2.1 Introduction

If you took an introductory biology course that marched you through the animal phyla, you may have seen a figure that looks like Figure 2.1, which demonstrates where you fit into the larger animal kingdom. Humans, like other vertebrates, belong to the phylum Chordata.

Chordates are united by a number of synapomorphies, or shared derived characteristics that were inherited from a common ancestor. Shared refers to characters or traits that the organisms have in common. Derived refers to when the trait evolved—sometime after the chordate lineage split from the common ancestor they shared with the echinoderms. The key with the chordate synapomorphies is that they possess them at some point in their lifetimes (Figure 2.2). Among these are

1. A dorsal hollow nerve tube (or dorsal hollow nerve cord)—dorsal indicates that a structure is opposite the belly (or ventral) side of the organism. In humans, this is our spinal cord.
2. A notochord—this stiff rod lies ventral to the nerve cord. In humans, the remnants of this are found in the intervertebral discs of the spinal column.
3. A postanal tail—“postanal” indicates that the tail occurs posterior to (or away from the face) the anus. If you have a cat or a dog, you can think about where their tails are. Humans tend not to have a visible tail past the embryo stage.

Box 2.1—Getting Oriented

We just used several important words—dorsal, ventral, and posterior. An important part of being able to discuss anatomy is to understand the road map of bodies. Just as we navigate a map by using compass directions (north, south, east, and west), we have specific terms that tell us where things are on animal bodies. We will first consider a quadrupedal animal, the kangaroo (Figure 2.3), as humans being bipedal and upright are a special case. However, when you finish this section, practice finding and using these terms on yourself or a pet.

We can start with four basic directions: Ventral refers to the belly side of the body, whereas dorsal refers to the back (think of where a dorsal fin is on a shark—the iconic triangle that cuts above the water). Anterior refers to the head end of the animal and the face, whereas posterior refers to the tail end. You will also see these called cranial and caudal, respectively. If we’re already on the head, we switch our terminology to rostral (toward the nose) and caudal.

Unlike two-dimensional paper or computer maps, kangaroos are three-dimensional. We have to add in another pair of directional terms: Medial refers to the midline of the body, whereas lateral refers to sides (put your hands on your hips—those are lateral to your vertebral column, which is your midline).

We can also divide up our kangaroo into regions by planes, just as you would have an X-Y plane or X-Z plane in a 3D graph. If we split our kangaroo into two mirror images, the plane that divides them is called the sagittal plane, as it goes right down the midline. However, if we move that plane to divide our kangaroo into two unequal lateral halves, we call it a parasagittal plane. If we change directions and want to divide our kangaroo into dorsal and ventral halves, we do that with a frontal plane (sometimes called a dorsal plane). Similarly, we can divide our kangaroo into anterior and posterior halves with a transverse plane (also called a coronal plane).

What about humans? As we will see repeatedly, often human anatomy is given its own separate terminology even though things are homologous with other mammals. This is true for directions in the body as well (Figure 2.4). Because we’re upright and bipedal, our faces are facing the same direction as our bodies, and the heads and tails of humans are no longer aligned with the face. The standard in human anatomy is to use superior (cranial), inferior (caudal), anterior, and posterior as our four cardinal directions. Dorsal and ventral are not often used to describe directions in human bodies.

We also have appendages that stick off both humans and our kangaroo. While it is true that if you move from the armpits to the fingers, you might be moving more laterally, we use special terms for the appendages: Proximal is closer to the trunk of the body, and distal is further out from it. In other words, your armpits are more proximal than your fingers, and your fingers are more distal than your armpits.

We have another important directional thing to discuss—left versus right. Consider where the left and right sides of your body are relative to you versus someone standing across from you and facing you. Your left side is on your left side; however, the left side of the person standing across from you is on your right. When we use left and right in an anatomical context, we are always talking about the animal’s or the subject’s own left and right, not the left and right of the person examining the animal or subject.

To return to our map analogy, maps also name regions of land, such as towns or countries. We have names for body regions too, which are based on human anatomy (Figure 2.5). Some of these terms are also applied to other vertebrates. While there are too many to list here, you will see some of these come up again.

The chordates are also deuterostomes (superphylum Deuterostomia), as are the members of phylum Echinodermata (sea stars, sea urchins, sea cucumbers, sand dollars, and crinoids) and phylum Hemichordata (acorn worms and pterobranchs). We will briefly discuss these organisms more below, but it’s worth asking why we are talking about sea stars in a book about vertebrates. Recall that our first core concept was evolution (see Chapter 1)—what we see in living organisms is due to descent with modification. Therefore, it is helpful to understand our closest living relatives, as different as they may seem, as a way to understand how natural selection favored particular traits and why. That being said, we also have to remember that any extant (i.e., living and not extinct) representatives of these groups have had a very long time for natural selection to act and make changes. If we want to know what our earliest ancestors looked like, we cannot necessarily look to living taxa. The fossil record may not be much help either, particularly if these organisms had few hard parts to make it through the fossilization process. Thus, we need to understand the evolutionary relationships of all the deuterostomes and the features we use to construct hypotheses about those relationships.

Box 2.2—How to Read a Phylogenetic Tree

A phylogenetic tree (also referred to as an evolutionary tree or a cladogram) is a visual way of depicting a hypothesis about evolutionary relationships among the taxa (sing. = taxon, a group of organisms given a taxonomic name such as species or family) included in the tree. How the taxa are distributed on that tree depends on the data used (e.g., morphological characteristics or genetic information) and the algorithm chosen to build the tree; this is why trees represent evolutionary hypotheses and not definitive answers.

Understanding the hypotheses represented by these trees requires being able to read them properly. This is something that even PhDs can struggle with, so we’re going to make sure everyone is on the same page. Figure 2.6A shows the anatomy of a tree, which is our first step. Taxa, like the shark and the frog, are typically at the tips of the branches, much like leaves on the branch of an actual living tree outside. As you move down the branches away from the tips, branches converge at nodes. Nodes represent a hypothetical common ancestor from which the tip-taxa diverged. As you keep moving away from the branch tips and toward the root of the tree, it’s similar to moving backward through time. Nodes higher up in the tree are more recent common ancestors than those in the lower parts of the tree, closer to the root.

The trick to reading the tree, once we have a handle on the tree anatomy, is to read from the tips down toward the roots and to pay attention to the nodes (common ancestors). To practice, let’s figure out which organism is more closely related to the frog in Figure 2.6A—the fish or the sheep? Begin by finding the frog and sheep on the tree, and literally put an index finger on each taxon. Now trace their respective branches down the branches away from the tips until they meet at node X and make note of the node’s location in the tree. Go back to the branch tips in Figure 2.6A and find the frog and fish. Repeat the same tracing motion; your fingers should have met at node Y. Node X is closer to the branch tips and farther from the root than node Y; thus, the frog and sheep have a more recent common ancestor than the frog and fish. This tells us that the frog and sheep are more closely related than the frog and fish, as they more recently diverged from their common ancestor.

The most common mistake people make is reading across the branch tips and thinking that how close taxa names are to each other tells you anything about evolutionary relationships. For example, in Figure 2.6A, one would make the erroneous conclusion that lizards are equally related to dinosaurs as to frogs. However, as you now know, it is the pattern of branching and nodes that indicates those evolutionary relationships. Because of this, we can rotate branches on the various nodes and get a tree that looks completely different from the original if we only read across the tips, but if we follow the branching and node pattern, we won’t be fooled. Examine the trees in Figures 2.6A and 2.6B and take the time to follow the branches—these are the same exact evolutionary relationships.

We have one more piece of terminology to discuss—clades. Clades are groups that are monophyletic, which means they include an ancestral lineage (which often is represented by a node and is sometimes called a common ancestor) and all its descendants. Looking at Figure 2.6A, if we wanted to make a clade that includes node X and all its descendants, we would have to include the frog, ram, lizard, T. rex, and chicken. Because clades are just monophyletic groups, they don’t always match up with a taxonomic level (e.g., phylum, family). Ideally, all our taxonomic levels would be monophyletic clades because they reflect a complete evolutionary history of the taxa included in that clade. Unfortunately, many taxonomic groups were established prior to this idea of monophyletic groups. “Reptiles” are a great example. If we go back to Figure 2.6A, most folks would only include the lizard and T. rex as reptiles. However, if we are also going to include all the descendants of the common ancestor, we should also be including chickens! As you’ll read in Chapter 3, birds evolved from a dinosaur ancestor.

2.2 The Deuterostomes

While genomic data supports the idea that the deuterostomes (echinoderms, hemichordates, chordates) are indeed closely related, their physical similarities are not at all apparent in their adult forms. After all, there are no chordates with pentaradial (five-sided) symmetry, which is a hallmark of the echinoderms. The Ambulacraria (Echinodermata + Hemichordata) haven’t shared a common ancestor with the Chordata since about 660–550 million years ago (abbreviated as Ma or MYA) and thus have had a lot of time for natural selection to work on these different evolutionary lineages.

However, if we examine the embryonic development of deuterostomes, it is easier to understand why these seemingly disparate groups are united (Figure 2.7).

The similarity begins rather early in development, in those initial stages where the fertilized egg (zygote) is undergoing a series of cell division events (cleavage). In animals that have protostome development (generally called protostomes—e.g., annelids, arthropods, molluscs), cleavage follows a particular spiraling pattern in which new cells are offset from their predecessors. The deuterostomes, on the other hand, do not follow the spiral pattern. Instead, they exhibit what’s called radial cleavage, wherein new cells sit directly atop their predecessors. If we fast-forward a bit, eventually these embryonic cells continue to divide and arrange themselves into a hollow ball with three germ layers called a gastrula (see Chapter 4 for more detail on embryonic development). The hollow space is the start of the gut cavity, called an archenteron. A gut needs an opening for food to enter (a mouth) and another for waste to leave (an anus). This is where we see our next embryonic difference. Protostomes literally translates to “first mouth”—the first opening (the blastopore) that forms here becomes the mouth. Deuterostome translates to “second mouth”—the first opening instead becomes the anus, and the mouth forms later. There are other developmental characteristics that unite the deuterostomes as well, such as how the mesoderm forms. We must issue a word of warning here, though—some of these “deuterostome developmental traits” have been found to exist in at least one protostome species, so we cannot strictly say that only deuterostomes have these traits.

What other features might unite the deuterostomes? So far the only confirmed candidate is pharyngeal gill slits—the pharynx is the region between your oral cavity (mouth) and esophagus. Humans tend not to have pharyngeal gill slits past the embryonic stage, and we do see these in extinct adult echinoderms (although these have been lost in our extant echinoderms). Luckily, this is something that does get preserved in the fossil record occasionally. Some scientists have proposed that Hox genes, which help control anterior-posterior body patterning, are a good place to find genetic features that may unite the deuterostomes. In particular, within the deuterostomes examined so far, Hox9/10 appears to have split off from other Hox genes in its cluster and undergone some duplication events and changes. Alas, we generally cannot Jurassic Park our way into the fossil record and look at the genes of fossilized organisms. At the time of this writing, the oldest DNA recovered and sequenced from fossilized remains comes from some mammoth specimens that are somewhere between 1 and 2 million years old.

Ambulacraria

The Ambulacraria includes two clades—the echinoderms and the hemichordates. Let’s begin with the clade that you’re probably more familiar with: phylum Echinodermata (Greek = “spiny skin”; Figure 2.8). These marine invertebrates come in a range of sizes and shapes and include sea stars, brittle stars, sea urchins, sand dollars, sea cucumbers, crinoids (sea lilies), and several extinct forms. Their wildly different morphologies come with different lifestyles: carnivores, detritivores, herbivores, and filter feeders, living on top of the substrate or underneath it (and sometimes swimming). Underlying this are a number of unifying characteristics—a calcite endoskeleton, larvae with bilateral (twofold) symmetry (Figure 2.9), and adults with pentaradial (fivefold) symmetry (Figure 2.8’s sea star is a great example).

Phylum Hemichordata consists of two classes of marine invertebrates—Pterobranchia (Figure 2.10) and Enteropneusta (Figure 2.11)—that look wildly different from each other. The pterobranchs are small filter feeders (microscopic to 1 cm long) that build tubes of collagen that they live within. The enteropneusts are also known as “acorn worms.” Most of these worm-shaped extant species live in or on top of the sediments of the sea floor and either filter feed or are detritivores. Unlike the pterobranchs, they tend to range from centimeters to 1.5 meters long. Just like we saw with the echinoderms, the hemichordates share some common features. Unlike the echinoderms, they do possess a dorsal nerve cord (Figure 2.12), although it is not necessarily hollow like we see in the chordates. Both classes also possess a muscular preoral organ that encloses the heart-kidney complex. In pterobranchs, this is the cephalic shield, and in enteropneusts, this is the proboscis (Figure 2.11).

What unites these very different phyla, Echinodermata and Hemichordata, under the Ambulacraria? Molecular data support this grouping, particularly a set of microRNAs and a subset of Hox genes. There are also larval characteristics (Figure 2.13). Specifically, there are ciliated cells that form a preoral larval feeding band that creates a current to bring food to the larva’s mouth, in addition to a perioral feeding band that moves food into the esophagus. The larvae of both phyla also have similar neuron structures that aren’t seen in other taxa. Finally, despite outward appearances, there is some organizational similarity between the two phyla: The coelom, or body cavity, is divided into three sections by a series of coelomic sacs that run anterior to posterior.

Phylum Chordata

There are three subphyla included in phylum Chordata: Urochordata (tunicates, sea squirts, and salps), Cephalochordata (lancelets), and Vertebrata (things with vertebrae). A glance at Figure 2.14 will once again show that this phylum contains animals that look wildly different from each other. Recall the start of this chapter, where we stated that there are three synapomorphies that the chordates demonstrate at some point in their lives: a dorsal hollow nerve tube, a stiff notochord, and a postanal tail.

Let’s first briefly introduce the Vertebrata so that you have them in mind as you consider the other chordates. Vertebrates have a head skeleton (often called the skull) that is cartilaginous at some point and surrounds a brain. Several neurological features are specific to vertebrates. These include unique motor and sensory nerves, embryonic neural crest cells, and cranial ectodermic placodes. Neural crest cells, which arise from the dorsal portion of the developing central nervous system, are particularly special. They are highly migratory, meaning that they don’t necessarily stay where they originate during development. They are multipotent cells, which means that they can form a lot of different things. A partial list includes the cells that make up your skeletal tissues, various types of nerve cells, and the melanocytes (cells that produce the pigment melanin) in your skin. The cranial ectodermic placodes (also known as neurogenic placodes), which are associated with the formation of the head, form things like the sensory structure in your inner ear and nose, the lens of your eye, and sensory cells. During embryonic development, which we’ll cover in more detail in Chapter 4, the internal organs of vertebrates develop from a different process than the rest of the deuterostomes. Finally, the Vertebrata have, well, vertebrae—skeletal elements associated with the dorsal nerve cord. We will see in Chapter 3 that the hagfishes do not have “true” vertebrae, but they have vertebrae-like elements that are homologous to the vertebrae in other vertebrates.

The subphylum Urochordata, sometimes referred to as the Tunicata as an alternate subphylum name, consists of roughly 3,000 living marine species. Some adults look like potatoes, others look like clumps of vases, and still others look like long chains of jellylike structures (Figure 2.15). Most urochordates are filter feeders. We will use tunicates as our representative urochordate here. Water enters the branchial siphon, which leads to the mouth and then the pharyngeal basket. Food is caught in mucous sheets within the basket and passed along to the stomach. Water leaves via the atrial siphon.

None of the adult urochordates are recognizable as chordates because they do not retain the three chordate synapomorphies as adults. As we saw with the ambulacrarians, a lot of evolutionary time has passed, and the adult forms we see now are highly modified compared to their early chordate ancestors. However, urochordates do have those synapomorphies as larvae! These are easiest to see in the tunicates, where the larvae resemble tadpoles (Figure 2.16). The features we saw in the adult tunicate are largely present in what looks like a head region, superficially—siphons, digestive organs, and other organs are all present. However, there is also a muscular tail, complete with a dorsal hollow nerve cord and notochord. When it is time for the tunicate larva to settle, it undergoes metamorphosis and resorbs its tail, nerve cord, and notochord. The cerebral ganglion, which is homologous (sharing a common ancestry) to the vertebrate brain and is responsible for controlling larval movement, also regresses.

The cephalochordates, or lancelets, consist of about 20 extant species that live in marine or brackish environments. Unlike with the urochordates, there isn’t much variability across species—they look vaguely fishlike and are under 5 cm long. They tend to spend most of their time buried in the sediment, except for their heads, and are capable of swimming. The lancelets demonstrate the three chordate synapomorphies as both larvae and adults. They also have characteristics that seem very vertebrate-like. For example, the anterior portion of the nerve cord is somewhat enlarged, and at least part of it is considered homologous to parts of the vertebrate brain. The muscles in the body wall are arranged in chevron-shaped blocks called myotomes (also known as myomeres), and we see a similar arrangement in fishes (Figure 2.17).

The fossil record of cephalochordates and urochordates is almost nonexistent. There is a fossil urochordate from the Cambrian (543 million years ago) that looks very similar to modern tunicates. However, similarly aged fossils that can be confidently assigned to Cephalochordata have not been found. Thus, the fossil record is not much help in figuring out chordate relationships. Given the anatomy of the extant nonvertebrate chordates, we probably would expect that the vertebrates are more closely related to the cephalochordates than the urochordates. Alas, this is not the case! Molecular data indicate that urochordates are more closely related to vertebrates than cephalochordates (Figure 2.18). This is why it’s also important to look at the larval urochordates—they actually share more characteristics with vertebrates than the cephalochordates do. For example, motor neurons connect to muscles in the same way in both vertebrates and urochordates but in a different way in cephalochordates. The microscopic structure of the notochord is also more similar in the larval urochordates and vertebrates. Last, it is possible that urochordates have neural-crest-like cells and ectodermal placodes like vertebrates do. However, this is still being explored.

2.3 What Did the Early Vertebrates Look Like?

While we learn about most of our vertebrate groups in Chapter 3, let’s pause in the Cambrian period for a moment. We just mentioned that we don’t have much in the way of early urochordates or cephalochordates in the fossil record. What about the Vertebrata? Some wonderful fossils from the Chengjiang formation in China that are about 516 million years old look very “fishy” in body shape and have fins (Figure 2.19). They also have all the chordate characteristics we’ve discussed, so there’s no doubt that they are chordates. However, they also have fairly well-defined heads that include branchial bars (supports for the gills) and a pair of eyes. These fossils do not show evidence of jaws, but as we will see in Chapter 3, vertebrates did not always have jaws (and some still don’t).

2.4 Summary

The chordates, which include the vertebrates, are united by three synapomorphies (dorsal hollow nerve cord, notochord, and postanal tail). They share developmental characteristics with both echinoderms and hemichordates. The vertebrates are united by neural crest cells, cranial ectodermal placodes, and vertebrae.

2.5 Further Reading

1. “Chengjiang Fossil Site.” UNESCO World Heritage Centre. Accessed July 22, 2024. https://whc.unesco.org/en/list/1388/.
2. “Homeotic Genes and Body Patterns.” Genetic Science Learning Center. Accessed July 22, 2024. https://learn.genetics.utah.edu/content/basics/hoxgenes.
3. Janvier, Phillipe. “Facts and fancies about early fossil chordates and vertebrates,” Nature 520 (2015): 483–489.
4. Naglu, Karma, Selina R. Cole, David F. Wright, and Camilla Souto. “Worms and gills, plates and spines: The evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development.” Biological Reviews 98 (2023): 316–351.

2.6 References

1. Bursca, Richard C. and Gary J. Brusca. Invertebrates. Sunderland: Sinaur Associates, 1990.
2. Cameron, C. B. “A phylogeny of hemichordates based on morphological characters.” Canadian Journal of Zoology 83 (2005): 196–215.
3. Martik, Megan L. and Marianne E. Bronner. “Riding the crest to get a head: Neural crest evolution in vertebrates.” Nature Reviews Neuroscience 22 (2021): 616–626.
4. Martín-Durán, José M., Yale J. Passamaneck, Mark Q. Martindale, and Andreas Hejnol. “The developmental basis for the recurrent evolution of deuterostomy and protostomy.” Nature Ecology and Evolution 1 (2017): article 005.
5. Naglu, Karma, Selina R. Cole, David F. Wright, and Camilla Souto. “Worms and gills, plates and spines: The evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development.” Biological Reviews 98 (2023): 316–351.
6. Ota, Kinya G., Sotoko Fujimoto, Yasuhiro Oisi, and Shigero Kurantani. “Identification of vertebra-like elements and their possible differentiation from sclerotomes in the hagfish.” Nature Communications 2 (2011): 373.
7. Peterson, Kevin J., and Douglas J. Eernisse. “The phylogeny, evolutionary developmental biology, and paleobiology of the Deuterostomia: 25 years of new techniques, new discoveries, and new ideas.” Organisms, Diversity, & Evolution 16 (2016): 401–418.
8. Ruppert, Edward E. “Key characters uniting hemichordates and chordates: Homologies or homoplasies?” Canadian Journal of Zoology 83 (2005): 8–23.
9. Swalla, Billie J., and Andrew B. Smith. “Deciphering deuterostome phylogeny: Molecular, morphological and paleontological perspectives.” Philosophical Transactions of the Royal Society of London B 363 (2008): 1557–1568.
10. van der Valk, Tom, Patrícia Pečnerová, David Díez-del-Molino, et al. “Million-year-old DNA sheds light on the genomic history of mammoths.” Nature 591 (2021): 265–269.