Editing Chordate (section)

=== Overview ===

[[File:Haikouichthys4.png|thumb|''[[Haikouichthys]]'', from about {{ma|518}} in China, may be the earliest known fish.<ref name="ShuConwayMorrisHan2003Haikouichthys" />]]

There is still much ongoing differential (DNA sequence based) comparison research that is trying to separate out the simplest forms of chordates. As some lineages of the 90% of species that lack a backbone or notochord might have lost these structures over time, this complicates the classification of chordates. Some chordate lineages may only be found by DNA analysis, when there is no physical trace of any chordate-like structures.<ref>{{citation|title=Why we have a spine when over 90% of animals don't|publisher=BBC|author=Josh Gabbatiss|date=15 August 2016|url=http://www.bbc.com/earth/story/20160812-why-we-have-a-spine-when-over-90-of-animals-dont}}</ref>

Attempts to work out the evolutionary relationships of the chordates have produced several hypotheses. The current consensus is that chordates are [[monophyletic]] (meaning that the Chordata includes all and only the descendants of a single common ancestor, which is itself a chordate) and that the [[vertebrate]]s' nearest relatives are tunicates. Recent identification of two [[conserved signature indels]] (CSIs) in the proteins cyclophilin-like protein and mitochondrial inner membrane protease ATP23, which are exclusively shared by all vertebrates, [[tunicate]]s and [[cephalochordate]]s also provide strong evidence of the monophyly of Chordata.<ref name=":0" />

All of the earliest chordate [[fossil]]s have been found in the Early [[Cambrian]] [[Chengjiang fauna]], and include two species that are regarded as [[fish]], which implies that they are vertebrates. Because the fossil record of early chordates is poor, only [[molecular phylogenetics]] offers a reasonable prospect of dating their emergence. However, the use of molecular phylogenetics for dating evolutionary transitions is controversial. It has proven difficult to produce a detailed classification within the living chordates. Attempts to produce evolutionary "[[phylogenetic tree|family trees]]" shows that many of the traditional [[class (biology)|classes]] are [[paraphyletic]].{{cn|date=December 2024}}

<div style="float:right; width:auto; border:solid 1px silver; padding:2px; margin:2px">
<div style="width:auto; border:solid 1px silver; padding:5px">
{{clade
  |label1=[[Deuterostome]]s
  |1={{clade
           |1={{clade
              |label1=[[Ambulacraria|Ambulacrarians]]
              |1={{clade
                  |1=[[Hemichordate]]s <span style="{{MirrorH}}">[[File:Ptychodera flava in New Caledonia, Encyclopaedia Britannica (1911) rotated.png|45px]]</span>
                  |2=[[Echinoderm]]s [[File:Starfish (PSF).png|30px]]
                 }}
              |label2='''Chordates'''
              |2={{clade
                  |1=[[Cephalochordate]]s [[File:Branchiostoma cultellus.jpg|75px]]
                  |label2=[[Olfactores]]
                  |2={{clade
                       |1=[[Tunicate]]s <span style="{{MirrorH}}">[[File:PSM V44 D080 Salpa.jpg|35px]]</span>
                       |2=[[Vertebrate]]s [[File:Ichthyostega_BW_(flipped).jpg|70px]]
                     }}
                 }}
             }}
         }}
}}
</div>Diagram of the [[cladogram|evolutionary relationships]] of chordates<ref name="Ruppert2005"/></div>

While this has been well known since the 19th century, an insistence on only monophyletic taxa has resulted in vertebrate classification being in a state of flux.<ref>{{cite journal|last= Holland|first=N. D.|date= 22 November 2005|title= Chordates|journal= Curr. Biol. |volume=15|issue= 22|pages=R911–4|doi=10.1016/j.cub.2005.11.008|pmid=16303545|doi-access=free|bibcode=2005CBio...15.R911H }}</ref>

The majority of animals more complex than [[jellyfish]] and other [[cnidarians]] are split into two groups, the [[protostome]]s and [[deuterostome]]s, the latter of which contains chordates.<ref name=Erwin20002>{{cite journal|author1=Erwin, Douglas H. |author2=Eric H. Davidson |date= 1 July 2002 |title=The last common bilaterian ancestor|journal=Development|volume=129|pages=3021–3032|url=http://dev.biologists.org/cgi/content/full/129/13/3021|pmid=12070079|issue=13|doi=10.1242/dev.129.13.3021 }}</ref> It seems very likely the {{ma|555|million-year-old}} ''[[Kimberella]]'' was a member of the protostomes.<ref name=Fedonkin2007>{{The Rise and Fall of the Ediacaran Biota|chapter=New data on ''Kimberella'', the Vendian mollusc-like organism (White sea region, Russia): palaeoecological and evolutionary implications |author=Fedonkin, M.A. |author2=Simonetta, A |author3=Ivantsov, A.Y.|pages=157–179|doi=10.1144/SP286.12}}</ref><ref name=Butterfield2006>{{cite journal|author=Butterfield, N.J.|date=December 2006|title=Hooking some stem-group "worms": fossil lophotrochozoans in the Burgess Shale|journal=BioEssays|volume=28|issue=12|pages=1161–6|doi=10.1002/bies.20507|pmid=17120226|s2cid=29130876}}</ref> If so, this means the protostome and deuterostome lineages must have split some time before ''Kimberella'' appeared—at least {{ma|558}}, and hence well before the start of the Cambrian {{ma|Cambrian}}.<ref name=Erwin20002 /> Three enigmatic species that are possible very early tunicates, and therefore deuterostomes, were also found from the [[Ediacaran]] period – ''[[Ausia (animal)|Ausia fenestrata]]'' from the Nama Group of [[Namibia]], the sac-like ''[[Yarnemia|Yarnemia ascidiformis]]'', and one from a second new ''Ausia''-like genus from the Onega Peninsula of northern [[Russia]], ''[[Burykhia|Burykhia hunti]]''. Results of a new study have shown possible affinity of these Ediacaran organisms to the ascidians.<ref name=Vickers-Rich>Vickers-Rich P. (2007). "Chapter 4. The Nama Fauna of Southern Africa". In: Fedonkin, M. A.; Gehling, J. G.; Grey, K.; Narbonne, G. M.; Vickers-Rich, P. "The Rise of Animals: Evolution and Diversification of the Kingdom Animalia", Johns Hopkins University Press. pp. 69–87</ref><ref name=Oslo_2008>Fedonkin, M. A.; Vickers-Rich, P.; Swalla, B.; Trusler, P.; Hall, M. (2008). "A Neoproterozoic chordate with possible affinity to the ascidians: New fossil evidence from the Vendian of the White Sea, Russia and its evolutionary and ecological implications". HPF-07 Rise and fall of the Ediacaran (Vendian) biota. International Geological Congress - Oslo 2008.</ref> ''Ausia'' and ''Burykhia'' lived in shallow coastal waters slightly more than 555 to 548 million years ago, and are believed to be the oldest evidence of the chordate lineage of metazoans.<ref name=Oslo_2008/> The Russian Precambrian fossil ''[[Yarnemia]]'' is identified as a tunicate only tentatively, because its fossils are nowhere near as well-preserved as those of ''Ausia'' and ''Burykhia'', so this identification has been questioned.{{cn|date=December 2024}} 

[[File:BlueWhaleSkeleton.jpg|thumb|A skeleton of the [[blue whale]], the largest animal, extant or extinct, ever discovered. Mounted outside the Long Marine Laboratory at the [[University of California, Santa Cruz]]. The largest blue whale ever reliably recorded measured 98ft (30m) long.]]
[[File:Peregrine Falcon 12.jpg|thumb|A [[peregrine falcon]], the world's fastest animal. Peregrines use gravity and aerodynamics to achieve their top speed of around 242mph (390km/h), as opposed to locomotion.]] 
Fossils of one major deuterostome group, the [[echinoderm]]s (whose modern members include [[starfish]], [[sea urchin]]s and [[crinoid]]s), are quite common from the start of the Cambrian, 542 million years ago.<ref name="Bengtson2004">{{cite journal |author=Bengtson, S. |editor1=Lipps, J.H. |editor2=Waggoner, B.M. |title=Early skeletal fossils |year=2004 |journal=The Paleontological Society Papers: Neoproterozoic – Cambrian Biological Revolutions |volume=10 |pages=67–78 |url=http://www.nrm.se/download/18.4e32c81078a8d9249800021554/Bengtson2004ESF.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://www.nrm.se/download/18.4e32c81078a8d9249800021554/Bengtson2004ESF.pdf |archive-date=2022-10-09 |url-status=live |access-date=2008-07-18|doi=10.1017/S1089332600002345 }}</ref> The Mid Cambrian fossil ''[[Rhabdotubus johanssoni]]'' has been interpreted as a [[pterobranch]] hemichordate.<ref>{{cite journal|author1=Bengtson, S. |author2=Urbanek, A. |date=October 2007|title=''Rhabdotubus'', a Middle Cambrian rhabdopleurid hemichordate |journal=Lethaia|volume=19 |issue=4| pages=293–308 |doi=10.1111/j.1502-3931.1986.tb00743.x|url=http://www3.interscience.wiley.com/journal/120025616/abstract|archive-url=https://archive.today/20121216150238/http://www3.interscience.wiley.com/journal/120025616/abstract|archive-date=2012-12-16}}</ref> Opinions differ about whether the [[Chengjiang fauna]] fossil ''[[Yunnanozoon]]'', from the earlier Cambrian, was a hemichordate or chordate.<ref name="ChenHangLi1996">{{cite journal |author=Shu, D. |author2=Zhang, X. |author3=Chen, L. |date=April 1996|title=Reinterpretation of Yunnanozoon as the earliest known hemichordate|journal=Nature| volume=380|pages=428–430|doi=10.1038/380428a0 |issue=6573 |bibcode=1996Natur.380..428S |s2cid=4368647}}</ref><ref name="ChenHangLi1999">{{cite journal|author1=Chen, J-Y. |author2=Hang, D-Y. |author3=Li, C.W. |title=An early Cambrian craniate-like chordate|journal=Nature |pages=518–522 |date=December 1999 |doi=10.1038/990080 |volume=402|issue=6761 |bibcode=1999Natur.402..518C|s2cid=24895681 }}</ref> Another 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.<ref name="ChenHangLi1999" /> ''[[Haikouichthys]]'' and ''[[Myllokunmingia]]'', also from the Chengjiang fauna, are regarded as [[fish]].<ref name="ShuConwayMorrisHan2003Haikouichthys">{{cite journal|author1=Shu, D-G. |author2=Conway Morris, S. |author3=Han, J. |name-list-style=amp |title=Head and backbone of the Early Cambrian vertebrate Haikouichthys|journal=Nature |volume=421|pages=526–529 |date=January 2003|doi=10.1038/nature01264 |pmid=12556891|issue=6922|bibcode=2003Natur.421..526S|s2cid=4401274 }}</ref><ref>{{cite journal |author1=Shu, D-G. |author2=Conway Morris, S. |author3=Zhang, X-L. |title=Lower Cambrian vertebrates from south China |journal=Nature |volume=402 |date=November 1999 |url=http://www.bios.niu.edu/davis/bios458/Shu1.pdf |access-date=2008-09-23 |doi=10.1038/46965 |page=42 |issue=6757 |bibcode=1999Natur.402...42S |s2cid=4402854 |archive-url=https://web.archive.org/web/20090226122732/http://www.bios.niu.edu/davis/bios458/Shu1.pdf |archive-date=26 February 2009}}</ref> ''[[Pikaia]]'', discovered much earlier (1911) but from the Mid Cambrian [[Burgess Shale]] (505 Ma), is also regarded as a primitive chordate.<ref>{{cite journal |author1=Shu, D-G. |author2=Conway Morris, S. |author3=Zhang, X-L. |title=A ''Pikaia''-like chordate from the Lower Cambrian of China|journal=Nature|volume=384 |pages= 157–158 |date=November 1996|doi=10.1038/384157a0 |issue=6605|bibcode=1996Natur.384..157S|s2cid=4234408 }}</ref> On the other hand, fossils of early chordates are very rare, since invertebrate chordates have no bones or teeth, and only one has been reported for the rest of the Cambrian.<ref name="ConwayMorris2008Metaspriggina">{{cite journal |last=Conway Morris |first=S.|year=2008 |title=A Redescription of a Rare Chordate,'' Metaspriggina walcotti'' Simonetta and Insom, from the Burgess Shale (Middle Cambrian), British Columbia, Canada |journal=Journal of Paleontology |volume=82 |issue=2|pages=424–430|doi=10.1666/06-130.1|bibcode=2008JPal...82..424M |s2cid=85619898|url=http://jpaleontol.geoscienceworld.org/cgi/content/extract/82/2/424|access-date=2009-04-28}}</ref> The best known and earliest unequivocally identified Tunicate is ''[[Shankouclava|Shankouclava shankouense]]'' from the Lower Cambrian [[Maotianshan Shale]] at Shankou village, Anning, near [[Kunming]] ([[Northern and southern China|South China]]).<ref name=Jun-Yuan2003>{{cite journal|author1=Chen, Jun-Yuan |author2=Huang, Di-Ying |author3=Peng, Qing-Qing |author4=Chi, Hui-Mei |author5=Wang,Xiu-Qiang |author6=Feng, Man |year=2003 |title=The first tunicate from the Early Cambrian of South China |journal=[[Proceedings of the National Academy of Sciences]] |volume=100 |pmid=12835415 |issue=14 |pages=8314–8318 |pmc=166226 |doi=10.1073/pnas.1431177100 |bibcode=2003PNAS..100.8314C |doi-access=free }}</ref>

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, [[embryology|embryological]], and paleontological data have produced different "family trees". Some closely linked chordates and hemichordates, but that idea is now rejected.<ref name="Ruppert2005" /> Combining such analyses with data from a small set of [[ribosome]] [[RNA]] genes eliminated some older ideas, but opened up the possibility that tunicates (urochordates) are "basal deuterostomes", surviving members of the group from which echinoderms, hemichordates and chordates evolved.<ref name="WinchellSullivanCameronSwallaMallatt2002">{{cite journal |author1=Winchell, C. J. |author2=Sullivan, J. |author3=Cameron, C. B. |author4=Swalla, B. J. |author5=Mallatt, J. |name-list-style=amp | title=Evaluating Hypotheses of Deuterostome Phylogeny and Chordate Evolution with New LSU and SSU Ribosomal DNA Data| journal=Molecular Biology and Evolution |volume=19 |pages=762–776 |date=1 May 2002 | pmid=11961109| issue=5 |doi=10.1093/oxfordjournals.molbev.a004134|doi-access=free }}</ref> Some researchers believe that, within the chordates, craniates are most closely related to cephalochordates, but there are also reasons for regarding tunicates (urochordates) as craniates' closest relatives.<ref name="Ruppert2005" /><ref name="BlairHedges2005">{{cite journal |author1=Blair, J. E. |author2=Hedges, S. B.| title=Molecular Phylogeny and Divergence Times of Deuterostome Animals |journal=Molecular Biology and Evolution|date=November 2005 |volume=22|issue=11 |pages=2275–2284 |doi=10.1093/molbev/msi225| pmid=16049193|doi-access=free}}</ref>

Since early chordates have left a poor fossil record, attempts have been made to calculate the key dates in their evolution by [[molecular phylogenetics]] techniques—by analyzing biochemical differences, mainly in RNA. One such study suggested that deuterostomes arose before {{ma|900}} and the earliest chordates around {{ma|896}}.<ref name="BlairHedges2005"/> However, molecular estimates of dates often disagree with each other and with the fossil record,<ref name="BlairHedges2005" /> and their assumption that the [[molecular clock]] runs at a known constant rate has been challenged.<ref name="Ayala1999MolClockMirages">{{cite journal |author= Ayala, F. J. |date=January 1999 |title=Molecular clock mirages |journal=[[BioEssays]] |volume=21 |issue=1 |pages=71–75 |doi=10.1002/(SICI)1521-1878(199901)21:1<71::AID-BIES9>3.0.CO;2-B |pmid=10070256}}</ref><ref name="SchwartzMaresca20006DoMolClocksRun">{{cite journal |author1=Schwartz, J. H. |author2=Maresca, B. |date=December 2006 |title=Do Molecular Clocks Run at All? A Critique of Molecular Systematics |journal=Biological Theory |volume=1 |pages=357–371|doi=10.1162/biot.2006.1.4.357 |issue=4|citeseerx=10.1.1.534.4060|s2cid=28166727 }}</ref>

Traditionally, Cephalochordata and Craniata were grouped into the proposed clade "Euchordata", which would have been the sister group to Tunicata/Urochordata. More recently, Cephalochordata has been thought of as a sister group to the "Olfactores", which includes the craniates and tunicates. The matter is not yet settled.{{cn|date=December 2024}}

A specific relationship between vertebrates and [[tunicate]]s is also strongly supported by two CSIs found in the proteins predicted exosome complex RRP44 and serine palmitoyltransferase, that are exclusively shared by species from these two subphyla but not [[cephalochordate]]s, indicating vertebrates are more closely related to tunicates than cephalochordates.<ref name=":0" />