stone tools.

import numpy as np
# Brain size in hominins over time (approximate values from the table above)
age_myr = np.array([7.0, 3.4, 1.9, 1.0, 0.2])     # million years ago
brain = np.array([350, 450, 600, 1000, 1350])     # cm^3
slope, intercept = np.polyfit(-age_myr, np.log(brain), 1)
print(f"average growth rate: {slope:.3f} per million years (natural log units)")
print(f"brain size doubling time: about {np.log(2)/slope:.1f} million years")
for a, b in zip(age_myr, brain):
    print(f"{a:4.1f} million years ago: {b:5d} cm3")

average growth rate: 0.188 per million years (natural log units)
brain size doubling time: about 3.7 million years
 7.0 million years ago:   350 cm3
 3.4 million years ago:   450 cm3
 1.9 million years ago:   600 cm3
 1.0 million years ago:  1000 cm3
 0.2 million years ago:  1350 cm3

The simple fit hides an uneven history: brain size changed little for millions of years among the australopiths, then rose rapidly in the genus Homo over the last two million years. Body size also increased, and part of the change reflects larger bodies.

Out of Africa, and interbreeding

Fossils and genetics agree that Homo sapiens evolved in Africa and that modern humans spread out of Africa beginning roughly 60,000 to 70,000 years ago, eventually reaching every continent except Antarctica. African populations hold the most genetic diversity of any people, as expected if other populations descend from subsets that left Africa (a series of founder effects, lesson 3).

Ancient DNA has transformed the story. In 2010 Svante Pääbo's team published the Neanderthal genome; Pääbo received the 2022 Nobel Prize in Physiology or Medicine for this work. It showed that people outside Africa carry about 1 to 2 percent Neanderthal DNA, from interbreeding after modern humans left Africa. DNA from a finger bone in Denisova Cave in Siberia revealed another group, the Denisovans, who contributed DNA especially to people of Oceania and parts of Asia. Some of this inherited DNA was useful: a Denisovan gene variant helps Tibetans live at high altitude.

People reached the Americas at least 15,000 years ago, and footprints at White Sands National Park in New Mexico suggest perhaps 21,000 to 23,000 years ago, crossing from Siberia via the Bering land bridge and moving south along the Pacific coast or through an ice-free corridor east of the Rockies. Genetic studies of ancient and present-day people show that the ancestors of Native American peoples came from these first populations. In the United States, the Native American Graves Protection and Repatriation Act governs human remains and ancestral objects, and research involving ancient DNA increasingly follows the CARE principles for Indigenous data governance and is conducted in partnership with tribes.

Human evolution did not stop with the origin of our species. Lactase persistence, the ability to digest milk sugar as an adult, spread through natural selection in dairying populations in Europe, Africa and the Middle East within the last 10,000 years. Variants protecting against malaria, such as the sickle-cell allele, are common where malaria has long been present. Skin color varies with the intensity of ultraviolet light, balancing protection of folate against the need to make vitamin D. All living humans belong to one species with very low genetic diversity compared with chimpanzees, and most human genetic variation is found within, not between, populations.