Editing Sponge (section)

=== Relationships to other animal groups ===

{{cladogram
 |title=Simplified family tree showing [[Calcarea|calcareous sponges]] as closest to more complex animals<ref name="Borchiellini_2001"/>
 |clades={{clade
     |label1=[[Opisthokonta]]
     |1={{clade
       |1=[[Fungi]]
       |2={{clade
        |1=[[Choanoflagellate]]s
        |label2=[[Metazoa]]
        |2={{clade
          |1=[[Glass sponge]]s
          |2={{clade
           |1=[[Demosponge]]s
           |2={{clade
             |1=[[Calcarea|Calcareous sponges]]
             |label2=[[Eumetazoa]]
             |2={{clade
              |1=[[Ctenophora|Comb jellies]]
              |2={{clade
                |1=[[Placozoa]]
                |2={{clade
                 |1=[[Cnidaria]]<br />(jellyfish, etc.)
                 |2=other [[metazoa]]ns
                 }}
                }}
              }}
             }}
           }}
          }}
        }}
       }}
     }}
}}
{{cladogram
 |title=Simplified family tree showing [[Homoscleromorpha]] as closest to more complex animals<ref name="Sperling_2007"/>
 |clades={{clade
     |label1=[[Eukaryotes]]
     |1={{clade
       |1=[[Plant]]s
       |2=[[Fungi]]
       |label3=[[Metazoa]]
       |3={{clade
        |1=Most [[demosponge]]s
        |2={{clade
          |1=[[Calcarea|Calcareous sponges]]
          |2={{clade
           |1=[[Homoscleromorpha]]
           |label2=[[Eumetazoa]]
           |2={{clade
             |1=[[Cnidaria]]<br />(jellyfish, etc.)
             |2=other [[metazoa]]ns
             }}
           }}
          }}
        }}
       }}
     }}
}}
In the 1990s, sponges were widely regarded as a [[monophyletic]] group, all of them having descended from a [[last universal common ancestor|common ancestor]] that was itself a sponge, and as the "sister-group" to all other [[animals|metazoans]] (multi-celled animals), which themselves form a monophyletic group. On the other hand, some 1990s analyses also revived the idea that animals' nearest evolutionary relatives are [[choanoflagellate]]s, single-celled organisms very similar to sponges' [[choanocytes]] – which would imply that most Metazoa evolved from very sponge-like ancestors and therefore that sponges may not be monophyletic, as the same sponge-like ancestors may have given rise both to modern sponges and to non-sponge members of Metazoa.<ref name="Borchiellini_2001">{{cite journal |last1=Borchiellini |first1=C. |last2=Manuel |first2=M. |last3=Alivon |first3=E. |last4=Boury-Esnault |first4=N. |last5=Vacelet |first5=J. |last6=Le Parco |first6=Y. |title=Sponge paraphyly and the origin of Metazoa |journal=Journal of Evolutionary Biology |volume=14 |issue=1 |pages=171–179 |date=January 2001 |pmid=29280585 |doi=10.1046/j.1420-9101.2001.00244.x |doi-access=free }}</ref>

Analyses since 2001 have concluded that [[Eumetazoa]] (more complex than sponges) are more closely related to particular groups of sponges than to other sponge groups. Such conclusions imply that sponges are not monophyletic, because the [[most recent common ancestor|last common ancestor]] of all sponges would also be a direct ancestor of the Eumetazoa, which are not sponges. A study in 2001 based on comparisons of [[ribosome]] [[DNA]] concluded that the most fundamental division within sponges was between [[glass sponge]]s and the rest, and that Eumetazoa are more closely related to [[Calcarea|calcareous sponges]] (those with calcium carbonate spicules) than to other types of sponge.<ref name="Borchiellini_2001"/> In 2007, one analysis based on comparisons of [[RNA]] and another based mainly on comparison of spicules concluded that demosponges and glass sponges are more closely related to each other than either is to the calcareous sponges, which in turn are more closely related to Eumetazoa.<ref name="Müller_2007"/><ref>{{cite journal |last1=Medina |first1=Mónica |last2=Collins |first2=Allen G. |last3=Silberman |first3=Jeffrey D. |last4=Sogin |first4=Mitchell L. |title=Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=98 |issue=17 |pages=9707–12 |date=August 2001 |pmid=11504944 |pmc=55517 |bibcode=2001PNAS...98.9707M |doi=10.1073/pnas.171316998 |doi-access=free }}</ref>

Other anatomical and biochemical evidence links the Eumetazoa with [[Homoscleromorpha]], a sub-group of demosponges. A comparison in 2007 of [[cell nucleus|nuclear]] [[DNA]], excluding glass sponges and [[Ctenophora|comb jellies]], concluded that:
* [[Homoscleromorpha]] are most closely related to Eumetazoa;
* calcareous sponges are the next closest;
* the other demosponges are evolutionary "aunts" of these groups; and
* the [[chancelloriidae|chancelloriids]], bag-like animals whose fossils are found in [[Cambrian]] rocks, may be sponges.<ref name="Sperling_2007">{{cite journal |last1=Sperling |first1=E. A. |last2=Pisani |first2=D. |last3=Peterson |first3=K. J. |year=2007 |title=Poriferan paraphyly and its implications for Precambrian paleobiology |journal=Journal of the Geological Society of London |volume=286 |issue=1 |pages=355–368 |doi=10.1144/SP286.25 |bibcode=2007GSLSP.286..355S |s2cid=34175521 |url=http://www.dartmouth.edu/~peterson/Sperling,%20Pisani%20and%20Peterson.pdf |url-status=dead |access-date=2008-11-04 |archive-url=https://web.archive.org/web/20090509061759/http://www.dartmouth.edu/~peterson/Sperling,%20Pisani%20and%20Peterson.pdf |archive-date=May 9, 2009}}</ref>
The [[sperm]] of Homoscleromorpha share features with the sperm of Eumetazoa, that sperm of other sponges lack. In both Homoscleromorpha and Eumetazoa layers of cells are bound together by attachment to a carpet-like basal membrane composed mainly of "typ&nbsp;IV" [[collagen]], a form of collagen not found in other sponges – although the [[spongin]] fibers that reinforce the mesohyl of all demosponges is similar to "type&nbsp;IV" collagen.<ref name="Exposito_2002">{{cite journal |last1=Exposito |first1=Jean-Yves |last2=Cluzel |first2=Caroline |last3=Garrone |first3=Robert |last4=Lethias |first4=Claire |title=Evolution of collagens |journal=The Anatomical Record |volume=268 |issue=3 |pages=302–16 |date=November 2002 |pmid=12382326 |doi=10.1002/ar.10162 |doi-access=free }}</ref>

[[File:Bathocyroe fosteri.jpg|thumb|left|A [[ctenophora|comb jelly]] ]]
The analyses described above concluded that sponges are closest to the ancestors of all Metazoa, of all multi-celled animals including both sponges and more complex groups. However, another comparison in 2008 of 150&nbsp;genes in each of 21&nbsp;genera, ranging from fungi to humans but including only two species of sponge, suggested that [[ctenophora|comb jellies]] ([[ctenophora]]) are the most basal lineage of the Metazoa included in the sample.<ref name="Dunn_2008">{{cite journal |last1=Dunn |first1=Casey W. |last2=Hejnol |first2=Andreas |last3=Matus |first3=David Q. |last4=Pang |first4=Kevin |last5=Browne |first5=William E. |last6=Smith |first6=Stephen A. |last7=Seaver |first7=Elaine |last8=Rouse |first8=Greg W. |last9=Obst |first9=Matthias |last10=Edgecombe |first10=Gregory D. |last11=Sørensen |first11=Martin V. |last12=Haddock |first12=Steven H. D. |last13=Schmidt-Rhaesa |first13=Andreas |last14=Okusu |first14=Akiko |last15=Kristensen |first15=Reinhardt Møbjerg |last16=Wheeler |first16=Ward C. |last17=Martindale |first17=Mark Q. |last18=Giribet |first18=Gonzalo |display-authors=6 |title=Broad phylogenomic sampling improves resolution of the animal tree of life |journal=Nature |volume=452 |issue=7188 |pages=745–9 |date=April 2008 |pmid=18322464 |doi=10.1038/nature06614 |bibcode=2008Natur.452..745D |s2cid=4397099 }}</ref><ref name="Hejnol_2009">{{cite journal |last1=Hejnol |first1=Andreas |last2=Obst |first2=Matthias |last3=Stamatakis |first3=Alexandros |last4=Ott |first4=Michael |last5=Rouse |first5=Greg W. |last6=Edgecombe |first6=Gregory D. |last7=Martinez |first7=Pedro |last8=Baguñà |first8=Jaume |last9=Bailly |first9=Xavier |last10=Jondelius |first10=Ulf |last11=Wiens |first11=Matthias |last12=Müller |first12=Werner E. G. |last13=Seaver |first13=Elaine |last14=Wheeler |first14=Ward C. |last15=Martindale |first15=Mark Q. |last16=Giribet |first16=Gonzalo |last17=Dunn |first17=Casey W. |display-authors=6 |title=Assessing the root of bilaterian animals with scalable phylogenomic methods |journal=Proceedings. Biological Sciences |volume=276 |issue=1677 |pages=4261–70 |date=December 2009 |pmid=19759036 |pmc=2817096 |doi=10.1098/rspb.2009.0896 }}</ref><ref name="Ryan_2013">{{cite journal |last1=Ryan |first1=Joseph F. |last2=Pang |first2=Kevin |last3=Schnitzler |first3=Christine E. |last4=Nguyen |first4=Anh-Dao |last5=Moreland |first5=R. Travis |last6=Simmons |first6=David K. |last7=Koch |first7=Bernard J. |last8=Francis |first8=Warren R. |last9=Havlak |first9=Paul |author10=NISC Comparative Sequencing Program |last11=Smith |first11=Stephen A. |last12=Putnam |first12=Nicholas H. |last13=Haddock |first13=Steven H. D. |last14=Dunn |first14=Casey W. |last15=Wolfsberg |first15=Tyra G. |last16=Mullikin |first16=James C. |last17=Martindale |first17=Mark Q. |last18=Baxevanis |first18=Andreas D. |display-authors=6 |title=The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution |journal=Science |volume=342 |issue=6164 |page=1242592 |date=December 2013 |pmid=24337300 |pmc=3920664 |doi=10.1126/science.1242592 }}</ref><ref name="Moroz_2014">{{cite journal |last1=Moroz |first1=Leonid L. |last2=Kocot |first2=Kevin M. |last3=Citarella |first3=Mathew R. |last4=Dosung |first4=Sohn |last5=Norekian |first5=Tigran P. |last6=Povolotskaya |first6=Inna S. |last7=Grigorenko |first7=Anastasia P. |last8=Dailey |first8=Christopher |last9=Berezikov |first9=Eugene |last10=Buckley |first10=Katherine M. |last11=Ptitsyn |first11=Andrey |last12=Reshetov |first12=Denis |last13=Mukherjee |first13=Krishanu |last14=Moroz |first14=Tatiana P. |last15=Bobkova |first15=Yelena |last16=Yu |first16=Fahong |last17=Kapitonov |first17=Vladimir V. |last18=Jurka |first18=Jerzy |last19=Bobkov |first19=Yuri V. |last20=Swore |first20=Joshua J. |last21=Girardo |first21=David O. |last22=Fodor |first22=Alexander |last23=Gusev |first23=Fedor |last24=Sanford |first24=Rachel |last25=Bruders |first25=Rebecca |last26=Kittler |first26=Ellen |last27=Mills |first27=Claudia E. |last28=Rast |first28=Jonathan P. |last29=Derelle |first29=Romain |last30=Solovyev |first30=Victor V. |last31=Kondrashov |first31=Fyodor A. |last32=Swalla |first32=Billie J. |last33=Sweedler |first33=Jonathan V. |last34=Rogaev |first34=Evgeny I. |last35=Halanych |first35=Kenneth M. |last36=Kohn |first36=Andrea B. |display-authors=6 |title=The ctenophore genome and the evolutionary origins of neural systems |journal=Nature |volume=510 |issue=7503 |date=2014 |issn=0028-0836 |pmid=24847885 |pmc=4337882 |doi=10.1038/nature13400 |pages=109–114|bibcode=2014Natur.510..109M }}</ref> If this is correct, either modern comb jellies developed their complex structures independently of other Metazoa, or sponges' ancestors were more complex and all known sponges are drastically simplified forms. The study recommended further analyses using a wider range of sponges and other simple Metazoa such as [[Placozoa]].<ref name="Dunn_2008"/>

However, reanalysis of the data showed that the computer algorithms used for analysis were misled by the presence of specific ctenophore genes that were markedly different from those of other species, leaving sponges as either the sister group to all other animals, or an ancestral paraphyletic grade.<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 |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 United States of America |volume=112 |issue=50 |pages=15402–15407 |date=December 2015 |pmid=26621703 |pmc=4687580 |doi=10.1073/pnas.1518127112 |doi-access=free |bibcode=2015PNAS..11215402P }}</ref><ref>{{Cite book |title=Spineless: the science of jellyfish and the art of growing a backbone |last= Berwald |first=Juli |publisher=Riverhead Books |year=2017|isbn=9780735211261}}{{page needed|date=October 2018}}</ref> 'Family trees' constructed using a combination of all available data – morphological, developmental and molecular – concluded that the sponges are in fact a monophyletic group, and with the [[cnidarian]]s form the sister group to the bilaterians.<ref name="Schierwater_2009">{{cite journal |last1=Schierwater |first1=Bernd |last2=Eitel |first2=Michael |last3=Jakob |first3=Wolfgang |last4=Osigus |first4=Hans-Jürgen |last5=Hadrys |first5=Heike |last6=Dellaporta |first6=Stephen L. |last7=Kolokotronis |first7=Sergios-Orestis |last8=DeSalle |first8=Rob |title=Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis |journal=PLOS Biology |volume=7 |issue=1 |pages=e20 |date=January 2009 |pmid=19175291 |pmc=2631068 |doi=10.1371/journal.pbio.1000020 |doi-access=free }}</ref><ref name="Kapli_2020">{{cite journal |last1= Kapli |first1=P. |last2=Telford |first2=M.J. |title=Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha |journal=Science Advances |volume=6 |issue=50 |pages=eabc5162 |date=December 2020 |pmid=33310849 |pmc=7732190 |doi=10.1126/sciadv.abc5162 |doi-access=free |bibcode=2020SciA....6.5162K }}</ref>

A very large and internally consistent alignment of 1,719&nbsp;proteins at the metazoan scale, published in 2017, showed that (i)&nbsp;sponges – represented by Homoscleromorpha, Calcarea, Hexactinellida, and Demospongiae – are monophyletic, (ii)&nbsp;sponges are sister-group to all other multicellular animals, (iii)&nbsp;ctenophores emerge as the second-earliest branching animal lineage, and (iv)&nbsp;[[placozoans]] emerge as the third animal lineage, followed by [[Planulozoa|cnidarians sister-group to bilaterians]].<ref name="Simion_2017">{{cite journal |last1=Simion |first1=Paul |last2=Philippe |first2=Hervé |last3=Baurain |first3=Denis |last4=Jager |first4=Muriel |last5=Richter |first5=Daniel J. |last6=Di Franco |first6=Arnaud |last7=Roure |first7=Béatrice |last8=Satoh |first8=Nori |last9=Quéinnec |first9=Éric |last10=Ereskovsky |first10=Alexander |last11=Lapébie |first11=Pascal |last12=Corre |first12=Erwan |last13=Delsuc |first13=Frédéric |last14=King |first14=Nicole |last15=Wörheide |first15=Gert |last16=Manuel |first16=Michaël |display-authors=6 |title=A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals |journal=Current Biology |volume=27 |issue=7 |pages=958–967 |date=April 2017 |pmid=28318975 |doi=10.1016/j.cub.2017.02.031 |url=https://hal.archives-ouvertes.fr/hal-01681528/file/Simion_etal2017_CurrBiol_proofs.pdf |type=<!-- Submitted manuscript --> |doi-access=free |bibcode=2017CBio...27..958S |access-date=2018-11-04 |archive-date=2020-04-25 |archive-url=https://web.archive.org/web/20200425191351/https://hal.archives-ouvertes.fr/hal-01681528/file/Simion_etal2017_CurrBiol_proofs.pdf |url-status=live }}</ref>

In March&nbsp;2021, scientists from Dublin found additional evidence that sponges are the sister group to all other animals,<ref>{{cite journal |last1= Redmond |first1=A.K. |last2=McLysaght |first2=A. |title=Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding |journal=Nature Communications |volume=12 |issue=1 |pages=1783 |date=March 2021 |pmid=33741994 |pmc=7979703 |doi=10.1038/s41467-021-22074-7 |doi-access=free |bibcode=2021NatCo..12.1783R }}</ref> while in May&nbsp;2023, Schultz et al. found patterns of irreversible change in genome synteny that provide strong evidence that [[ctenophora|ctenophores]] are the sister group to all other animals instead.<ref>{{cite journal |last1=Schultz |first1=Darrin T. |last2=Haddock |first2=Steven H. D. |last3=Bredeson |first3=Jessen V. |last4=Green |first4=Richard E. |last5=Simakov |first5=Oleg |last6=Rokhsar |first6=Daniel S. |title=Ancient gene linkages support ctenophores as sister to other animals |journal=Nature |volume=618 |issue=7963 |pages=110–117 |date=June 2023 |pmid=37198475 |pmc=10232365 |doi=10.1038/s41586-023-05936-6 |bibcode=2023Natur.618..110S }}</ref>