Editing Sponge (section)

== Evolutionary history ==

=== Fossil record ===
{{see also|Huainan biota}}

[[File:Raphidonema faringdonense 070715a.jpg|thumb|left|''[[Raphidonema (sponge)|Raphidonema faringdonense]]'', a fossil sponge from the [[Cretaceous]] of England]]
{{Annotated image |float=right|caption=[[Archaeocyathid]] structure|image=Archaeocyatha.png|width=150|image-width=150|height=235|image-top=-5|annotations=
{{Annotation|4|11|'''1'''}}
{{Annotation|9|60|'''2'''}}
{{Annotation|17|87|'''3'''}}
{{Annotation|27|124|'''4'''}}
{{Annotation|141|14|'''5'''}}
{{Annotation|139|64|'''6'''}}
{{Annotation|117|124|'''7'''}}
{{Annotation|2|175|'''1''':&nbsp;Gap&nbsp; '''2''':&nbsp;Central&nbsp;cavity&nbsp; '''3'''&nbsp;Internal wall&nbsp; '''4''':&nbsp;Pore (''all'' walls have pores)&nbsp; '''5'''&nbsp;Septum&nbsp; '''6'''&nbsp;Outer wall&nbsp; '''7'''&nbsp;Holdfast}}
}}

[[File:Nevadacoelia wistae.jpg|left|thumb|''[[Nevadacoelia|Nevadacoelia wistae]]'', a fossil [[Anthaspidellidae|anthaspidellid]] [[demosponge]] from the early [[Ordovician]] of [[Nevada]] ]]

Although [[molecular clock]]s and [[biomarker]]s suggest sponges existed well before the [[Cambrian explosion]] of life, [[silica]] spicules like those of demosponges are absent from the fossil record until the Cambrian.<ref>{{cite journal |last1=Sperling |first1=E. A. |last2=Robinson |first2=J. M. |last3=Pisani |first3=D. |last4=Peterson |first4=K. J. |date=January 2010 |title=Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200&nbsp;Myr missing Precambrian fossil record of siliceous sponge spicules |journal=Geobiology |volume=8 |issue=1 |pages=24–36 |pmid=19929965 |doi=10.1111/j.1472-4669.2009.00225.x |bibcode=2010Gbio....8...24S |s2cid=41195363 }}</ref> An unsubstantiated 2002 report exists of spicules in rocks dated around {{ma|750}}.<ref>{{cite book|last1= Reitner |first1=J |last2=Wörheide |first2=G. |contribution=Non-lithistid fossil Demospongiae – origins of their palaeobiodiversity and highlights in history of preservation |editor1=Hooper, J.N. |editor2=Van Soest, R.W. |year=2002 |title=Systema Porifera: A Guide to the Classification of Sponges |publisher=Kluwer Academic Plenum |location=New York, NY |url=http://webdoc.sub.gwdg.de/pub/geo/geobiologie/2005/reitner/2002-porifera.pdf |archive-url=https://web.archive.org/web/20081216220745/http://webdoc.sub.gwdg.de/pub/geo/geobiologie/2005/reitner/2002-porifera.pdf |archive-date=2008-12-16 |url-status=live |access-date=November 4, 2008}}</ref> Well-preserved [[fossil]] sponges from about {{ma|580}} in the [[Ediacaran]] period have been found in the [[Doushantuo Formation]].<ref>{{cite journal|last1=Li|first1=Chia-Wei|last2=Chen|first2=Jun-Yuan|last3=Hua|first3=Tzu-En|title=Precambrian sponges with cellular structures|journal=Science|date=February 1998|volume=279|issue=5352|pages=879–882|doi=10.1126/science.279.5352.879|pmid=9452391|bibcode=1998Sci...279..879L}}</ref> These fossils, which include: spicules; [[pinacocyte]]s; [[porocyte]]s; [[archeocyte]]s; [[sclerocyte]]s; and the internal cavity, have been classified as demosponges. The Ediacaran record of sponges also contains two other genera: the stem-hexactinellid ''[[Helicolocellus]]'' from the [[Dengying Formation]]<ref>{{cite journal |last1=Wang |first1=Xiaopeng |last2=Liu |first2=Alexander G. |last3=Chen |first3=Zhe |last4=Wu |first4=Chengxi |last5=Liu |first5=Yarong |last6=Wan |first6=Bin |last7=Pang |first7=Ke |last8=Zhou |first8=Chuanming |last9=Yuan |first9=Xunlai |last10=Xiao |first10=Shuhai |title=A late-Ediacaran crown-group sponge animal |journal=Nature |date=27 June 2024 |volume=630 |issue=8018 |pages=905–911 |doi=10.1038/s41586-024-07520-y|pmid=38839967 |bibcode=2024Natur.630..905W }}</ref> and the possible stem-archaeocyathan ''[[Arimasia]]'' from the [[Nama Group]].<ref name=arimasia>{{cite journal |last1=Runnegar |first1=Bruce |last2=Gehling |first2=James G. |last3=Jensen |first3=Sören |last4=Saltzman |first4=Matthew R. |title=Ediacaran paleobiology and biostratigraphy of the Nama Group, Namibia, with emphasis on the erniettomorphs, tubular and trace fossils, and a new sponge, Arimasia germsi n. gen. n. sp. |journal=Journal of Paleontology |date=October 2024 |volume=98 |issue=S94 |pages=1–59 |doi=10.1017/jpa.2023.81|bibcode=2024JPal...98S...1R }}</ref> These genera are both from the "Nama assemblage" of Ediacaran biota, although whether this is due to a genuine lack beforehand or preservational bias is uncertain. Fossils of [[glass sponge]]s have been found from around {{ma|540}} in rocks in Australia, China, and Mongolia.<ref name="Müller_2007">{{cite journal |last=Müller |first=W. E. G. |author2=Jinhe Li |last3=Schröder |first3=H. C. |author4=Li Qiao |author5=Xiaohong Wang |year=2007 |title=The unique skeleton of siliceous sponges (Porifera; Hexactinellida and Demospongiae) that evolved first from the Urmetazoa during the Proterozoic: a review |journal=Biogeosciences |volume=4 |issue=2 |pages=219–232 |bibcode=2007BGeo....4..219M |doi=10.5194/bg-4-219-2007 |doi-access=free }}</ref> Early Cambrian sponges from Mexico belonging to the genus ''Kiwetinokia'' show evidence of fusion of several smaller spicules to form a single large spicule.<ref>{{cite journal |last= McMenamin |first=M.A. |year=2008 |title=Early Cambrian sponge spicules from the Cerro Clemente and Cerro Rajón, Sonora, México |journal=[[Geologica Acta]] |volume=6 |issue=4 |pages=363–367 }}</ref> [[Calcium carbonate]] spicules of [[Calcarea|calcareous sponges]] have been found in Early Cambrian rocks from about {{ma|530|523}} in Australia. Other probable demosponges have been found in the Early [[Cambrian]] [[Chengjiang fauna]], from {{ma|525|520}}.<ref name="Li_1998">{{cite journal |last1=Li |first1=Chia-Wei |last2=Chen |first2=Jun-Yuan |last3=Hua |first3=Tzu-En |date=February 1998 |title=Precambrian sponges with cellular structures |journal=Science |volume=279 |issue=5352 |pages=879–82 |pmid=9452391 |doi=10.1126/science.279.5352.879 |bibcode=1998Sci...279..879L |s2cid=38837724 }}</ref> Fossils found in the Canadian Northwest Territories dating to {{ma|890}} may be sponges; if this finding is confirmed, it suggests the first animals appeared before the Neoproterozoic oxygenation event.<ref name="Turner_2021">{{cite journal |last=Turner |first=E.C. |title=Possible poriferan body fossils in early Neoproterozoic microbial reefs |journal=Nature |volume=596 |issue=7870 |pages=87–91 |date=August 2021 |pmid=34321662 |pmc=8338550 |doi=10.1038/s41586-021-03773-z |doi-access=free |bibcode=2021Natur.596...87T }}</ref>
[[File:Sauerstoffgehalt-1000mj2.png|thumb|left|Oxygen content of the atmosphere over the last billion years. If confirmed, the discovery of fossilized sponges dating to 890&nbsp;million years ago would predate the Neoproterozoic Oxygenation Event.]]

Freshwater sponges appear to be much younger, as the earliest known fossils date from the Mid-[[Eocene]] period about {{ma|48|40}}.<ref name="Müller_2007"/> Although about 90% of modern sponges are [[demosponges]], fossilized remains of this type are less common than those of other types because their skeletons are composed of relatively soft spongin that does not fossilize well.<ref name="Kazmierczak_2004">{{cite web |title=Demospongia |publisher=[[University of California, Berkeley|U.C. Berkeley]] |department=[[University of California Museum of Paleontology]] |place=Berkeley, CA |url=http://www.ucmp.berkeley.edu/porifera/demospongia.html |access-date=2008-11-27 |url-status=live |archive-url=https://web.archive.org/web/20131018230738/http://www.ucmp.berkeley.edu/porifera/demospongia.html |archive-date=October 18, 2013}}</ref>
The earliest sponge symbionts are known from the [[Llandovery epoch|early Silurian]].<ref name="Vinn_2015">{{cite journal |last1=Vinn |first1=Olev |last2=Wilson |first2=Mark A. |last3=Toom |first3=Ursula |last4=Mõtus |first4=Mari-Ann |year=2015 |title=Earliest known rugosan-stromatoporoid symbiosis from the Llandovery of Estonia (Baltica) |journal=Palaeogeography, Palaeoclimatology, Palaeoecology |volume=31 |pages=1–5 |bibcode=2015PPP...431....1V |doi=10.1016/j.palaeo.2015.04.023 |url=https://www.researchgate.net/publication/275657612 |access-date=2015-06-18 |archive-date=2024-04-10 |archive-url=https://web.archive.org/web/20240410181408/https://www.researchgate.net/publication/275657612_Earliest_known_rugosan-stromatoporoid_symbiosis_from_the_Llandovery_of_Estonia_Baltica |url-status=live }}</ref>

A chemical tracer is [[24-Isopropylcholestane|24-isopropyl cholestane]], which is a stable derivative of 24-isopropyl [[cholesterol]], which is said to be produced by [[demosponge]]s but not by [[eumetazoa]]ns ("true animals", i.e. [[cnidaria]]ns and [[bilateria]]ns). Since [[choanoflagellate]]s are thought to be animals' closest single-celled relatives, a team of scientists examined the [[biochemistry]] and [[gene]]s of one [[choanoflagellate]] species. They concluded that this species could not produce 24-isopropyl cholesterol but that investigation of a wider range of choanoflagellates would be necessary in order to prove that the fossil 24-isopropyl cholestane could only have been produced by demosponges.<ref>{{cite journal |last1=Kodner |first1=Robin B. |last2=Summons |first2=Roger E. |last3=Pearson |first3=Ann |last4=King |first4=Nicole |last5=Knoll |first5=Andrew H. |date=July 2008 |title=Sterols in a unicellular relative of the metazoans |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=29 |pages=9897–9902 |pmid=18632573 |pmc=2481317 |doi=10.1073/pnas.0803975105 |bibcode=2008PNAS..105.9897K |doi-access=free }}</ref>
Although a previous publication reported traces of the chemical 24-isopropyl cholestane in ancient rocks dating to {{ma|1800}},<ref>{{cite journal |last1=Nichols |first1=S. |last2=Wörheide |first2=G. |date=April 2005 |title=Sponges: New views of old animals |journal=Integrative and Comparative Biology |volume=45 |issue=2 |pages=333–334 |pmid=21676777 |doi=10.1093/icb/45.2.333 |citeseerx=10.1.1.598.4999 }}</ref> recent research using a much more accurately dated rock series has revealed that these biomarkers only appear before the end of the [[Marinoan glaciation]] approximately {{ma|635}},<ref>{{cite journal |last1=Love |first1=Gordon D. |last2=Grosjean |first2=Emmanuelle |last3=Stalvies |first3=Charlotte |last4=Fike |first4=David A. |last5=Grotzinger |first5=John P. |last6=Bradley |first6=Alexander S. |last7=Kelly |first7=Amy E. |last8=Bhatia |first8=Maya |last9=Meredith |first9=William |last10=Snape |first10=Colin E. |last11=Bowring |first11=Samuel A. |last12=Condon |first12=Daniel J. |last13=Summons |first13=Roger E. |display-authors=6 |date=February 2009 |title=Fossil steroids record the appearance of Demospongiae during the Cryogenian period |journal=Nature |volume=457 |issue=7230 |pages=718–721 |pmid=19194449 |doi=10.1038/nature07673 |bibcode=2009Natur.457..718L |s2cid=4314662 |url=https://authors.library.caltech.edu/14867/2/Love2009p34510.1038nature07673_supp.pdf |access-date=2019-08-01 |archive-url=https://web.archive.org/web/20180724144041/https://authors.library.caltech.edu/14867/2/Love2009p34510.1038nature07673_supp.pdf |archive-date=2018-07-24 |url-status=dead }}</ref> and that "Biomarker analysis has yet to reveal any convincing evidence for ancient sponges pre-dating the first globally extensive Neoproterozoic glacial episode (the Sturtian, ~{{ma|713}} in Oman)". While it has been argued that this 'sponge biomarker' could have originated from marine algae, recent research suggests that the algae's ability to produce this biomarker evolved only in the [[Carboniferous]]; as such, the biomarker remains strongly supportive of the presence of demosponges in the Cryogenian.<ref name="Antcliffe_2013">{{cite journal |author=Antcliffe, J.B. |year=2013 |editor=Stouge, S. |title=Questioning the evidence of organic compounds called sponge biomarkers |journal=Palaeontology |volume=56 |issue=5 |pages=917–925 |doi=10.1111/pala.12030 |doi-access=free |bibcode=2013Palgy..56..917A }}</ref><ref>{{cite journal |author=Gold, D.A. |title=The slow rise of complex life as revealed through biomarker genetics |journal=Emerging Topics in Life Sciences |volume=2 |issue=2 |pages=191–199 |date=September 2018 |pmid=32412622 |doi=10.1042/ETLS20170150 |s2cid=90887224 }}</ref><ref>{{cite journal |last1=Gold |first1=David A. |last2=Grabenstatter |first2=Jonathan |last3=de Mendoza |first3=Alex |last4=Riesgo |first4=Ana |last5=Ruiz-Trillo |first5=Iñaki |last6=Summons |first6=Roger E. |date=March 2016 |title=Sterol and genomic analyses validate the sponge biomarker hypothesis |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=113 |issue=10 |pages=2684–2689 |pmid=26903629 |pmc=4790988 |doi=10.1073/pnas.1512614113 |bibcode=2016PNAS..113.2684G |doi-access=free }}</ref>

[[Archaeocyathid]]s, which some classify as a type of coralline sponge, are very common fossils in rocks from the Early [[Cambrian]] about {{ma|530|520}}, but apparently died out by the end of the Cambrian {{ma|490}}.<ref name="Li_1998"/>
It has been suggested that they were produced by: sponges; [[cnidaria]]ns; [[algae]]; [[foraminifera]]ns; a completely separate [[phylum]] of animals, Archaeocyatha; or even a completely separate [[Kingdom (biology)|kingdom]] of life, labeled Archaeata or Inferibionta. Since the 1990s, archaeocyathids have been regarded as a distinctive group of sponges.<ref name="Rowland_2001">{{cite journal |author1= Rowland, S.M. |author2=Stephens, T. |year=2001 |title=Archaeocyatha: A history of phylogenetic interpretation |journal=Journal of Paleontology |volume=75 |issue=6 |pages=1065–1078 |jstor=1307076 |doi=10.1666/0022-3360(2001)075<1065:AAHOPI>2.0.CO;2}}</ref>

{{clear left}}
{{Annotated image|float=left|caption=[[Halkieriid]] sclerite structure<ref name="Porter_2008"/> |image=Halkieriid sclerite structure 300.png |width=210 |height=96 |image-width=200 |image-left=0 |image-top=0
|annotations =
{{Annotation|141|44|{{=}} skin}}
{{Annotation|141|64|{{=}} [[aragonite]]}}
{{Annotation|141|84|{{=}} flesh}}
}}
It is difficult to fit [[chancelloriid]]s into classifications of sponges or more complex animals. An analysis in 1996 concluded that they were closely related to sponges on the grounds that the detailed structure of chancellorid sclerites ("armor plates") is similar to that of fibers of spongin, a [[collagen]] [[protein]], in modern keratose (horny) [[demosponge]]s such as ''[[Darwinella (sponge)|Darwinella]]''.<ref>{{cite journal |author1=Butterfield, N.J. |author2=Nicholas, C.J. |year=1996 |title=Burgess Shale-type preservation of both non-mineralizing and "shelly" Cambrian organisms from the Mackenzie Mountains, northwestern Canada |journal=Journal of Paleontology |volume=70 |issue=6 |pages=893–899 |jstor=1306492 |doi=10.1017/S0022336000038579 |bibcode=1996JPal...70..893B |s2cid=133427906 }}</ref> However, another analysis in 2002 concluded that chancelloriids are not sponges and may be intermediate between sponges and more complex animals, among other reasons because their skins were thicker and more tightly connected than those of sponges.<ref name="Janussen_2002">{{cite journal |last1=Janussen |first1=Dorte |last2=Steiner |first2=Michael |last3=Maoyan |first3=Zhu |year=2002 |title=New well-preserved scleritomes of Chancelloridae from the early Cambrian Yuanshan Formation (Chengjiang, China) and the middle Cambrian Wheeler Shale (Utah, USA) and paleobiological implications |journal=Journal of Paleontology |volume=76 |issue=4 |pages=596–606 |doi=10.1666/0022-3360(2002)076<0596:NWPSOC>2.0.CO;2|bibcode=2002JPal...76..596J |s2cid=129127213 }} free text at {{cite news |last=Janussen |first=D. |year=2002 |title=(full text without images) |journal=[[Journal of Paleontology]] |url=http://findarticles.com/p/articles/mi_qa3790/is_200207/ai_n9134583/pg_1?tag=artBody;col1 |access-date=2008-08-04 |archive-date=December 10, 2008 |url-status=dead |archive-url=https://web.archive.org/web/20081210092130/http://findarticles.com/p/articles/mi_qa3790/is_200207/ai_n9134583/pg_1?tag=artBody%3Bcol1}}</ref> In 2008, a detailed analysis of chancelloriids' sclerites concluded that they were very similar to those of [[halkieriid]]s, mobile [[bilaterian]] animals that looked like [[slug]]s in [[chain mail]] and whose fossils are found in rocks from the very Early Cambrian to the Mid Cambrian. If this is correct, it would create a dilemma, as it is extremely unlikely that totally unrelated organisms could have developed such similar sclerites independently, but the huge difference in the structures of their bodies makes it hard to see how they could be closely related.<ref name="Porter_2008">{{cite journal |last=Porter |first=S.M. |year=2008 |title=Skeletal microstructure indicates Chancelloriids and Halkieriids are closely related |journal=[[Palaeontology (journal)|Palaeontology]] |volume=51 |issue=4 |pages=865–879 |doi=10.1111/j.1475-4983.2008.00792.x |bibcode=2008Palgy..51..865P |doi-access=free}}</ref>

=== 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>