Animals: Vertebrates

Learning Objectives

  1. Place and identify chordates (including vertebrates) on a phylogenetic tree within the domain Eukarya
  2. Identify and describe key adaptations of chordates (notochord, dorsal hollow nerve cord, pharyngeal slits, and post-anal tail)
  3. Identify and use key adaptations to differentiate between vertebrate groups, including, including Fishes (bony and cartilaginous), Amphibians, and Amniotes (reptiles, birds, and mammals)
  4. Explain how adaptations in tetrapods facilitated colonization of land and how adaptations in early amniotes facilitated colonization of drier land habitats
  5. Organize the appearance and/or flourishing of major vertebrate groups in chronological order in geologic time, including Fishes, Amphibians, and Amniotes (reptiles, birds, and mammals)

Chordates on the Phylogenetic Tree of Life

Chordates form a clade within the Deuterostomes, and are most closely related to Echinoderms (starfish, sea urchins, sand dollars, etc.).

A phylogenetic tree representing one hypothesis for animal evolutionary relationships, with chordates emphasized in green. Image credit: Shana Kerr

Evolutionary Adaptations Shared by all Chordates

The information below is adapted from OpenStax Biology 2e 29.1, OpenStax Biology 29.3, OpenStax Biology 29.4, , OpenStax Biology 29.6, CK-12 Biology Advanced Concepts 16.7 Vertebrate Evolution – Advanced, CK-12 Biology for High School 12.5 Vertebrate Evolution

CK-12 Foundation is licensed under CK-12 Curriculum Materials License

Chordates include both invertebrate and vertebrate species, but all vertebrates share the following traits at some point during their developmental/larval or adult stages:

  • Notochord: Chordates are named for the notochord, a flexible, rod-shaped structure that arises from mesodermal tissue during embryonic development. The notochord is found in the embryonic stage of all chordates and in the adult stage of some chordate species. It is located between the digestive tract and the nerve cord, and it provides support throughout the length of the body.
  • Dorsal hollow nerve cord: The dorsal hollow nerve cord arises from ectodermal tissue that rolls into a hollow tube during development. In chordates, it is located dorsal (along the back) from the notochord. In contrast, other animal phyla have solid (rather than hollow) nerve cords that are located either ventrally (along the belly) or laterally (on the sides). The nerve cord found in most chordate embryos develops into the brain and spinal cord, which compose the central nervous system.
  • Pharyngeal slits: The pharyngeal slits are openings in the pharynx (the region just behind the mouth) that extend to the outside environment. In organisms that live in aquatic environments, pharyngeal slits allow for the exit of water that enters the mouth during feeding.
    • Some invertebrate chordates use the pharyngeal slits to filter food out of the water that enters the mouth.
    • In vertebrate fishes, the pharyngeal slits are modified into gill supports and/or jaw supports.
    • In tetrapods (amphibians, reptiles, birds, and mammals), the slits are modified into components of the ear and tonsils.
  • Muscular post-anal tail: The muscular post-anal tail is a posterior elongation of the body, extending beyond the anus. The tail contains skeletal elements and muscles which provide a source of locomotion in aquatic species. In some terrestrial vertebrates, the tail also helps with balance, courting, and signaling when danger is near. In apes and humans, the post-anal tail is vestigial, meaning it is reduced in size and nonfunctional.

The image below shows these traits on a cartoon of a generalized chordate:

Chordate features. In chordates, four common features appear at some point during development: a notochord, a dorsal hollow nerve cord, pharyngeal slits, and a post-anal tail. Image credit: OpenStax Biology 2e

Evolutionary Adaptations among Chordate and Vertebrate Lineages

Chordates make up just over 3% of all animal species, but the include the largest animal species on Earth. Below is a phylogenetic tree visualizing chordate evolutionary relationships. Viewing the tree, note that not all chordates are vertebrates! There are three groups of non-vertebrate chordates: cephalochordates (lancelets), urochordates (tunicates), and

A phylogenetic tree showing evolutionary relationships among chordate groups. Note: 1) placement of Hyperoartia (lampreys) within Vertebrata is debated; 2) there is recent evidence suggesting that cartilaginous fishes evolved from bony fish but lost the mineralized skeleton; this hypothesis is currently under debate. Image credit: Shana Kerr
A simplified phylogenetic tree of vertebrate evolution. Image credit: CK-12 Foundation, CK-12 Biology for High School 12.5 Vertebrate Evolution

All chordates possess the four traits described above: notochord, dorsal hollow never chord, pharyngeal slits, and a muscular post-anal tail. In addition, they are triploblastic deuterostomes that evolved from an ancestor with cephalization (see the reading on Invertebrate Animals for a review of these concepts). New adaptations arose in different chordate lineages as they diverged over time, including a cranium (skull), vertebral column, jaw, bony skeleton, lungs, lobed fins, four limbs, amniotic egg, endothermy, feathers, wings, hair, and milk production. In the section below, we will discuss the evolution of different chordate groups with emphasis on these evolutionary adaptations.

Before we walk through these details, here is the Crash Course take on Chordates (please note, as entertaining as Hank Green may be, there is no such thing as a “living fossil”):

  • Craniata are chordates with a cranium (skull). We take it for granted that vertebrates have skulls; however, this is not universally true:
    • One of the earliest known craniates was Haikouichthys, with fossils dating to approximately 518 MYA during the Cambrian explosion; Haikouichtys was approximately 1 inch long, and had a defined skull with a distinct head and tail, but no evidence of a vertebral column.
    • Modern day Myxini (hagfish) are non-vertebrate chordates that are the only living species that has a skull but no vertebral column. Hagfish do have some rudimentary vertebrae-like structures and there is some evidence that they may have evolved from a vertebra-bearing ancestor, but lost this trait. The hagfish skeleton consists of the skull and the notochord. Hagfish are jawless.
Reconstruction of Haikouichthys, the earliest known craniate. Image credit: Nobu
  • Vertebrata are chordates that have a vertebral column, which is the defining evolutionary feature of this group. The vertebral column is composed of a series of separate bones joined together as a backbone. In adult vertebrates, the vertebral column replaces the notochord, which is only seen in the embryonic stage. Fishes were the earliest vertebrates, with jawless species being the earliest and jawed species evolving later. Jawless fishes are called agnathostomes (“a” = “without” and “gnathos” = “jaw”)
    • One of the earliest known possibly-vertebrate species was Myllokunmingia, with a single known fossil dating to approximately 518-490 MYA, although it is not universally accepted that Myllokunmingia was a true vertebrate. Myllokunmingia was approximately 1 inch long. Fishes are active feeders, rather than sessile (non-motile), suspension feeders.
    • Living agnathostomes (jawless fishes) such as Hyperaortia (lampreys), are craniates with a vertebral column that represent a vertebrate linage that diverged from other vertebrate lineages over 500 million years ago. Lampreys lack fins, causing them to look tubular.
Artist illustration of the craniate Myllokunmingia, a possible early vertebrate (under debate). Image credit: Giant Blue Anteater
  • Gnathostomes or ‘jaw-mouths‘ are vertebrates that possess jaws; a jaw is a hinged structure attached to the cranium that allows an animal to grasp and tear its food. Evolution of the jaw approximately 430 MYA was one of the most significant developments in early vertebrate evolution, facilitating an evolutionary arms race between predators, competitors, and prey. In addition to jaws, early gnathostomes also possessed two sets of paired fins, allowing the fishes to maneuver accurately and become mobile predators. These two traits allowed early gnathostomes to exploit food resources that were unavailable to jawless fishes. Most modern fishes are gnathostomes (jawed).
    • A famous example of early gnathostomes are the placoderms, which were a diverse group of jawed fish with an abundance of fossils dating from approximately 430 – 360 MYA. Placoderms were large (up to ~29 feet long) predators with bony plates forming armor over their heads, but their internal skeletons were typically composed of cartilage (with one noteworthy exception discovered in 2020).
External anatomy of the placoderm Coccosteus decipiens. Image credit: Nobu Tamura (
  • Chondrichthyes (cartilaginous fish) are living jawed fishes (gnathostomes) that possess paired fins and a skeleton made of cartilage, including sharks, rays, skates, sawfishes and a few dozen species of fishes called chimaeras (ghost sharks). Cartilaginous fish first appear in the fossil record approximately 395 MYA and may have evolved from one group of early placoderms. Some recent fossil evidence suggests that the possibly-placoderm ancestors of cartilaginous fish once had bony endoskeletons but lost this trait over evolutionary time, replacing their bony skeleton with a skeleton of cartilage; this hypothesis is currently under debate in the scientific community.

  • Osteichthyes (bony fishes) contain mineralized (bony) skeletons. Fish with bony endoskeletons appear in the fossil record approximately 420 MYA; bony fish may have evolved from another group of placoderms, distinct from the ancestors of cartilaginous fish. The vast majority of living fishes belong to this group, which consists of approximately 30,000 species, making it the largest class of vertebrates in existence today. The ‘bony fish’ group includes the Actinopterygii (ray-finned fishes), and Sarcopterygii (lobe-finned fishes).
    • Lungs: Interestingly, early bony fish were the first group to evolve lungs, which later evolved into swim bladders which are present in modern-day fish (NOT the other way around). What were lungs doing in ancient bony fish? There are a number of hypotheses, but one of the most prominent is that early lungs allowed fish to “gulp” air in oxygen-poor conditions; this air could then supplement oxygen obtained from gills and circulated in the circulatory system.

  • Sarcopterygii (lobe-finned fishes): Lobed fins were a important adaptation that later allowed evolution of tetrapods (four-legged vertebrates). Lobed fins differ from the fins of ray-finned fishes in that the fin extends from a fleshy, lobe-like structure that resembles a limb bud and is connected to the body by a single bone.
    • Lobe-finned fishes first appear in the fossil record approximately 425 MYA.
    • Most lobe-finned fishes are now extinct, but living species include coelacanths and lungfishes.
Evolution of fishes from the Cambrian to the present as a spindle diagram. The width of the spindles are proportional to the number of families as a rough estimate of diversity. The diagram is based on Benton, M. J. (2005) Vertebrate Palaeontology, Blackwell, 3rd edition, Fig 2.10 on page 35 and Fig 3.25 on page 73, as well as this source, and this Wikimedia Commons file. Image credit:
  • Tetrapods (four-limbed vertebrates): The earliest fossil evidence of tetrapods are now-extinct amphibian species dating to nearly 400 million years ago. Evolution of tetrapods from lobe-finned freshwater fishes represented a significant change in body plan from one suited to organisms that respired and swam in water, to organisms that breathed air and moved onto land; these changes occurred over a span of 50 million years.
    • Tiktaalik roseae is a famous fossil of a “tetrapod-like fish” that lived in a shallow water environment about 375 million years ago. Tiktaalik seems likely represent an intermediate form between fishes having lobe fins and tetrapods having limbs.
    • Among the earliest known true tetrapods include Ichthyostega and Acanthostega. Both were aquatic species (not truly terrestrial), and may have had both gills and lungs. They also had four limbs, with the skeletal structure of limbs found in present-day tetrapods, including amphibians. However, the limbs could not be pulled in under the body and would not have supported their bodies well out of water. They probably lived in shallow freshwater environments, and may have taken brief terrestrial excursions.
Simplified phylogeny spanning the fish–tetrapod transition, illustrating the major anatomical changes. In the color coding, blue denotes an aquatic adaptation, and yellow to red colors represent adaptations for walking and weight support. Image credit: Per E. Ahlberg,

Watch the video below about the importance of the fossil Tiktaalik to our understanding of tetrapod evolution:

  • Amphibia: Modern-day amphibians are vertebrate tetrapods that include frogs, salamanders, and caecilians. The term amphibian loosely translates from the Greek as ‘dual life’ which is a reference to the metamorphosis that many frogs and salamanders undergo and their mixture of aquatic and terrestrial environments in their life cycle. Most amphibian species must remain forever associated with a moist environment, at a minimum in early development as eggs. In addition to breathing with lungs, amphibians can also exchange gas through their moist and permeable skin, which is kept moist through mucus glands in the skin.
    • Early amphibians were predators who dominated the terrestrial landscape, but were limited to wet and swampy areas. Early amphibians grew as large as 18 feet in length.
Artist reconstruction of Prionosuchus plummeri of the Permian, thought to be the largest amphibian that ever lived. Image credit: ДиБгд at Russian Wikipedia
  • Amniota: The amniotes, which include modern-day reptiles, birds, and mammals, are distinguished from amphibians by their terrestrially-adapted amniotic egg, which is protected by amniotic membranes (fluid-filled membranes which function in embryonic development). A solid eggshell surrounds the membrane-enclosed embryos and provides protection to the developing organism. The evolution of the amniotic egg approximately 300 to 360 million years ago was key to allowing tetrapods to reproduce on land and marked the beginning of a flourishing population of terrestrial tetrapods.
    • There are many many lineages of amniotes (including many extinct groups), but here we will emphasize two important groups of amniotes: the sauropsids (ancestors of lizards, snakes, turtles, crocodilians, dinosaurs, and birds), and the synapsids (ancestors of mammals).
Cladogram of the Tetrapoda, with clade Sauropsida in green with red dashed outline, and Reptilia in blue with blue. Class Reptilia includes the ancestors of birds and mammals and is therefore paraphyletic. Image credit:
Maksim Dolgun
. Based on File:Phylogenetic-Groups.svg by TotoBaggins at English Wikipedia.
  • Reptilia (within Sauropsidia): The earliest known true reptile is the now-extinct Hylonomus, a small lizard-like animal approximately 8-10 inches long (including its tail). Unlike modern reptiles, Hylonomus was an anapsid, meaning it had a solid skull without any holes (or “temporal openings”) on the side. This skull structure is important because it affects the way muscles connect from the jaw to the skull, influencing jaw strength and movements; having no holes means smaller jaw muscles and thus less jaw strength.
Top: Hylonomus lyelli, an early reptile from the Late Carboniferous of Nova Scotia, Canada, pencil drawing. Image credit: Nobu Tamura ( Bottom: Anapsid skull. The large opening/hole is the eye socket, and the region behind the eye socket is lacking any temporal openings. Image credit: Preto(m).
  • Reptiles became the dominant terrestrial vertebrates, and a clade of sauropsids called diapsids are the ancestors of lizards, snakes, turtles, crocodilians, dinosaurs, and birds. Diapsids are defined by the presences of two temporal openings (holes) in each side of the skull; this structure allows for attachment of larger, stronger jaw muscles and wider jaw opening, compared to amniotes lacking these holes in the skull.
    • Reptiles use lungs to breathe and have scaly skin containing the protein keratin and waxy lipids, which reduced water loss from the skin. This thick, impermeable skin means that reptiles cannot use their skin for respiration, like amphibians, and thus all breathe with lungs.
    • Reptiles, like fish and amphibians, are ectothermic, meaning their main source of body heat comes from the environment. In addition to being ectothermic, reptiles are categorized as poikilotherms, or animals whose body temperatures vary rather than remain stable. Reptiles have behavioral adaptations to help regulate body temperature, such as basking in sunny places to warm up and finding shady spots or going underground to cool down. The advantage of ectothermy is low metabolic energy needed to survive (e.g., about 10% of a similarly-sized endotherm).
Diapsid skull. The large hole is the eye socket, and the region behind the eye has two temporal openings. Image credit: Preto(m).
  • Aves (within Sauropsidia): Birds are the only group of dinosaurs that are still living, evolving from a group of dinosaurs called theropods. (Even though birds are descended from dinosaurs, which are reptiles, we will consider birds as a group distinct from reptiles for the purpose of this discussion with the understanding that this designation does not accurately reflect phylogenetic history and relationships.)
    • One important fossil of an animal intermediate to dinosaurs and birds is Archaeopteryx, which is from the Jurassic period. Archaeopteryx is important in establishing the relationship between birds and dinosaurs, because it is an intermediate fossil, meaning it has characteristics of both dinosaurs and birds. Some scientists propose classifying it as a bird, but others prefer to classify it as a dinosaur. The fossilized skeleton of Archaeopteryx looks like that of a dinosaur, and it had teeth whereas birds do not, but it also had feathers modified for flight, a trait associated only with birds among modern animals. Fossils of older feathered dinosaurs exist, but the feathers do not have the characteristics of flight feathers.
    • The most obvious characteristic that sets birds apart from other modern vertebrates is the presence of feathers, which are modified scales. In addition to allowing for flights, feathers are also very effective insulation, trapping air in spaces between each feather to decrease the rate of heat loss. Feather coloration can play roles in camouflage or social signaling.
    • Birds are endothermic, meaning they produce their own body heat via their metabolism. Compared to ectothermy, endothermy requires more energy and thus more food. Because birds fly, they require large amounts of energy, necessitating an especially high metabolic rate.
A photo of an original fossil of Archaeopteryx Lithographica. It is often considered the oldest known true bird. The specimen is displayed at the Museum für Naturkunde in Berlin. Image credit: H. Raab (User: Vesta)
  • Mammalia (within Synapsidia): Mammals evolved from a group of reptile-like amniotes called synapsids. Synapsids are defined by the presences of a single hole in in each side of the skull. Similar to diapsids (ancestors of modern-day reptiles), the structure of the synapsid skull allows for attachment of larger, stronger jaw muscles and wider jaw opening, compared to amniotes lacking this hole in the skull. Mammals evolved from a group of synapsids called therapsids, and the cynodonts are the group of therpasids that include the most recent common ancestor of all mammals.
Synapsid skull. The large hole is the eye socket, and the region behind the eye has one temporal opening. Image credit: Preto(m).
  • Mammals are amniotes that retain features of the amniotic egg, even though only one group (the monotremes) still lay eggs. All mammals produce milk from mammary glands for their offspring.
  • The skeletal system of mammals possesses many unique features. Unlike other vertebrates, the lower jaw of mammals consists of just one bone; the additional jaw bones found in other vertebrates have been modified to function in hearing and form the three small bones in the mammalian ear, and is one way of distinguishing fossil mammals from fossils of other synapsids. The musculature of the jaw is also unique in mammals, allowing side-to-side movement of the jaw which makes chewing possible; chewing is unique to mammals.
    And finally, most mammals have different types and shapes of teeth rather than just one type and shape of tooth as in other amniotes.
  • The presence of hair is one of the most obvious visual features of a mammal (even whales and dolphins have hair). Like feathers in birds, hairs are heavily modified scales; hair, feathers, and scales are homologous structures of amniotes. Like feathers in birds, hair is effective insulation, trapping air in spaces between each hair to decrease the rate of heat loss. Hair coloration can also play roles in camouflage or social signaling.
  • Also like birds, mammals are endothermic, meaning they generate their own body heat via metabolic processes, and hair provides insulation to retain heat generated by metabolic work. Because the common ancestor of mammals and birds was ectothermic, endothermy evolved independently in mammals and birds; it is not a homologous trait.
Endothermy in mammals (Mammalia) and birds (Aves) evolved independently in these lineages; the trait is not homologous (indicated in purple above). Image source:, based on work by based on image by Stanislav Traykov Jan 28, 2005
  • Living mammals belong to just three clades: eutherians (including placental mammals, like us), marsupials (metatherians) which have live birth but no placenta, and the young develop within a pouch (eg., kangaroo, opossum), and monotremes (australosphenidans) which lay eggs (platypus and echidna). Many other clades of mammals are now extinct.
Phylogeny and diversification patterns of major mammal lineages after Luo (2007). The only three living mammal lineages are Monotremes (descendants of Australosphenida in pink), marsupials (decendants of  metatherians in blue), and placental mammals (descendants of Eutherians in red). Image credit: Williamson TE, Brusatte SL, Wilson GP (2014) The origin and early evolution of metatherian mammals: the Cretaceous record. ZooKeys 465: 1-76. doi:10.3897/zookeys.465.8178

Vertebrate Evolution over Geologic Time

Taking the timeline you’ve seen before, let’s zoom in to look at key events that have occurred in the evolution of vertebrates.

Timeline of the Phanerozoic eon, including Eras and Periods, with dates in million years ago (MYA). Image credit: Shana Kerr
  • Paleozoic era: The Paleozoic sees the origin of craniates, vertebrates (including all fishes), tetrapods, and amniotes (including reptiles and mammal-like reptiles):
    • Cambrian period: Craniates (including Hyikouichthys) and vertebrates (including Myllokunmingia) appear in the fossil record record. All vertebrates are aquatic in this period.
    • Devonian period: The Devonian is called the age of fishes because of the great diversity and abundance of fish that appear in the fossil record at this time, including jawless fish, cartilaginous fish, bony fish, ray-finned fish, lobe-finned fish, and of course the now-extinct placoderms. Placoderms went extinct shortly after the end of the Devonian, in the early Carboniferous. Tetrapods also first appear in the fossil record in the Devonian, but they do not become abundant until the Carboniferous.
    • Carboniferous period: Amphibian tetrapods flourish during the Carboniferous, becoming the dominant predators on land. Amniotes also first appear in the fossil record in the Carboniferous, but they do not become abundant until the Permian.
    • Permian period: Amniotes flourish during the Perminan, and therapsids (mammal-like reptiles) first appear in the fossil record at this time. Many lineages of fish and tetrapods are lost at the end-Permian mass extinction, which marks the end of the Paleozoic era.
  • Mesozoic era: The Mesozoic sees the origin of dinosaurs, mammals, and, bird-like dinosaurs, and birds:
    • Triassic period: Both dinosaurs and mammals (non-placental) appear during the Triassic.
    • Jurassic period: Placental mammals and therapods (bird-like dinosaurs) first appear in the Jurassic.
    • Cretaceous period: Birds appear in the fossil record during the Cretaceous, and dinosaurs flourish during this period. All non-avian dinosaurs become extinct during the end-Cretaceous mass extinction, which marks the end of the Mesozoic era.
  • Cenozoic era: We will not break the Cenozoic down into periods, but the Cenozoic sees the flourishing of placental mammals, and the origin of cetaceans (eg., whales, dolphins), primates, great apes, and Homo sapiens.

The spindle diagram below provides a visual for some of the events described above, with geologic periods of and eras of the Phanerozoic on the left.

Evolution of Vertebrate from the Cambrium to the present at a class level as a traditional spindle diagram. The width of the spindle represents the number of families as a rough estimate of diversity. The figures representing classes are (from left): Agnatha, Chondrichthyes, Osteichthyes, Amphibia, Reptilia, Aves, and Mammalia. The two extinct classes are Placodermi and Acanthodii. All classes interpreted traditionally. Note that number of families is an imperfect measure of diversity. Reptilia in particular should probably have been shown as far more diverse in the Mesozoic. Image modified from Petter Bøckman, based on Benton, M. J. (1998) The quality of the fossil record of vertebrates. P. 269–303, in Donovan, S. K. and Paul, C. R. C. (eds), The adequacy of the fossil record, Fig. 2. Wiley, New York, 312 p.

Keep in mind that the origins, or emergence, of a group may not align with when the group flourishes. Often, extinction events and the evolution of other organisms can open up new niches into which organisms will diversify.

Key events in vertebrate evolution (in blue). Image credit: Chrissy Spencer; adapted by Shana Kerr