Chordata

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Chordata is the phylum of animals that includes humans, and as a result, it tends to receive a disproportionate amount of attention compared to the others. There are over 81,000 living species of chordates, with over 95% of them being vertebrates. The earliest known chordate fossils are around 530 million years old and were formed during the Cambrian explosion, although the phylum is likely to have originated earlier. As chordates, or more specifically vertebrates, are the most abundant land animals besides arthropods, they were the focus of most of the early attempts at taxonomy. Paleontological and genetic evidence would prove these models to be wildly inaccurate, but many misconceptions fueled by them remain.

Characteristics

There are five synapomorphies, or shared traits, that all chordates share and are believed to have come from their last common ancestor. Lancelets have all of these traits throughout their lives, while for other chordates, some of these traits may only appear in the embryo stage. These traits are for the most part exclusive to chordates, although hemichordates have analogues to some of these.

Notochord

A thin section of a lancelet. The notochord is the circular thing in the middle.

The trait that gave the phylum its name, the notochord is a semi-flexible rod across the length of chordates. Lancelets keep these throughout their entire lives, and rely on muscles to move the notochord. Tunicates have a notochord only in their larval stage, while in vertebrates the notochord is only present in embryos and gets supplanted by the vertebral column in development. The notochord is a source of signals to the rest of the body and is important to skeletal development in vertebrates.

Dorsal nerve cord

Located on the upper side of the notochord, the hollow dorsal nerve cord develops into the spine and brain of most chordates. This is unique to chordates, as other animal phyla have a ventral nerve cord in the center of the body, although hemichordates have both a dorsal and ventral nerve cord.

Pharyngeal gill arches or slits

Like many other animals, chordates have a pharynx, but what makes chordates (and hemichordates) unique is that they have slits in their pharynx. Lancelets and fish use their pharynx to take in oxygen from the water, while in humans these slits typically close in adults (if not, it requires surgery) but they help with the organization of blood vessels, bones, and glands in the upper body.

Post-anal tail

All chordates have a tail that extends past the anus, giving more space for the notochord and dorsal nerve cord. Tails also help for locomotion for marine chordates and balance for terrestrial ones. In certain tetrapods such as humans, the tail is vestigial.

Endostyle/thyroid

All chordates have one of these glands, with lancelets, tunicates, and lamprey larvae having endostyles and all other extant chordates having thyroids. Both of these glands are responsible for absorbing iodine.

Groups

This acorn worm isn't actually a chordate; it's a hemichordate instead.

Chordates, like hemichordates and echinoderms, are deuterostomes, which means that their blastopore develops into an anus, as opposed to a mouth as with protostomes such as arthropods, molluscs, and annelids. Chordates later split into three subphyla, cephalochordata, tunicata, and vertebrata. Cephalochordates split from the others first, so tunicates and vertebrates share a clade, olfactores, which are defined by their more advanced olfactory system (a.k.a. their sense of smell). Hemichordates, which include acorn worms, were once considered to be a subphylum of chordates, as they have some analogous features, such as gill slits, a dorsal nerve chord, and a stomochord that is similar to a notochord. However, as DNA evidence has shown them to more closely related to echinoderms (sea stars, sea urchins, sea cucumbers, sea lilies, etc.), they are now placed in their own phylum.

Cephalochordata

The internal anatomy of a lancelet. See if you can find the five traits that make this a chordate.

Cephalochordates, also known as lancelets or amphioxi, are small fish-like filter-feeding invertebrates that are considered to be the most primative extant chordates, with a fossil record dating back to the Burgess Shale. There are around thirty known extant species of lancelets. They have no vertebrae and have poorly developed sense organs, but they have a muscular notochord and the other traits associated with chordates. Lancelets reproduce by external reproduction, with planktonic larvae that eventuality develop into benthic adults that live in the sand.

Lancelets are eaten as food by several cultures, mainly in East Asia, and they supposedly taste like anchovies. They are widely studied in order to gain insights into the evolutionary history of vertebrates, as they were once thought to be the closest invertebrate relative of vertebrates, although genetic analysis has revealed the below-mentioned tunicates to be more closely related instead.

Tunicata

Microcosmus sabatieri, a species of sea squirt also called a sea fig.

Quite a bit more diverse than the lancelets with about 3,000 species, the tunicates are another group of mostly benthic marine filter-feeding invertebrates. The most well-known tunicates are the sea squirts, so named for their habit of "squirting" water when removed from the sea. Like lancelets, they are sometimes eaten by humans, although many species of tunicates are poisonous, containing high levels of vanadium and sulfuric acid. Some other, less well-known tunicates include colonial pyrosomes (aka "sea pickles"), planktonic larvaceans, and the stalked sea tulips, which have a symbiotic relationship with sponges.

The chordate features of a tunicate are more apparent when you look at their tadpole-like larvae.

At first glance, tunicates look nothing like other chordates, and it can be surprising to learn that these are the invertebrates that are most similar to humans. However, it makes more sense when you look at their larvae, which look similar to tadpoles. These larvae do not have mouths and thus cannot eat, however within a few days the tunicate will begin to metamorphose after the larvae attatches to a hard surface in most species. During the metamorphasis, the notochord merges with the rest of the body, and afterwards, with the exception of free-floating species, the tunicates become completely sessile. Some tunicates bud to produce colonies, while others live alone.

Vertebrata

The vertebrates, or animals with a backbone, are the largest group of chordates, with a fossil record dating back to the Cambrian Chengjiang laggerstätten. Historically split into mammals, birds, reptiles, amphibians, and fish, this taxonomy was found to be wildly inaccurate for several reasons that we'll get to later. This subphylum contains the largest animals known to have existed, as well as the only animals known to have edited RationalWiki.^{[citation NOT needed]} As the first vertebrates were likely jawless fish (see below), this means that every vertebrate can be accurately called a fish.

Agnatha

The mouth of a sea lamprey, looking like something out of a horror film.

This is an infraphylum consisting of the jawless fish, and it is sister to gnathostomes, which contains all other extant vertebrate species. Although they used to be a lot more diverse in the past, there are only two remaining extant groups: Myxini or hagfishes and Hyperoartia or lampreys, both of the taxa Cyclostomata. Some extinct groups include the conodonts, the primative Myllokunmingiida, and the Ostracoderms, which were the most diverse group.

Modern jawless fishes have a skeleton made of cartilage and a third pineal eye to help detect light, but they lack side fins or a stomach. Lampreys lack gill openings and have their gills behind their mouth and eyes. They are parasites that use their tongue to put holes in a fish's skin so they can suck their prey's bodily fluids. They have become invasive in many places, with a single lamprey being capable of killing 40 pounds of fish per year. Hagfish, on the other hand, are slimy scavengers with four hearts that also occasionally prey on marine invertebrates, although their slow metabolism means they don't have to eat often. Being almost blind, they rely primarily on their senses of touch and smell, which is helped out by their sensing tentacles on their mouths. While hagfish have a partial cranium and a notochord, they don't actually have any vertebrae, meaning there was a debate as to whether these are vertebrates at all, although since hagfish were found to be closely related to lampreys, excluding them would make the group paraphyletic. Their gills form lens-shaped pouches, which makes them different from those of lampreys or any other extant fish, which have holobranchs.

Chondrichthyes

A sawfish (not to be confused with a saw shark). Its "saw" contains thousands of Ampullae of Lorenzini that allow it to detect the electric fields of other organisms.

Also known as the "cartilaginous fishes" (although it would be more accurate to say "jawed cartilaginous fishes" since lampreys and hagfishes also have skeletons (or just a skull in the hagfishes' case) made of cartilage), this class includes two subclasses: Elasmobranchii, which contains sharks, rays, skates, and sawfishes, and Holocephali, of which the only living representatives are the chimaeras or "ghost sharks". They likely descended from acanthodians or "spiny sharks". They first appeared in the Silurian, and many species that live today are remarkably similar to those that lived hundreds of millions of years ago.

Most of their skeletons are made of cartilage; the only part with calcium is their teeth, which tend to be by far the most common part to fossilize. Like the bony fish, chondrichthyes have paired fins, but unlike them, they lack swim bladders, meaning they must constantly be in motion. Additionally, all chondrichthyes are capable of electroreception, or the ability to sense changes in electricity of their surroundings; only a handful of modern-day bony fish like sturgeons can do the same.

Actinopterygii

The bichir, a living fossil usually found in streams in Africa but can sometimes come ashore to search for insects.

Under the superclass Osteichthyes (bony fish) and sister to the below Sarcopterygii, the "ray-finned fishes" are the most diverse class of chordates, comprising a slight majority of vertebrate species. They are separated from other kinds of fish by their lepidotrichia, which are webs of fins supported by bony spines. Additionally, unlike jawless or cartilaginous fish, they have swim bladders, which provide buoyancy and allow the fish to stay in place in the water without using energy.

There are two subclasses of ray-finned fish: Cladistia and Actinopteri. Cladistia contains the bichirs and reedfish, a group of fish that share some traits with the below lobe-finned fishes and can even live on land for short periods of time. Actinopteri can be further split into Chondrostei (sturgeons and paddlefish) and Neopterygii. Sturgeons and paddlefish both have their skeletons made partially from cartilage, and their fins look more like those of sharks than other ray-finned fishes. Finally, Neopterygii can be split into Holostei, gars and bowfins, and Teleostei, which contains sea horses, anglerfish, eels, ocean sunfish, and every other ray-finned fish you can think of. Gars and bowfins are long, tough, predatory freshwater fish that can inhabit oxygen-poor waters as they can breathe air through their gills. Teleosts are separated from the other ray-finned fish by their movable premaxilla, allowing their jaws to protrude from their mouths.

Sarcopterygii

A fossil of Eusthenopteron, an extinct genus of lobe-finned fish that is closely related to tetrapods.

The lobe-finned fishes, as these are commonly called, are distinguished by their fleshy fins, which became limbs in tetrapods. While they were more diverse in the past, there are only two extant subclasses of lobe-finned fishes: Actinistia, which contains coelacanths, and Rhipidistia, which contains lungfish and tetrapods (see below). Coelacanths are living fossils that have several traits that are unique to them among living chordates, among them an oil-filled swim bladder and incompletely formed vertebrae. Lungfish are another ancient order of fish dating back to the Devonian that can breathe air using their modified swim bladders.

Tetrapoda

An axolotl, an example of a batrachomorph tetrapod.

Finally, the group including goats, dinosaurs, monkeys, and other iconic animals. This group was considered so important that half of the six groups of animals in the original Linnaen taxonomy were tetrapods! This group was classically divided into mammals, birds, reptiles, and amphibians. However, this system was proven inaccurate for a variety of reasons. Firstly, there was still a lot of gray area with these categories; for instance, "mammal-like reptiles" like Dimetrodon were grouped in with reptiles, despite being more closely related to mammals than any extant reptiles. Secondly, birds were found to be the direct descendants of dinosaurs, despite dinosaurs being grouped in with reptiles. Thirdly, the group "amphibians" is paraphyletic, as all tetrapods have ancestors that would classically be considered to be "amphibians". This meant that this system, while being intuitive to humans, did not reflect the realities of their evolutionary relation, so a new system had to be found.

Today, tetrapoda is split into two subgroups, Batrachomorpha and Reptiliomorpha. Batrachomorpha includes all modern amphibians as well as extinct ones that are more closely related to modern-day frogs than they are to snakes or humans. Reptiliomorpha is the opposite, containing all animals related more closely to snakes than to frogs, with all modern-day reptilomorphs being in Amniota. Amniota is split into Synapsida, which contains mammals and their ancestors up to the synapsid-sauropsid split, and Sauropsida, which contains all modern-day reptiles, including birds, as well as their ancestors up to the synapsid-sauropsid split.

Evolutionary history

Development of notochord

How chordates developed from earlier deuterostomes is still a topic of debate in biology, and our understanding of the topic has shifted quite a bit in the last couple of decades alone. When looking for how the first chordates may have evolved, it is useful to look at the chordates' closest relatives (hemichordates and echinoderms) and see what they have in common using morphological, chemical, and genetic data. By doing this, and looking back to the protostomes that they likely split from, it can be inferred that the notochord and dorsal nerve cord likely developed from the ventral nerve cord, while the deuterostome mouth that the three phyla share likely developed from amphistomy, or the division of blastopores in embryos, similarly to what happens with nematodes.

Development of vertebrae

Chemical analysis suggests that the invertebrate to vertebrate transition was preceded by a whole gene duplication, which allowed the copies of the genes to take on many mutations without impeding the primary set of genes, allowing such a massive evolutionary leap. Unlike the deuterostome-chordate transition, there are some known fossils that illustrate this transition well, such as Haikouichthys. The exact placement of Haikouichthys is still a little controversial, as some consider it to be the earliest known vertebrate while others consider it to be of a more broadly-defined clade like Craniata. Nevertheless, the animal definitely has important vertebrate features like a skull and dorsal fin.

Development of jaws

During embryonic development of gnathostomes, the front pharyngeal arch develops into a jaw, while the rest of them develop into gills. This suggests that the jaw has its origin as a specialized gill. Among the earliest known fish to have jaws are the now extinct placoderms (also known as "armoured fish"), although their jaws had bony plates rather than any true "teeth".

Development of limbs

The evolution of limbs is perhaps the most important milestone in tetrapod evolution, but before tetrapods could develop limbs, their ancestors needed to develop paired fins. There have been a few competing theories on how paired fins first developed, but recently discovered fossils of Tujiaaspis, a jawless fish in the taxa Galeaspida, suggest that paired fins developed from an earlier fin on top of the animal folding over both sides of the fish and later splitting into two paired fins on opposite sides. The fin-to-limb transition is perhaps best illustrated by Tiktaalik, a lobe-finned fish right in the middle of it, and an analysis of its skeleton shows that it already had muscles propping it up in its fins and asymetries between its two pairs of fins that allowed it to better be able to walk.