Talk:Chordate/sandbox

Chordates (phylum Chordata) are a group of animals that includes the vertebrates, together with several closely related invertebrates. They are united by having, at some time in their life cycle, a notochord, a hollow dorsal nerve cord, pharyngeal slits, an endostyle, and a post-anal tail. The phylum Chordata consists of three subphyla: Urochordata, represented by tunicates; Cephalochordata, represented by lancelets;and Craniata, which includes Vertebrata. The Hemichordata have been presented as a fourth chordate subphylum, but they are now usually treated as a separate phylum. Urochordate larvae have a notochord and a nerve cord but these are lost in adulthood. Cephalochordates have a notochord and a nerve cord but no brain or specialist sense organs, and a very simple circulatory system. Craniates are the only sub-phylum whose members have skulls. In all craniates except for Hagfish, the dorsal hollow nerve cord has been surrounded with cartilaginous or bony vertebrae and the notochord generally reduced; hence hagfish are not regarded as vertebrates. The chordates and three sister phyla, the Hemichordata, the Echinodermata and the Xenoturbellida, make up the deuterostomes, one of the two superphyla which encompass all fairly complex animals.

Attempts to work out the evolutionary relationships of the chordates have produced several hypotheses, but the current consensus is that chordates are monophyletic, in other words contain all and only the descendants of a single common ancestor which is itself a chordate, and that craniates' nearest relatives are cephalochordates. All of the earliest chordate fossils have been found in the Early Cambrian Chengjiang fauna, and include two species that are regarded as fish, which implies that these are vertebrates. Because the fossil record of chordates is poor, only molecular phylogenetics offers a reasonable prospect of dating their emergence. However the use of molecular phylogeneticss for dating evolutionary transitions is controversial.

It has also proved difficult to produce a detailed classification within the living chordates. Attempts to produce evolutionary "family trees" give results that differ from traditional classes because several of those classes are not monophyletic. As a result vertebrate classification is in a state of flux.

Definition
Chordates form a phylum - a grouping of animals with a shared bodyplan - defined by having at some stage in their lives all of the following:
 * a notochord, in other words a fairly stiff rod of cartilage that extends along the inside of the body and helps the animal to swim by flexing its tail.
 * a dorsal neural tube, which develops into the spinal cord, the main commmunications trunk of the nervous system, in fish and other vertebrates
 * pharyngeal slits. The pharynx is the part of the throat immediately behind the mouth. In fish the slits are modified to form gills, but in other chordates they are part of a filter feeding system that extracts particles of food from the water in which the animals live.
 * a muscular tail that extends backwards behind the anus.
 * an endostyle. This groove in the ventral wall of the pharynx produces mucus to gather food particles, helps in transporting food to the esophagus, and stores iodine. It may be a precursor of the vertebrate thyroid gland.

Sub-divisions
There are three major groupings within the chordates:

Craniates have distinct skulls. Michael J. Benton comments that "craniates are characterized by their heads, just as chordates, or possibly all deuterostomes, are by their tails." Most are vertebrates, in which the notochord is relaced by the spinal column. This consists of a series of bony or cartilaginous cylindrical vertebrae, generally with neural arches that protect the spinal chord and with projections that link the vertebrae. Hagfish have incomplete braincases and no vertebrae, and are therefore not regarded as vertebrates, but as members of the craniates, the group from which vertebrates are thought to have evolved. The position of lampreys is ambiguous. They have complete braincases and rudimentary vertebrae, and therefore may be regarded as vertebrates and true fish. However molecular phylogenetics, which uses biochemical features to classify organisms, has produced both results that group them with vertebrates and others that group them with hagfish.

Cephalochordates are small, "vaguely fish-shaped" animals that lack brains, clearly-defined heads and specialized sense organs. These burrowing filter-feeders may be either the closest living relatives of craniates or surviving members of the group from which all other chordates evolved.

Most tunicates appear as adults in two major forms, both of which are bags of jelly that lack the standard features of chordates: "sea squirts" are sessile and consist mainly of water pumps and filter feeding apparatus; salps float in mid-water, feeding on plankton, and have a two-generation cycle in which one generation is solitary and the next forms chain-like colonies. However all tunicate larvae have the standard chordate features, including long, tadpole-like tails; they also have rudimentary brains, light sensors and tilt sensors. The third main group of tunicates, Appendicularia (also known as Larvacea) retain tadpole-like shapes and active swimming all their lives, and were for a long time regarded as larvae of sea squirts or salps. Because of their larvae's long tails tunicates are also called urochordates ("tail chordates").

Closest non-chordate relatives
Hemichordates ("half chordates") have some features similar to those of chordates: branchial openings that open into the pharynx and look rather like gill slits; stomochords, similar in composition to notochords but running in a circle round the "collar", which is ahead of the mouth; and a dorsal nerve cord – but also a smaller ventral nerve cord. There are two living groups of hemichordates. The solitary enteropneusts, commonly known as "acorn worms", have long probosces and worm-like bodies with up to 200 branchial slits, are up to 2.5 m long, and burrow though seafloor sediments. Pterobranchs are colonial animals, often less than 1 mm long individually, whose dwellings are inter-connected. Each filter feeds by means of a pair of branched tentacles, and has a short, shield-shaped proboscis. The extinct graptolites, colonial animals whose fossils look tiny hacksaw blades, lived in tubes similar to those of pterobranchs.

Echinoderms differ from chordates' other relatives in three conspicuous ways: instead of having bilateral symmetry they have radial symmetry, like wheels; their bodies are supported by skeletons made of calcite, a material not used by chordates, and these skeleton enclose their bodies but are also covered by a thin skin; they have tube feet. The feet are powered by another unique feature of echinoderms, a water vascular system of canals that also function as a "lung" and are surrounded by muscles that act as pumps. Crinoids look rather like flowers, and use their feather-like arms to filter food particles out of the water; most live anchored to rocks, but a few can move very slowly. Other echinoderms are mobile and take a variety of body shapes, for example starfish, sea urchins and sea cucumbers.

Origins
The majority of animals more complex than jellyfish and other Cnidarians are split into two groups, the protostomes and deuterostomes, and chordates are deuterostomes. It seems very likely that  Kimberella was a member of the protostomes. If so, this means that the protostome and deuterostome lineages must have split some time before Kimberella appeared - at least, and hence well before the start of the Cambrian. The Ediacaran fossil Ernettia, from about, may represent a deuterostome animal.

Fossils of one major deuterostome group, the echinoderms (whose modern members include starfish, sea urchins and crinoids) are quite common from the start of the Cambrian,. The Mid Cambrian fossil Rhabdotubus johanssoni has been interpreted as a pterobranch hemichordate. Opinions differ about whether the Chengjiang fauna fossil Yunnanozoon, from the earlier Cambrian, was a hemichordate or chordate. Another Chenjiang fossil, Haikouella lanceolata, also from the Chengjiang fauna, is interpreted as a chordate and possibly a craniate, as it shows signs of a heart, arteries, gill filaments, a tail, a neural chord with a brain at the front end, and possibly eyes - although it also had short tentacles round its mouth. Haikouichthys and Myllokunmingia, also from the Chenjiang fauna, are regarded as fish. Pikaia, discovered much earlier but from the Mid Cambrian Burgess Shale, is also regarded as a primitive chordate. On the other hand fossils of early chordates are very rare, since non-vertebrate chordates have no bones or teeth, and none have been reported for the rest of the Cambrian.

A consensus family tree of the chordates The evolutionary relationships between the chordate groups and between chordates as a whole and their closest deuterostome relatives have been debated since 1890. Studies based on anatomical, embryological, and paleontological data have produced different "family trees". Some closely linked chordates and hemichordates, but that idea is now rejected. Combining such analyses with data from a small set of ribosome RNA genes eliminated some older ideas, but open the possibility that tunicates (urochordates) are "basal deuterostomes", in other words surviving members of the group from which echinoderms, hemichordates and chordates evolved. Most researchers agree that, within the chordates, craniates are most closely related to cephalochordates, but there also reasons for regarding tunicates (urochordates) as craniates' closest relatives. One other phylum, Xenoturbellida, appears to be basal within the deuterostomes, in other words closer to the original deuterostomes than to the chordates, echinoderms and hemichordates.

Since chordates have left a poor fossil record, attempts have been made to calculate the key dates in their evolution by molecular phylogenetics techniques, in other words by analysing biochemical differences, mainly in RNA. One such study suggested that deuterostomes arose before and the earliest chordates around. However molecular estimates of dates often disagree with each other and with the fossil record, and their assumption that the molecular clock runs at a known constant rate has been challenged.

Taxonomy
The following schema is from the third edition of Vertebrate Palaeontology. While it is structured so as to reflect evolutionary relationships (similar to a cladogram), it also retains the traditional ranks used in Linnaean taxonomy.


 * Phylum Chordata
 * Subphylum Tunicata (Urochordata)— (tunicates, 3,000 species)
 * Subphylum Cephalochordata (Acraniata)— (lancelets, 30 species)
 * Subphylum Vertebrata (Craniata) (vertebrates — animals with backbones; 57,674 species)
 * Class 'Agnatha'Paraphyletic (jawless vertebrates; 100+ species)
 * Subclass Myxinoidea (hagfish; 65 species)
 * Subclass Petromyzontida (Lampreys)
 * Subclass Conodonta
 * Subclass Pteraspidomorphi (Paleozoic jawless fish)
 * Order Anaspida
 * Order Thelodonti (Paleozoic jawless fish)
 * Infraphylum Gnathostomata (jawed vertebrates)
 * Class Placodermi (Paleozoic armoured forms)
 * Class Chondrichthyes (cartilaginous fish; 900+ species)
 * Class Acanthodii (Paleozoic "spiny sharks")
 * Class Osteichthyes (bony fishes; 30,000+ species)
 * Subclass Actinopterygii (ray-finned fish; about 30,000 species)
 * Subclass Sarcopterygii (lobe-finned fish)
 * Superclass Tetrapoda (four-legged vertebrates; 18,000+ species)
 * Class Amphibia (amphibians; 6,000 species)
 * Series Amniota (with amniotic egg)
 * Class Sauropsida — (reptiles; 8,225+ species)
 * Class Aves (birds; 8,800–10,000 species)
 * Class Synapsida (mammal-like "reptiles"; 4,500+ species)
 * Class Mammalia (mammals; 5,800 species)

Phylogeny
Notes:
 * Lines show probable evolutionary relationships, including extinct taxa, which are denoted with a dagger, †. Some are invertebrates. Chordata is a phylum.
 * The positions (relationships) of the Lancelet, Tunicate, and Craniata clades are as reported in the scientific journal Nature.