Introduction to Chordates & Fish Anatomy - De Anza College

Introduction to Chordates & Fish Anatomy 

Biology 6A / Brian McCauley & Bruce Heyer 

November 19 & 20, 2007 

Today’s lab has two parts: 

• Introduction to Chordates: an introduction to the key characteristics of the phylum 

Chordata, with just a few specimens to study. 

• Fish anatomy: dissection of some fresh fish in order to learn their external and internal 

anatomy. 

The next two labs will also be dedicated to this phylum: one lab for mammalian anatomy as seen 

in fetal pigs, and one lab for vertebrate skeletons. 

Chordate characteristics 

TISSUES: • Three well-defined tissue layers in embryo. 

SYMMETRY: • Bilateral, with cephalization. 

BODY CAVITY: • Coelom 

PROTO/DEUTEROSTOME: • Deuterostome: the blastopore formed during gastrulation 

eventually becomes the anus; the mouth forms later. 

DIGESTIVE TRACT: • Complete digestive tract. 

CIRCULATORY SYSTEM • Closed in vertabrates; open in a few others. 

OTHER FEATURES • Segmented body. Vertebrae, for example. 

• Endoskeleton 

• Notochord: a connective-tissue body stiffener 

• Dorsal tubular nerve cord – forms brain and spinal cord. 

• Pharyngeal pouches and slits – gill related structures that 

may appear and then disappear early in development. 

• Postanal tail. In many worms, the anus is at the very tip 

end of the animal’s body; chordates typically have a tail 

beyond the anus. 

Brian McCauley & Bruce Heyer 11/18/07 Page 1 of 13

Early development of chordates 

The defining features of chordates appear early in development. 

Gastrulation 

Like other animals, chordates 

progress through blastula 

and gastrula stages. 

Gastrulation not only forms 

the beginning of the digestive 

tract, it also forms the three 

embryonic tissue types: 

endoderm, mesoderm, and 

ectoderm. 

The diagram at right shows 

gastrulation in a frog. The 

process is somewhat similar 

to gastrulation in echinoderms 

(as shown in last 

week’s handout on animal 

tissues and development). 

However, chordate 

gastrulation is somewhat 

more complex, partly 

because the early embryo is 

more asymmetrical and more 

filled in with cells. 

Chordates are deuterostomes. 

This means that the 

blastopore (the opening into 

the archenteron that forms 

during gastrulation) becomes the anus; the mouth forms later. Echinoderms are also 

deuterostomes, but annelids and arthropods are protostomes. In those phyla, the blastopore 

becomes the mouth, and the anus forms later. This is one of the reasons that chordates are 

considered to be more closely related to echinoderms than to arthropods. 

Notochord formation 

The notochord, one of the unique defining characteristics of chordates, is a semi-stiff rod of 

connecting tissue that forms in the embryo and to guide the development of the vertebral 

column (backbone) of vertebrates, along with other structures. In your own body, the notochord 

has mostly disappeared; the only remnants are the cartilaginous disks between your vertebrae 

Neurulation 

Neurulation forms the dorsal hollow nerve cord in a developmental event that bears some 

resemblance to gastrulation. The dorsal hollow nerve cord is another unique feature of 

chordates. 

Following gastrulation, the presence of a notochord induces neurulation of the overlying dorsal 

ectoderm. This third stage of morphogenesis is unique to chordates. The ectoderm above the 

notochord thickens to form the neural plate. This plate then invaginates to form a furrow along 

the anterior-posterior axis. The folds along the groove eventually seal over the furrow to form the 


neural tube that in turn develops into the dorsal hollow nerve cord. This nerve cord 

eventually develops into the central nervous system, including the spinal cord and brain. 

By contrast, in non-chordate animals the main nerve cord is solid and usually ventral. 

The diagram below (fig. 47.14 from Campbell) shows neurulation and associated events in a 

frog. 

Chordate development specimens: 

Models of frog development & neurulation. Note the stages of development following 

gastrulation. Identify the subsequent appearance of the notochord, neural plate, and 

finally the neural tube and neural crest. Compare to Campbell Fig. 47.14. 

Slides of 13-hour & 18-hour developing chick embryos. Compare the developing chick 

to the models of frog morphogenesis and identify the corresponding homologous structures 

named above. Refer to the Photo Atlas Fig. 2.16. 

☛ (CAUTION: We will be examining today several slides of this series showing stages of 

development in the chick embryo. The slides with the later stages are thick and can only be 

viewed at low power. Don’t break them by using a higher power objective.) 

Non-vertebrate chordates: urochordates and cephalochordates 

Urochordates and cephalochordates are in the phylum Chordata, but they aren’t vertebrates; in 

fact, you might not immediately recognize them as belonging to your own phylum. 

Urochordates (tunicates) 

Tunicates (also called sea squirts) are marine suspension feeders. They live in the ocean, pump 

water though their gut, and capture small particles of food suspended in the water. They are 

different from vertebrates in many respects: 

No cephalization of the dorsal nerve tube – in other words, no brain. 

Open circulatory system that can even reverse its direction of flow. 


Pharyngeal arches and slits form a ciliated filter basket (pharynx) used for gas exchange 

and suspension feeding. Water is drawn in through an incurrent siphon and pumped out through 

an excurrent siphon, passing through the slits in the pharynx. A sheet of mucus is used to 

capture suspended particles. The arches of the pharynx are vascularized, and serve for gas 

exchange as well as food capture. 

Many urochordates are sessile; they spend their adult lives glued to the bottom of the ocean. 

The diagram above (fig.34.4 from Campbell shows adult tunicates in (a) and (b), and a larval 

tunicate in (c). 

While urochordates differ from vertebrates in many ways, they also show the defining 

characteristics of the phylum Chordata, including the notochord, and the dorsal hollow nerve 

cord. 

We don’t have many urochordate specimens in the lab, but: 

Preserved specimens of adult ascidians. Identify the incurrent siphon, the filter 

basket formed by the pharyngeal arches, the atrium, and the excurrent siphon. 

Where is the notochord 

Cephalochordates (Amphioxus, or lancelets) 

The lancelets (Class Cephalochordata) resemble 

fish larvae, but they never develop bones. They are 

chordates, but not vertebrates. 

The notochord remains throughout life and serves 

as a semi-rigid endoskeleton. Mesodermal blocks 

develop segmented muscle bands called 

myotomes. The atrial aperture (atriopore) is 

directed posteriorly, and the anus is located outside 

the atrium posterior to the atriopore. A pre-anal 

ventral fin and post-anal caudal fin aid mobility as 

the lancelet burrows tail-down into sandy substrate 

projecting its oral aperture and ventral filter basket 

up into the water column. 

The diagram at right (fig.34.5 from Campbell) shows 

most of the features you should be able to see in 

our microscope slides of a lancelet. Note that there 

is a pathway that water passes through, called the 


atrium; this is separate from the intestine. As water is pumped through the atrium, it is forced 

through the pharyngeal slits, where food particles are captured. The food particles are then 

passed into the digestive tract. 

Slides with w.m. & c.s. of the lancelet Amphioxus. Identify the following structures: 

tentacles, mouth, notochord, dorsal nerve cord, pharynx with slits, atrium, intestine, tail, 

muscle segments (myotomes). 

Vertebrates 

The vertebrates (phylum Chordata, subphylum Vertebrata) include fish, amphibians, reptiles 

(including birds) and mammals. All these animals have the basic characteristics of chordates, 

with some added twists: 

• The anterior region of the dorsal hollow nerve cord expands to become a brain and is 

encased within a skeletal cranium. 

• Mesodermal blocks develop not only myotomes, but a segmented vertebral column that 

protects the posterior region of the dorsal nerve cord (spinal cord) and replaces the 

notochord. The cranium and vertebral column comprise the axial skeleton of vertebrates 

allowing an elaborate central nervous system and powerful muscle action with a flexible 

body. 

• The development of a brain has further spurred the development of more sophisticated 

cephalic sensory organs, especially eyes, nostrils and ears. 

• To support their enhanced homeostasis, vertebrates also have a closed circulatory system 

with distinctive types of heart and kidneys, and a greater suite of endocrine organs. 

Vertebrate specimens: 

Slides of 21-hour through 48-hour developing chick embryos. Observe the dramatic 

cephalization of the dorsal hollow nerve cord with the distinction of brain from spinal 

cord and development of cephalic sensory organs, notably the eyes and ears. Note also the 

segmentation evident in the developing myomeres, and the early establishment of the 

segmented vertebral column. 

Slides of 2-day through 7-day developing chick embryos. Observe the limb buds 

developing into the appendicular skeleton. Locate each of the four extra-embryonic 

membranes and describe their respective functions. C.f., Campbell Fig. 47.17. 

Slide of lamprey ammocoetes larva. The ammocoete larva of lampreys resembles a 

lancelet in form and habit, but with the vertebrate modifications described above.How is this 

larva similar to the lancelet How is it different How does it differ from the adult lamprey 

Skeleton of a bony fish. Note the segmented axial endoskeleton. What is the function for 

the spines protruding from the vertebral segments Examine the hinged jaw, buccal 

chamber, and pharynx with gill arches. List and locate the unpaired and paired fins. 

Skeleton of a shark. Note the corresponding structures to those listed for the boney fish. 

How is the shark skeleton different from the boney fish (composition; attachment of fins) 

In a later lab, you’ll look at vertebrate skeletons in more detail, contrasting fish with mammals 

and other vertebrates. 


Fish Anatomy 

This part of the lab comes to you straight from the grocery store. You’ll have the opportunity to 

examine a variety of fresh fish. 

Fish Taxonomy 

The taxonomy of Chordates can be confusing, because there are traditional, well-known groups 

(like fish) that don’t reflect real evolutionary relationships. Most fish have traditionally been 

grouped in two classes within the phylum Chordata: Osteichtyes, or bony fish (which includes 

most kinds of fish) and the Chondrichthyes, or cartilaginous fish (which includes sharks and 

rays). However, the actual evolutionary relationships of fish are a bit more complex, as shown in 

the cladograms in Campbell, ch. 34. 

This lab will focus on the bony fish, traditionally classified as Osteichthyes. Most of the bony fish 

belong to a group within the Osteichthyes called the Actinopterygii. 


In this handout, you’ll see various diagrams with numerous anatomical features listed. Study 

them all, but the terms you’re likely to see on a lab exam are those listed in bold type in the text 

of this handout. You won’t be tested on everything in the diagrams. 

External anatomy 

Before you cut the fish open, see what you can learn from the outside. Note that different fish 

may have very different shapes, especially for their fins. Can you make any guesses about how 

your fish lives 

Look for the features shown in the diagram below. 


Fins: Note the caudal, dorsal, pelvic, pectoral, and anal fins. You’ll see very different shapes of 

these fins in the various fish we have in lab. 

Lateral line: You may see a pigmented stripe marking the location of the lateral line sense 

organs. Can you see any evidence of the lateral line canals or organs 

Inside the mouth: Look inside the mouth. Note where the water would go as it passes over the 

gills, and note where the food would go when the fish eats. Take a look at the tongue. How is it 

different from your tongue Note the teeth. Compare the teeth of the various fish in the room. 

Fish teeth come in a variety of syles, some of which are shown in the diagram on the next page. 

In addition to the teeth in the jaws, fish often have pharyngeal teeth located back in the 

throat. The pharyngeal teeth are derived from pharyngeal arches, one of the key chordate 

characteristics. Why do you suppose they would have these “extra” teeth 

While you’re looking in the mouth, look at the gill arches and the operculum. The gill arches 

are pharyngeal arches that support and protect the gills. The gill arches usually have gill rakers 

on the anterior (front) side. Gill rakers are small projections sticking out of the gill arch; they 

prevent the fish’s food from escaping out through the gills. Fish that eat large prey have widely 

spaced gill rakers; fish that eat tiny zooplankton have closely spaced, filter-like rakers. 


I have no idea what the captions say on the above figure (from 

http://gyeonggi.go.kr/fishs/fishs2.php). However, it’s a picture of a gill arch with gills on the 

posterior side (the right in this picture) and gill rakers on the anterior side (left). 

Note how opercular pumping might work in your fish. What would make the water enter the 

mouth What would make it pass out across the gills 

Nostrils: where does the water go when it passes through the fish’s nostrils 

Vent: Fish have a single opening, the vent, that serves as the anus and the urogenital opening. 

(Urogenital means urinary and genital – that is, the opening through which eggs or sperm pass 

during reproduction). Find the vent in your fish. The vent marks the posterior end of the body 

cavity; behind that, the fish is all tail. 

Gills 

Recall the structure of fish gills: 

Cut away the operculum so you have a good look at the gills and the inside of the mouth. Each 

gill is supported by a bony gill arch, with the spiny gill rakers projecting forward. Note the 

filaments of the gills, each with many lamellae. You will be able to see this better under the 

dissecting microscope. 

The fish’s blood must flow through the gills to get oxygenated, so the gills are filled with blood 

vessels. The heart is located just behind the gills, but you won’t be able to see it until you cut the 

body open. You’ll come back to the heart in a little while. 

Inside the body cavity 

Cut open the fish’s body along the ventral (belly) side. You’ll see all the internal organs sitting in 

the coelom. To get a better view, cut away one side of the body wall, removing the muscle, 

bone, and skin so you have an unobstructed view. Note the organs shown in the diagram below 

(diagram is from Campbell, ch. 34.) 


Digestive tract. The digestive tract of fish is similar to that of mammals. Food passes from the 

mouth down the esophagus to the stomach. You may be able to see pyloric ceca, which 

function as accessory digestive glands (mammals don’t have these). The liver is large; it 

secretes bile into the gall bladder, from which the bile passes into the intestine. The intestine 

is fairly long. You may find remnants of food in the stomach or the intestine. 

Just like mammals, fish have digestive tracts that are adapted to the food they eat. Herbivorous 

fish generally have longer intestines to aid in digestion and nutrient absorption from their low 

calorie food. Some also have a gizzard, a muscular organ that helps to mash up the food for 

better digestion. 


Swim bladder. The swim bladder is a large light-colored structure near the dorsal side of the 

body cavity. Bony fish can adjust their buoyancy by putting gas into the swim bladder. The most 

abundant gas in the swim bladder is oxygen, which comes from the blood. A specialized gas 

gland generates lactic acid, acidifying the blood in the gas gland and causing it to release its 

oxygen (remember the Bohr shift). This gland is accompanied by a specialized countercurrent to 

maintain the incredibly strong gradient of oxygen partial pressure between the swim bladder and 

the blood. Some fish can have over 100 atmospheres of oxygen partial pressure in the swim 

bladder, but their blood can never contain more O 2 pressure than the surrounding water, which 

never contains more O 2 pressure than the air (0.2 atm). 

Kidney & urinary bladder. Does your fish live in salt water or in fresh water Either way it has 

a kidney, but the function of the kidney is quite different in these two environments. The kidney 

is long and thin and dark; it is located along the very top of the body cavity. Urine produced by 

the kidney enters the urinary bladder, which exits into the same area as the anus and the gonad. 

Gonad. Most fish are either male or female, though some change sexes. You should be able to 

see either an ovary, which may be filled with large orange eggs, or a testis, filled with white 

sperm. 

Circulatory system. Remember that fish pump their blood once per circuit. The heart is 

located close to the gills, and blood passes through the gills and then through the systemic 

circulation before making it back to the heart. You may have to do a little extra dissection to find 

the heart; it’s typically just behind and beneath the gills. Note the direct blood flow from heart to 

gills. 

Other anatomical features 

Muscle. Fish have a lot of muscle. If you peel away the skin, you can see the sections of muscle 

that are familiar to anyone who eats fish. The muscle of fish provides a very clear example of the 

segmented mesoderm that is characteristic of chordates. Also note the rays of the fins. Most 

fish can pull their fins flat to the body or extend them. The fins are extended by rays that 

penetrate down into the fish’s muscle; the flexing muscle levers the rays into an upright position. 

Eyes. If you’re good at dissecting small things, you may be able to sort out the anatomy of the 

eye. It’s a bit squishy, but you may be able to find some of the features shown below: 


Note that in fish eyes there is usually a tapetum behind the retina; this silvery reflective layer 

bounces light back to the photoreceptor cells in the retina, allowing the fish to see better in low 

light. Many mammals also have this feature, but humans don’t. 

Brain. It takes a little work with scissors, but you can cut open the brain case and find the brain 

inside. You’ll probably have a hard time locating the different regions of the brain, but here’s a 

diagram: 

Note that there are large semicircular canals (balance organs) associated with the brain. 

Skeleton. Fish live in the water, and they don’t have to support all their weight with their 

skeletons. For this reason, fish skeletons are generally much weaker than mammalian skeletons. 

That’s why you can cut the skull open with scissors. Compare your fish to the mounted fish 

skeletons in lab. We’ll look at skeletons in more detail in a later lab. 



Terms and structures to remember: 

There are two parts to this lab: chordates in general, and the anatomy of fish. 

Chordates 

• Appendicular skeleton 

• Atrium 

• Axial skeleton 

• Cephalochordate 

• Chordata 

• Cranium 

• Deuterostome 

• Dorsal hollow nerve cord 

• Gastrulation 

• Myotomes (muscle segments) 

• Neurulation 

• Notochord 

• Pharynx; pharyngeal slits; pharyngeal basket 

• Tail 

• Urochordates 

• Vertebral column 

• Vertebrate 


You should be able to identify the following structures in any of the fish that are in today’s lab 

(remember, other groups may have different species of fish – you should look at them all). 

• Fins: pectoral, pelvic, dorsal, anal, caudal 

• Gills, gill arches, gill rakers 

• Gonad (ovary or testis) 

• Heart 

• Intestine 

• Kidney 

• Lateral line 

• Liver & gall bladder 

• Operculum 

• Pyloric ceca 

• Stomach 

• Swim bladder 

• Teeth and pharyngeal teeth 

• Vent

Introduction to Chordates & Fish Anatomy - De Anza College

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