Editing Ctenophora (section)

==Evolutionary history==

Despite their fragile, gelatinous bodies, [[fossil]]s thought to represent ctenophores – apparently with no tentacles but many more comb-rows than modern forms – have been found in [[Lagerstätte]]n as far back as the early [[Cambrian]], about {{ma|515}}. Nevertheless, a recent molecular phylogenetics analysis concludes that the common ancestor originated approximately 350&nbsp;million years ago ± 88&nbsp;million years ago, conflicting with previous estimates which suggests it occurred {{ma|Paleogene}} after the [[Cretaceous–Paleogene extinction event]].<ref name=Whelan2017/>

===Fossil record===

{{Further| Ctenorhabdotus capulus| Fasciculus vesanus| Xanioascus canadensis| Archaeocydippida hunsrueckiana| Paleoctenophora brasseli}}

Because of their soft, gelatinous bodies, ctenophores are extremely rare as fossils, and fossils that have been interpreted as ctenophores have been found only in [[Lagerstätte]]n, places where the environment was exceptionally suited to the preservation of soft tissue. Until the mid-1990s, only two specimens good enough for analysis were known, both members of the crown group, from the early [[Devonian]] (Emsian) [[geologic timescale|period]]. Three additional putative species were then found in the [[Burgess Shale]] and other Canadian rocks of similar age, about {{ma|505}} in the mid-[[Cambrian]] period. All three lacked tentacles but had between 24–80&nbsp;comb rows, far more than the eight typical of living species. They also appear to have had internal organ-like structures unlike anything found in living ctenophores. One of the fossil species first reported in 1996 had a large mouth, apparently surrounded by a folded edge that may have been muscular.<ref name=Morris1996/> Evidence from China a year later suggests that such ctenophores were widespread in the Cambrian, but perhaps very different from modern species – for example one fossil's comb-rows were mounted on prominent vanes.<ref>{{cite journal |last=Conway Morris |first=S. |author-link=Simon Conway Morris |year=2003 |title=The Cambrian "explosion" of metazoans and molecular biology: Would Darwin be satisfied? |journal=[[International Journal of Developmental Biology]] |volume=47 |issue=7–8 |pages=505–515 |pmid=14756326 |url=http://www.ijdb.ehu.es/fullaccess/fulltext.03078/ft505.pdf |access-date=2009-02-14 |archive-url=https://web.archive.org/web/20091224184258/http://www.ijdb.ehu.es/fullaccess/fulltext.03078/ft505.pdf
 |archive-date=2009-12-24}}</ref> The youngest fossil of a species outside the crown group is ''[[Daihuoides]]'' from the late Devonian, which belongs to a basal group that had been assumed to have gone extinct more than 140 million years earlier.<ref>{{cite journal | last1=Klug | first1=Christian | last2=Kerr | first2=Johanne | last3=Lee | first3=Michael S.Y. | last4=Cloutier | first4=Richard | year=2021 | title=A late-surviving stem-ctenophore from the Late Devonian of Miguasha (Canada) | journal=[[Scientific Reports]] | volume=11 | issue=1 | page=19039 | pmid=34561497 | pmc=8463547 | bibcode=2021NatSR..1119039K | doi=10.1038/s41598-021-98362-5 }}</ref>

The Ediacaran ''[[Eoandromeda]]'' could putatively represent a comb jelly.<ref name=Tang2011>{{Cite journal | last1=Tang | first1=F. | last2=Bengtson | first2=S. | last3=Wang | first3=Y. | last4=Wang | first4=X.L. | last5=Yin | first5=C.Y. | date=20 September 2011 | title=Eoandromeda and the origin of Ctenophora | journal=[[Evolution & Development]] | volume=13 | issue=5 | pages=408–414 | doi=10.1111/j.1525-142X.2011.00499.x | pmid=23016902| s2cid=28369431 }}</ref> It has eightfold symmetry, with eight spiral arms resembling the comblike rows of a ctenophore. If it is indeed ctenophore, it places the group close to the origin of the Bilateria.<ref>{{cite news |last1=Maxmen |first1=Amy |date=7 September 2011 |title=Ancient sea jelly shakes evolutionary tree of animals |magazine=[[Scientific American]] |url=https://www.scientificamerican.com/article/ancient-sea-jelly-makes-tree/ |access-date=21 June 2018 }}</ref>
The early Cambrian [[Sessility (zoology)|sessile]] [[frond]]-like fossil ''[[Stromatoveris]]'', from China's [[Chengjiang fauna|Chengjiang]] lagerstätte and dated to about {{ma|515}}, is very similar to [[Vendobionta]] of the preceding [[Ediacaran]] period. De-Gan Shu, [[Simon Conway Morris]], ''et al.'' found on its branches what they considered rows of cilia, used for [[filter feeding]]. They suggested that ''Stromatoveris'' was an evolutionary "aunt" of ctenophores, and that ctenophores originated from sessile animals whose descendants became swimmers and changed the cilia from a feeding mechanism to a propulsion system.<ref>{{cite journal |last1=Shu |first1=D.-G. |last2=Conway Morris |author2-link=Simon Conway Morris |first2=S. |last3=Han |first3=J. |last4=Li |first4=Y. |last5=Zhang |first5=X.L. |last6=Hua |first6=H. |last7=Zhang |first7=Z.F. |last8=Liu |first8=JN |last9=Guo |first9=J.F. |last10=Yao |first10=Y. |last11=Yasui |first11=K. |display-authors=6 |title=Lower Cambrian vendobionts from China and early diploblast evolution |journal=[[Science (journal)|Science]] |date=5 May 2006 |volume=312 |issue=5774 |pages=731–734 |doi=10.1126/science.1124565 |pmid=16675697 |bibcode=2006Sci...312..731S |s2cid=1235914 }}</ref> Other Cambrian fossils that support the idea of ctenophores having evolved from sessile forms are ''[[Dinomischus]]'', ''[[Daihua]]'', ''[[Xianguangia]]'' and ''[[Siphusauctum]]'' which also lived on the seafloor, had organic skeletons and cilia-covered tentacles surrounding their mouth, which have been found by [[cladistics|cladistic]] analysis as members of the ctenophore [[stem-group]]<ref>{{cite journal |last1=Zhao |first1=Yang |last2=Vinther |first2=Jakob |last3=Parry |first3=Luke A. |last4=Wei |first4=Fan |last5=Green |first5=Emily |last6=Pisani |first6=Davide |last7=Hou |first7=Xianguang |last8=Edgecombe |first8=Gregory D. |last9=Cong |first9=Peiyun |display-authors=6 |date=April 2019 |title=Cambrian sessile, suspension feeding stem-group Ctenophores and evolution of the comb jelly body plan |journal=[[Current Biology]] |lang=en |volume=29 |issue=7 |pages=1112–1125.e2 |doi=10.1016/j.cub.2019.02.036 |doi-access=free |pmid=30905603 |hdl=1983/40a6bcb8-a740-482c-a23c-7d563faea5c5 |hdl-access=free }}</ref><ref>{{Cite journal |last1=Zhao |first1=Yang |last2=Hou |first2=Xian-guang |last3=Cong |first3=Pei-yun |date=January 2023 |title=Tentacular nature of the 'column' of the Cambrian diploblastic ''Xianguangia sinica'' |journal=[[Journal of Systematic Palaeontology]] |lang=en |volume=21 |issue=1 |doi=10.1080/14772019.2023.2215787 |doi-access=free |bibcode=2023JSPal..2115787Z }}</ref>

520&nbsp;million-year-old Cambrian fossils also from Chengjiang in China show a now wholly extinct class of ctenophore, named "[[Scleroctenophora]]", that had a complex internal skeleton with long spines.<ref>{{cite web |last=Mindy |first=Weisberger |date=2015-07-10 |df=dmy-all |title=Ancient jellies had spiny skeletons, no tentacles |website=livescience.com |url=https://www.livescience.com/51515-ancient-comb-jellies-had-skeletons.html |lang=en}}</ref> The skeleton also supported eight soft-bodied flaps, which could have been used for swimming and possibly feeding. One form, ''[[Thaumactena]]'', had a streamlined body resembling that of [[Chaetognatha|arrow worms]] and could have been an agile swimmer.<ref name=Shu-Zhang-etal-2015/>

===Relationship to other animal groups===

The [[phylogenetic tree|phylogenetic]] relationship of ctenophores to the rest of [[Metazoa]] is very important to our understanding of the early evolution of animals and the origin of multicellularity. It has been the focus of debate for many years. Ctenophores have been purported to be the sister lineage to the [[Bilateria]],<ref name="Simonetta1991">{{cite book |editor1-first=Simon |editor1-last=Conway Morris |editor1-link=Simon Conway Morris |editor2-first=Alberto M. |editor2-last=Simonetta |year=1991 |title=The Early Evolution of Metazoa and the Significance of Problematic Taxa |publisher=Cambridge University Press |isbn=978-0-521-11158-4 |page=308 }}</ref><ref name=Nielsen1996>{{cite journal |last1=Nielsen |first1=Claus |last2=Scharff |first2=Nikolaj |last3=Eibye-Jacobsen |first3=Danny |date=April 1996 |title=Cladistic analyses of the animal kingdom |journal=[[Biological Journal of the Linnean Society]] |volume=57 |issue=4 |pages=385–410 |doi=10.1006/bijl.1996.0023 |doi-access=free|bibcode=1996BJLS...57..385N }}</ref> sister to the [[Cnidaria]],<ref name=Leuckart1848>{{cite book |last=Leuckart |first=Rudolf |year=1923 |title=Ueber die Morphologie und die Verwandtschaftsverhältnisse der wirbellosen thiere. Ein Beitrag zur Charakteristik und Classification der thierischen Formen |lang=de}}</ref><ref name=Haeckel1896>{{cite book |last=Haeckel |first=Ernst |author-link=Ernst Heinrich Philipp August Haeckel |year=1896 |title=Systematische Phylogenie der Wirbellosen Thiere |series=Invertebrata |volume=Part&nbsp;2: Des Entwurfs Einer Systematischen Stammesgeschichte |lang=de }}</ref><ref name=Hyman1940>{{cite book |last=Hyman |first=Libbie Henrietta |year=1940 |title=The Invertebrates |volume=I&nbsp;Protozoa through Ctenophora |publisher=McGraw Hill |isbn=978-0-07-031660-7}}</ref><ref name=Philippe2009>{{cite journal |last1=Philippe |first1=H. |last2=Derelle |first2=R. |last3=Lopez |first3=P. |last4=Pick |first4=K. |last5=Borchiellini |first5=C. |last6=Boury-Esnault |first6=N. |last7=Vacelet |first7=J. |last8=Renard |first8=E. |last9=Houliston |first9=E. |last10=Quéinnec |first10=E. |last11=Da Silva |first11=C. |last12=Wincker |first12=P. |last13=Le Guyader |first13=H. |last14=Leys |first14=S. |last15=Jackson |first15=D.J. |last16=Schreiber |first16=F. |last17=Erpenbeck |first17=D. |last18=Morgenstern |first18=B. |last19=Wörheide |first19=G. |last20=Manuel |first20=M.L. |display-authors=6 |date=28 April 2009 |title=Phylogenomics Revives Traditional Views on Deep Animal Relationships |journal=[[Current Biology]] |volume=19 |issue=8 |pages=706–712 |doi=10.1016/j.cub.2009.02.052 |doi-access=free |pmid=19345102 |s2cid=15282843 |bibcode=2009CBio...19..706P }}</ref> [[Placozoa]], and [[Bilateria]],<ref name=WallbergEtAl2004PhylogeneticPositionOfCtenophora>{{Cite journal |last1=Wallberg |first1=A. |last2=Thollesson |first2=M. |last3=Farris |first3=J.S. |last4=Jondelius |first4=U. |date=December 2004 |title=The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling |journal=Cladistics |volume=20 |issue=6 |pages=558–578 |doi=10.1111/j.1096-0031.2004.00041.x |pmid=34892961 |s2cid=86185156|doi-access=free }}</ref><ref name=Collins2002PhylogenyOfMedusozoa>{{cite journal |last=Collins |first=A.G. |year=2002 |title=Phylogeny of Medusozoa and the evolution of cnidarian life cycles |journal=[[Journal of Evolutionary Biology]] |volume=15 |issue=3 |pages=418–432 |s2cid=11108911 |doi=10.1046/j.1420-9101.2002.00403.x |doi-access=free }}</ref><ref name=Pick2010>{{cite journal |last1=Pick |first1=K.S. |last2=Philippe |first2=H. |last3=Schreiber |first3=F. |last4=Erpenbeck |first4=D. |last5=Jackson |first5=D.J. |last6=Wrede |first6=P. |last7=Wiens |first7=M. |last8=Alié |first8=A. |last9=Morgenstern |first9=B. |last10=Manuel |first10=M. |last11=Wörheide |first11=G. |display-authors=6 |date=September 2010 |title=Improved phylogenomic taxon sampling noticeably affects non-bilaterian relationships |journal=[[Molecular Biology and Evolution]] |volume=27 |issue=9 |pages=1983–1987 |doi=10.1093/molbev/msq089 |pmc=2922619 |pmid=20378579 }}</ref> and sister to all other animals.<ref name=Dunn2008/><ref name=Hejnol2009>{{Cite journal |last1=Hejnol |first1=A. |last2=Obst |first2=M. |last3=Stamatakis |first3=A. |last4=Ott |first4=M. |last5=Rouse |first5=G.W. |last6=Edgecombe |first6=G.D. |last7=Martinez |first7=P. |last8=Baguna |first8=J. |last9=Bailly |first9=X. |last10=Jondelius |first10=U. |last11=Wiens |first11=M. |last12=Muller |first12=W.E.G. |last13=Seaver |first13=E. |last14=Wheeler |first14=W.C. |last15=Martindale |first15=M.Q. |last16=Giribet |first16=G. |last17=Dunn |first17=C. W. |display-authors=6 |date=22 December 2009 |title=Assessing the root of bilaterian animals with scalable phylogenomic methods |journal=Proceedings of the Royal Society B: Biological Sciences |volume=276 |issue=1677 |pages=4261–4270 |doi=10.1098/rspb.2009.0896 |pmc=2817096 |pmid=19759036}}</ref>

[[Walter Garstang]] in his book [[Walter Garstang#Larval Forms and Other Zoological Verses|''Larval Forms and Other Zoological Verses'']] (''Mülleria and the Ctenophore'') even expressed a theory that [[ctenophore]]s were descended from a [[neotenic]] ''[[Mülleria]]'' larva of a [[polyclad]].<ref name="Garstang 1985">{{cite book |last=Garstang |first=Walter |author-link=Walter Garstang |chapter=Mülleria and the Ctenophore |title=Larval Forms, and Other Zoological Verses |publisher=Heinemann Educational Publishers |publication-place=Chicago |date=1985 |orig-date=1951 |isbn=978-0-226-28423-1 |page=}}</ref>

A series of studies that looked at the presence and absence of members of gene families and signalling pathways (e.g., [[homeobox]]es, [[nuclear receptor]]s, the [[Wnt signaling pathway]], and [[sodium channels]]) suggest that ctenophores are either sister to [[Cnidaria]], [[Placozoa]], and [[Bilateria]] or sister to all other animal phyla.<ref name="Ryan2010">{{Cite journal |last1=Ryan |first1=J. F. |last2=Pang |first2=K. |last3=Comparative Sequencing Program |last4=Mullikin |first4=J. C. |last5=Martindale |first5=M. Q. |last6=Baxevanis |first6=A. D. |last7=NISC Comparative Sequencing Program |year=2010 |title=The homeodomain complement of the ctenophore ''Mnemiopsis leidyi'' suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa |journal=[[EvoDevo]] |volume=1 |issue=1 |page=9 |doi=10.1186/2041-9139-1-9 |pmc=2959044 |pmid=20920347 |doi-access=free }}</ref><ref name="Reitzel2011">{{Cite journal |last1=Reitzel |first1=A. M. |last2=Pang |first2=K. |last3=Ryan |first3=J. F. |last4=Mullikin |first4=J. C. |last5=Martindale |first5=M. Q. |last6=Baxevanis |first6=A. D. |last7=Tarrant |first7=A. M. |year=2011 |title=Nuclear receptors from the ctenophore ''Mnemiopsis leidyi'' lack a zinc-finger DNA-binding domain: Lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily? |journal=[[EvoDevo]] |volume=2 |issue=1 |page=3 |doi=10.1186/2041-9139-2-3 |pmc=3038971 |pmid=21291545 |doi-access=free }}</ref><ref name="Pang2011">{{Cite journal |last1=Pang |first1=K. |last2=Ryan |first2=J. F. |last3=NISC Comparative Sequencing Program |first3=<!-- comment to keep out citation bot --> |last4=Mullikin |first4=J. C. |last5=Baxevanis |first5=A. D. |last6=Martindale |first6=M. Q. |year=2010 |title=Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore ''Mnemiopsis leidyi'' |journal=[[EvoDevo]] |volume=1 |issue=1 |page=10 |doi=10.1186/2041-9139-1-10 |pmc=2959043 |pmid=20920349 |doi-access=free }}</ref><ref name="Liebeskind2011">{{Cite journal |last1=Liebeskind |first1=B. J. |last2=Hillis |first2=D. M. |last3=Zakon |first3=H. H. |year=2011 |title=Evolution of sodium channels predates the origin of nervous systems in animals |journal=Proceedings of the National Academy of Sciences of the USA |volume=108 |issue=22 |pages=9154–9159 |bibcode=2011PNAS..108.9154L |doi=10.1073/pnas.1106363108 |pmc=3107268 |pmid=21576472 |doi-access=free}}</ref> 
Several more recent studies comparing complete sequenced genomes of ctenophores with other sequenced animal genomes support ctenophores as sister to all other animals.<ref name=Ryan2013>{{Cite journal |last1=Ryan |first1=J.F. |last2=Pang |first2=K. |last3=Schnitzler |first3=C.E. |last4=Nguyen |first4=A.-D. |last5=Moreland |first5=R.T. |last6=Simmons |first6=D.K. |last7=Koch |first7=B.J. |last8=Francis |first8=W.R. |last9=Havlak |first9=P. |last10=Smith |first10=S.A. |last11=Putnam |first11=N.H. |last12=Haddock |first12=S.H.D. |last13=Dunn |first13=C.W. |last14=Wolfsberg |first14=T.G. |last15=Mullikin |first15=J.C. |last16=Martindale |first16=M.Q. |last17=Baxevanis |first17=A.D. |display-authors=6 |date=13 December 2013 |title=The Genome of the Ctenophore ''Mnemiopsis leidyi'' and its Implications for Cell Type Evolution |journal=[[Science (journal)|Science]] |volume=342 |number=6164 |page=1242592 |doi=10.1126/science.1242592 |pmc=3920664 |pmid=24337300}}</ref><ref name=Moroz2014/><ref>{{cite journal |last1=Whelan |first1=Nathan V. |last2=Kocot |first2=Kevin M. |last3=Moroz |first3=Leonid L. |last4=Halanych |first4=Kenneth M. |date=5 May 2015 |title=Error, signal, and the placement of Ctenophora sister to all other animals |journal=Proceedings of the National Academy of Sciences of the USA |volume=112 |issue=18 |pages=5773–5778 |bibcode=2015PNAS..112.5773W |doi=10.1073/pnas.1503453112 |pmc=4426464 |pmid=25902535 |doi-access=free}}</ref><ref>{{cite journal |last1=Borowiec |first1=Marek L. |last2=Lee |first2=Ernest K. |last3=Chiu |first3=Joanna C. |last4=Plachetzki |first4=David C. |date=December 2015 |title=Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa |journal=BMC Genomics |volume=16 |issue=1 |page=987 |doi=10.1186/s12864-015-2146-4 |pmc=4657218 |pmid=26596625 |doi-access=free}}</ref> This position would suggest that neural and muscle cell types either were lost in major animal lineages (e.g., [[Porifera]] and [[Placozoa]]) or evolved independently in the ctenophore lineage.<ref name=Ryan2013/>

Other researchers have argued that the placement of Ctenophora as sister to all other animals is a statistical anomaly caused by the high rate of evolution in ctenophore genomes, and that [[Porifera]] is the earliest-diverging animal taxon instead (a "sponge sister" topology).<ref name="Pick2010" /><ref>{{cite journal |last1=Philippe |first1=Hervé |last2=Derelle |first2=Romain |last3=Lopez |first3=Philippe |last4=Pick |first4=Kerstin |last5=Borchiellini |first5=Carole |last6=Boury-Esnault |first6=Nicole |last7=Vacelet |first7=Jean |last8=Renard |first8=Emmanuelle |last9=Houliston |first9=Evelyn |last10=Quéinnec |first10=Eric |last11=da Silva |first11=Corinne |last12=Wincker |first12=Patrick |last13=Le Guyader |first13=Hervé |last14=Leys |first14=Sally |last15=Jackson |first15=Daniel J. |last16=Schreiber |first16=Fabian |last17=Erpenbeck |first17=Dirk |last18=Morgenstern |first18=Burkhard |last19=Wörheide |first19=Gert |last20=Manuel |first20=Michaël |display-authors=6 |date=April 2009 |title=Phylogenomics revives traditional views on deep animal relationships |journal=[[Current Biology]] |volume=19 |issue=8 |pages=706–712 |doi=10.1016/j.cub.2009.02.052 |doi-access=free |pmid=19345102 |s2cid=15282843 |bibcode=2009CBio...19..706P}}</ref><ref>{{cite journal |last1=Nosenko |first1=Tetyana |last2=Schreiber |first2=Fabian |last3=Adamska |first3=Maja |last4=Adamski |first4=Marcin |last5=Eitel |first5=Michael |last6=Hammel |first6=Jörg |last7=Maldonado |first7=Manuel |last8=Müller |first8=Werner E.G. |last9=Nickel |first9=Michael |display-authors=6 |date=April 2013 |title=Deep metazoan phylogeny: When different genes tell different stories |journal=[[Molecular Phylogenetics and Evolution]] |volume=67 |issue=1 |pages=223–233 |doi=10.1016/j.ympev.2013.01.010 |pmid=23353073 |bibcode=2013MolPE..67..223N}}</ref><ref>{{cite journal |last1=Pisani |first1=Davide |last2=Pett |first2=Walker |last3=Dohrmann |first3=Martin |last4=Feuda |first4=Roberto |last5=Rota-Stabelli |first5=Omar |last6=Philippe |first6=Hervé |last7=Lartillot |first7=Nicolas |last8=Wörheide |first8=Gert |display-authors=6 |date=15 December 2015 |title=Genomic data do not support comb jellies as the sister group to all other animals |journal=Proceedings of the National Academy of Sciences of the USA |volume=112 |issue=50 |pages=15402–15407 |bibcode=2015PNAS..11215402P |doi-access=free |doi=10.1073/pnas.1518127112 |pmc=4687580 |pmid=26621703}}</ref><ref name=Kapli_2020>{{cite journal |last1=Kapli |first1=Paschalia |last2=Telford |first2=Maximilian J. |date=11 December 2020 |title=Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha |journal=[[Science Advances]] |volume=6 |issue=10 |page=eabc5162 |bibcode=2020SciA....6.5162K |pmc=7732190 |doi=10.1126/sciadv.abc5162 |pmid=33310849}}</ref>They also have extremely high rates of [[Mitochondrion|mitochondrial]] evolution,<ref>{{cite journal | last1=Christianson | first1=L.M. | last2=Johnson | first2=S.B. | last3=Schultz | first3=D.T. | last4=Haddock | first4=S.H. | year=2021 | title=Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences | journal=[[Molecular Ecology Resources]] | volume=22 | issue=1 | pages=283–294 | doi=10.1111/1755-0998.13459 | pmid=34224654 | pmc=9290464}}</ref>and the smallest known RNA/protein content of the [[Mitochondrial DNA|mtDNA genome]] in animals.<ref>{{cite journal | last1=Kohn | first1=A.B. | last2=Citarella | first2=M.R. | last3=Kocot | first3=K.M. | last4=Bobkova | first4=Y.V. | last5=Halanych | first5=K.M. | last6=Moroz | first6=L.L. | year=2011 | title=Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, ''Pleurobrachia bachei'' | journal=[[Molecular Phylogenetics and Evolution]] | volume=63 | issue=1 | pages=203–207 | doi=10.1016/j.ympev.2011.12.009 | pmc=4024468 | pmid=22201557}}</ref> As such, the Ctenophora appear to be a basal [[diploblast]] clade. In agreement with the latter point, the analysis of a very large sequence alignment at the metazoan taxonomic scale (1,719&nbsp;proteins totalizing {{nobr|{{circa|{{gaps|400 000}} amino}}}} acid positions) in Simion ''et al.'' (2017) showed that ctenophores emerge as the second-earliest branching animal lineage, and sponges are sister to all other multicellular animals.<ref name=Simion2017/> Research on [[mucin]] genes shows that sponges have never had them while all other animals, including comb jellies, do.<ref>{{cite journal |last1=Bakshani |first1=Cassie R. |last2=Morales-Garcia |first2=Ana L. |last3=Althaus |first3=Mike |last4=Wilcox |first4=Matthew D. |last5=Pearson |first5=Jeffrey P. |last6=Bythell |first6=John C. |last7=Burgess |first7=J. Grant |date=4 July 2018 |title=Evolutionary conservation of the antimicrobial function of mucus: A first defence against infection |journal=[[npj Biofilms and Microbiomes]] |volume=4 |issue=1 |page=14 |doi=10.1038/s41522-018-0057-2 |pmc=6031612 |pmid=30002868}}</ref>

Despite all their differences, ctenophoran neurons share the same foundation as cnidarian neurons after findings shows that peptide-expressing neurons are probably ancestral to chemical neurotransmitters.<ref>{{cite journal |first1 =Eisuke |last1 =Hayakawa |first2 =Christine |last2 =Guzman |first3 =Osamu |last3 =Horiguchi |first4 =Chihiro |last4 =Kawano |first5 =Kurato |last5 =Mohri |first6 =Mei-Fang |last6 =Lin |first7 =Ryotaro |last7 =Nakamura |first8 =Erina |last8 =Kawai |first9 =Shinya |last9 =Komoto |first10=Kogiku |last10=Shiba |first11=Shuji |last11=Shigenobu |first12=Honoo |last12=Satake |first13=Kazuo |last13=Inaba |first14=Hiroshi |last14=Watanabe |display-authors=6 |date=October 2022 |orig-date=8 August 2022 |title=Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons |journal=[[Nature Ecology and Evolution]] |volume=6 |issue= 10|pages=1438–1448 |doi=10.1038/s41559-022-01835-7 |doi-access=free |pmid =35941202 |pmc =9525235 }}</ref>

The issue with the "rate of evolution" counterargument is that it mainly affects analyses based on the sequence of genes, not those based on gene family presence or synteny, both of which have produced results in support of the "Ctenophora sister" theory.<ref name=Schultz23/> Even with sequence-based analyses, the biases can also be corrected for: Whelan ''et al.'' (2017), using such an approach, strongly rejects the hypothesis that sponges are the sister group to all other extant animals and establishes the placement of Ctenophora as the sister group to all other animals, and disagreement with Simion ''et al.'' (2017) is explained by methodological problems in analyses in that work.<ref name="Whelan2017"/> [[Synteny]] analysis by Schultz ''et al.'' (2023) supports the same result.<ref name=Schultz23/>
Neither ctenophores nor [[Porifera|sponges]] possess [[Hypoxia-inducible factors|HIF pathways]],<ref>{{Cite journal |last1=Mills |first1=DB |last2=Francis |first2=WR |last3=Vargas |first3=S |last4=Larsen |first4=M |last5=Elemans |first5=CP |last6=Canfield |first6=DE |last7=Wörheide |first7=G |year=2018 |title=The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments |journal=eLife |volume=7 |doi=10.7554/eLife.31176 |pmc=5800844 |pmid=29402379 |doi-access=free }}</ref> their genome express only a single type of [[voltage-gated calcium channel]] unlike other animals which have three types,<ref>{{Cite journal |last1=Gauberg |first1=Julia |last2=Abdallah |first2=Salsabil |last3=Elkhatib |first3=Wassim |last4=Harracksingh |first4=Alicia N. |last5=Piekut |first5=Thomas |last6=Stanley |first6=Elise F. |last7=Senatore |first7=Adriano |date=2020-12-25 |title=Conserved biophysical features of the CaV2 presynaptic Ca2+ channel homologue from the early-diverging animal Trichoplax adhaerens |journal=The Journal of Biological Chemistry |volume=295 |issue=52 |pages=18553–18578 |doi=10.1074/jbc.RA120.015725 |doi-access=free |pmc=7939481 |pmid=33097592}}</ref> and they are the only known animal phyla that lack any true [[Hox gene]]s.<ref name=Moroz2014/> A few species from other phyla; the [[nemertea]]n pilidium larva, the larva of the [[phoronid]] species ''Phoronopsis harmeri'' and the [[acorn worm]] larva ''Schizocardium californicum'', do not depend on Hox genes in their larval development either, but need them during metamorphosis to reach their adult form.<ref>{{cite report |first=Allan |last=Spradling |date=14 May 2012 |section=Relationships of early metazoans |title=Evolution and Development |page=38 |type=presentation slides |series=Evo-Devo research program |publisher=[[Carnegie Institution for Science|Carnagie Science]] |place=Washington, DC |url=http://emb.carnegiescience.edu/sites/emb.carnegiescience.edu/files/evodevo12.pdf |via=carnegiescience.edu |access-date=8 October 2024 |archive-url=https://web.archive.org/web/20140302084415/http://emb.carnegiescience.edu/sites/emb.carnegiescience.edu/files/evodevo12.pdf |archive-date=2014-03-02 }} — technical introduction and review of genomic research, evolution, and taxonomy </ref><ref>{{cite journal | last1=Hiebert | first1=Laurel S. | last2=Maslakova | first2=Svetlana A. | year=2015 | title=Hox genes pattern the anterior-posterior axis of the juvenile but not the larva in a maximally indirect developing invertebrate, Micrura alaskensis (Nemertea) | journal=[[BMC Biology]] | volume=13 | page=23 | pmid=25888821 | pmc=4426647 | doi=10.1186/s12915-015-0133-5 | doi-access=free }}</ref><ref>{{Cite journal |last1=Gąsiorowski |first1=Ludwik |last2=Hejnol |first2=Andreas |year=2019 |title=Hox gene expression during the development of the phoronid Phoronopsis harmeri |journal=[[EvoDevo]] |volume=11 |page=2 |biorxiv=10.1101/799056 |doi=10.1186/s13227-020-0148-z |pmc=7011278 |pmid=32064072 |s2cid=208578827 |doi-access=free }}</ref> [[Innexin]] genes, which code for proteins used for [[intercellular communication]] in animals, also appears to have evolved independently in ctenophores.<ref>[https://academic.oup.com/mbe/article/40/2/msad025/7026321?login=false Independent Innexin Radiation Shaped Signaling in Ctenophores]</ref>

===Internal phylogeny ===

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{{clade
|1={{clade
 |1=[[Mertensiidae]] ([[Cydippida|cydippid]]s)
 |2={{clade
 |1=[[Platyctenida]]
 |2={{clade
 |1=[[Pleurobrachiidae]] (cydippids)
 |2={{clade
 |1=[[Lobata]]
 |2=[[Thalassocalycida]]
 |3=[[Cestida]]
 }}
 |3={{clade
 |1=[[Haeckeliidae]] (cydippids)
 |2=[[Beroida]]
 }}
 }}
 }}
 }}
}}
</div>Relationships within Ctenophora (2001).<ref name="PodarHaddockEtAl2001MolecularPhylogeneticFrameworkForCtenophora" /></div>

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{{clade
|1={{clade
 |1=''[[Euplokamis]]''
 |2={{clade
 |1=[[Platyctenida]]
 |2={{clade
 |1=[[Pleurobrachiidae]]
 |2={{clade
 |1=[[Mertensiidae]]
 |2={{clade
 |1={{clade
 |1=[[Dryodoridae]]
 |2=[[Beroida]]
 }}
 |2=[[Lobata]] <small>incl. [[Cestida]]</small>
 }}
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</div>Relationships within Ctenophora (2017).<ref name=Whelan2017/></div>

Since all modern ctenophores except the beroids have cydippid-like larvae, it has widely been assumed that their last common ancestor also resembled cydippids, having an egg-shaped body and a pair of retractable tentacles. Richard Harbison's purely morphological analysis in 1985 concluded that the cydippids are not monophyletic, in other words do not contain all and only the descendants of a single common ancestor that was itself a cydippid. Instead, he found that various cydippid [[family (biology)|families]] were more similar to members of other ctenophore [[order (biology)|orders]] than to other cydippids. He suggested that the last common ancestor of modern ctenophores was either cydippid-like or beroid-like.<ref>{{cite book|last=Harbison|first=G.R.|title=The Origins and Relationships of Lower Invertebrates|url=https://archive.org/details/originsrelations00morr|url-access=limited |editor=Conway Morris, S. |editor-link=Simon Conway Morris |editor2=George, J.D. |editor3=Gibson, R. |editor4=Platt, H.M.|publisher=Clarendon Press|year=1985 |pages=[https://archive.org/details/originsrelations00morr/page/n47 78]–100|chapter=On the classification and evolution of the Ctenophora|isbn=978-0-19-857181-0}}</ref> 

A molecular phylogeny analysis in 2001, using 26 species, including four recently discovered ones, confirmed that the cydippids are not monophyletic and concluded that the last common ancestor of modern ctenophores was cydippid-like. It also found that the genetic differences between these species were so small that the relationships between the Lobata, Cestida and Thalassocalycida remained uncertain. This suggests that the last common ancestor of modern ctenophores was relatively recent, and perhaps survived the [[Cretaceous–Paleogene extinction event]] {{ma|65.5}} while other lineages perished. When the analysis was broadened to include representatives of other phyla, it concluded that cnidarians are probably more closely related to bilaterians than either group is to ctenophores but that this diagnosis is uncertain.<ref name=PodarHaddockEtAl2001MolecularPhylogeneticFrameworkForCtenophora>{{cite journal |last1=Podar |first1=Mircea |last2=Haddock |first2=Steven H.D. |last3=Sogin |first3=Mitchell L. |last4=Harbison |first4=G. Richard |date=November 2001 |title=A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes |journal=[[Molecular Phylogenetics and Evolution]] |volume=21 |issue=2 |pages=218–230 |doi=10.1006/mpev.2001.1036 |pmid=11697917 |bibcode=2001MolPE..21..218P |citeseerx=10.1.1.384.6705 }}</ref> A  2017 study corroborates the paraphyly of [[Cydippida]] but finds that [[Lobata]] is paraphyletic with respect to [[Cestida]].<ref name=Whelan2017/>