View source for Talk:Ecdysozoa

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==Untitled==
Could we get some examples of classes/orders/species of ecdysozoa, so us less biologically aware folk have some idea which animals are being discussed here? -- [[User:JohnOwens|JohnOwens]] 18:14 Mar 21, 2003 (UTC)

== Removed PoV ==

I've taken out a lot of material which was not properly verified or written in a neutral manner. It appeared to have all been inserted by a single editor in an attempt to push a PoV. [[User:Jefffire|Jefffire]] 21:16, 23 September 2006 (UTC)

: I was that author. Strongly disagree. I provided all necessary references to the peer-revieved sources, so there was no original research involved. The references, by the way, are still visible in the current revision in the ''References'' section. If the controversy is still open, the one-sided Wikipedia article strongly supporting Ecdysosoa hypothesis is a POV-pushing ebterprise. AGF, please. I'll go take a lunch and come back to revert. [[User:Alexei Kouprianov|Alexei Kouprianov]] 11:28, 30 November 2006 (UTC)

: Well, here I am. Just to prove that the controversy really exists (bold added):
: <blockquote>'''Discussions about the phylogenetic placements of''' acoels and nemertodermatids (basal-most extant bilaterians or derived lophotrochozoans?), brachiopods and phoronids (lophotrochozoan protostomes or deuterostomes?), and '''arthropods and annelids (monophyly of Ecdysozoa or Articulata?) are among the more conspicuous of the current debates''' (e.g., Luter and Bartolomaeus, 1997; Ruiz-Trillo et al., 1999; Baguna et al., 2001; Wagele et al., 1999; Wagele and Misof, 2001; Zrzavy, 2001; De Rosa, 2001). The resolution of these debates will eventually be dependent upon the reconciliation of molecular and morphological phylogenetic evidence. However, before we can hope for such an overarching consensus, we first have to secure a more modest goal: to establish the contribution of a decade of morphological cladistic research towards our current understanding of metazoan relationships. ([http://www.findarticles.com/p/articles/mi_qa4054/is_200302/ai_n9184883/pg_1 Unleashing the force of cladistics? Metazoan phylogenetics and hypothesis testing.] ''Integrative and Comparative Biology,'' Feb 2003 by Jenner, Ronald A.)</blockquote>

: Other references are provided in the article. [[User:Alexei Kouprianov|Alexei Kouprianov]] 12:26, 30 November 2006 (UTC)

I've removed the ciliated sperm argument because ciliated sperm are now considered to be an acceptable part of the group ecdysozoa (much like humans can be primates despite lacking a tail).

I've also removed the "moulting" argument as it doesn't actually address any important issues. It's roughly equivalent to pointing out that snakes moult to. [[User:Jefffire|Jefffire]] 10:30, 15 December 2006 (UTC)

: Your comments reveal some deep misunderstanding of the argument, and I feel I need to explain it more thoroughly.

: Humans surely can be primates lacking a tail. Moreover, the reduction of the tail is a synapomorphy humans share with some but not all primates. The case you are discussing is far more complicated and the better illustration is as follows. Imagine that there is a whole new order of mammals lacking tails 'Acauditheria.' Then imagine that someone claims that this group is a sister group of 'Primates' because the latter lack tails too. Someone else objects: not all Primates lack tails, just the subordinate group of human-like apes; therefore, the absence of the tail can not be used in our classification as a shared derived character supporting the monophyly of 'Acauditheria' and 'Primates,' and, even though the two groups may be monophyletic, the lack of the tail renders no support for this hypothesis and the synapomorphies are to be sought elsewhere. The latter point is mine. If the arthropods vary with respect to this character displaying both the plesiomorphic (flagellate sperm) and apomorphic (amoeboid sperm) condition, one can not argue that amoeboid sperm is a synapomorphy of arthropods and roundworms unless this someone claims that arthropods are indeed paraphyletic to roundworms or that there is a major character reversal in all but few arthropods from amoeboid to the flagellate sperm.

: Moulting arument is relevant because it is not the position of snakes what makes us worry, bit the position of the annelids. It is the monopyly of annelida and arthropoda or paraphyly of annelida to arthropoda that is challenged by the ecdysosoa hypothesis, so this would be simply unfair to disregard the paper claiming that the two groups are not so much different in this crucial aspect. [[User:Alexei Kouprianov|Alexei Kouprianov]] 16:09, 28 December 2006 (UTC)

== Phylogenetic tree ==

I would like some feed back on this: would it be better to change the phylogenetic tree presented to that proposed by Dunn ''et al'' (which has better resolution), or to stick with that from the tree of life project? [[User:Jefffire|Jefffire]] ([[User talk:Jefffire|talk]]) 07:55, 23 April 2008 (UTC)
:Reliable sources that contain the most recent summaries would be nice. [[User:Shyamal|Shyamal]] ([[User talk:Shyamal|talk]]) 08:09, 23 April 2008 (UTC)
::Dunn ''et al'' is a large study with many contributors published in ''Nature''. To me it looks impeccable as an authoritative source, but I'm not an expert on molecular data. Of course, there is the issue of which of the two models used by Dunn is better, since they give slightly different results, but I'm looking into it. [[User:Jefffire|Jefffire]] ([[User talk:Jefffire|talk]]) 08:15, 23 April 2008 (UTC)

For anyone's interest, I've hashed together an example of what I've proposed [[http://en.wikipedia.org/wiki/User:Jefffire/phylotest]], based on the first of the tree prosed in the ''Nature'' paper. [[User:Jefffire|Jefffire]] ([[User talk:Jefffire|talk]]) 09:02, 23 April 2008 (UTC)

:"Dunn ''et al'' is a large study with many contributors published in ''Nature''" - the former is not necessarily an argument (in such a controversy), the latter certainly isn't. '''Nature'' and ''Science'' have by now been burned by bad research far too often - haw many papers there were retracted in the last 5 years, and how many in, say, ''Molecular Phylogenetics and Evolution''? In the present case, ''Molecular Biology and Evolution'' seems to be the journal to watch closely.

:In any case, what Wikipedia should do IMHO is to present both ''hypotheses'' with all the supporting and contradicting data, as an example of an ongoing scientific controversy. Researchers have really gotten desperate by now - see {{doi|10.1073/pnas.0409891102}} for an approach that "supports" Ecdysozoa on an entirely theoretical consideration. This is, I think, barely science anymore. (Similar examples can probably given for desperate attempts of researchers to rescue their beloved Coelomata, no matter the price)

:But ''no matter'' which methodological approach is followed, every scientists who likes Ecdysozoa can find data in support of them, and any scientists liking Coelomata can find data in support of them. Troubling. What can be observed is that support for Ecdysozoa seems to be a bit stronger than for Coelomata, but a) it was A LOT stronger 10 years ago, and b) no single approach has yet yielded an unequivocal result (i.e., there is no way that will support Ecdysozoa or Coelomata ''only''). The "first round" of the debate ended about 2003-2004, see {{doi|10.1016/j.cub.2004.03.022}} for a resume.

:I have briefly rounded up some of the more interesting newer works on the topic from the peer-reviewed literature. Of course, since the "peers" have a personal interest in the matter, this is less helpful here than elsewhere. But as you will see, the word is still very much out.

:In support of Ecdysozoa -
:* "Rare Coding Sequence Changes are Consistent with Ecdysozoa, not Coelomata" (2007) {{doi|10.1093/molbev/msm105}} [http://mbe.oxfordjournals.org/cgi/reprint/24/8/1604 PDF fulltext]
:* "The Complete Mitochondrial Genome of the Onychophoran ''Epiperipatus biolleyi'' Reveals a Unique Transfer RNA Set and Provides Further Support for the Ecdysozoa Hypothesis" (2008) {{doi|10.1093/molbev/msm223}} [http://mbe.oxfordjournals.org/cgi/reprint/24/12/2594 PDF fulltext] - see also below

:In support of Coelomata -
:* "Analysis of Rare Amino Acid Replacements Supports the Coelomata Clade" (2007) {{doi|10.1093/molbev/msm218}} [http://mbe.oxfordjournals.org/cgi/reprint/24/12/2594 PDF fulltext]
:* "Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements" (2007) {{aut|10.1093/molbev/msm029}} [http://mbe.oxfordjournals.org/cgi/reprint/24/4/1080 PDF fulltext] [http://mbe.oxfordjournals.org/cgi/content/full/msm029/DC1 Supplementary data]

:An interesting pair of articles which purportedly do "rigorous" analysis of the same kind of data and find it to "support" each authors' pet hypothesis:
:* "Rare Genomic Characters Do Not Support Coelomata: Intron Loss/Gain" (2008) {{doi|10.1093/molbev/msn035}} [http://mbe.oxfordjournals.org/cgi/reprint/25/4/620 PDF fulltext]
:* "A Rigorous Analysis of the Pattern of Intron Conservation Supports the Coelomata Clade of Animals" (2007) {{doi|10.1007/978-3-540-74960-8_14}} - doi:10.1093/molbev/msm223 does an equally "rigorous" analysis of the data and says no it doesn't 

:Papers that are perhaps more important than those favoring one proposed clade over the other. Bear in mind that a paper is some 20-40 months in the making, so everything that is published no is not necessarily taking into account complications discovered as early as 2005.
:* "The multimeric ''β-thymosin'' found in nematodes and arthropods is not a synapomorphy of the Ecdysozoa" (2004) {{doi|10.1111/j.1525-142X.2004.04013.x}}
:* "Animal Phylogeny: Fatal Attraction" (2005) {{doi|10.1016/j.cub.2005.04.001}}
:* "Molting polychaete jaws - ecdysozoans are not the only molting animals" (2005) {{doi|10.1111/j.1525-142X.2005.05039.x}}
:and especially:
:* "Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors?" (2007) {{doi|10.1093/molbev/msl137}} [http://mbe.oxfordjournals.org/cgi/reprint/24/1/6 PDf fulltext] [http://mbe.oxfordjournals.org/cgi/content/full/msl137/DC1 Supplementary data] 

:The last paper may be the single most important one here. I expect no study fulfilling the desiderata outlined there to come out before 2009 - and its take-home message is, bluntly: any study that does not take them into account is a rather pointless exercise anyway. To which from my experience with reviewing bird phylogenetic studies can add: a) wait til the ''[[Trichoplax]]'' genome data is available - it at least can't hurt since it's (probably) ''somewhere near'' the metazoan base b) it is sorely necessary to move away from the "standard model" taxa. Take about 2-3 advanced arthropods, nematodes, annelids and mollusks, and then as many of the basalmost lineages of arthropods, annelids, and nematodes as you can possibly get, plus 2-3 basal members of each and every lineage that has ever been considered a close relative of these. And don't expect single-gene trees to be informative.

:Comprehensive taxon sampling is an absolute must, see [http://digitallibrary.amnh.org/dspace/bitstream/2246/2890/1/N3337.pdf here] what you'll run into if you pick a handful of "model" taxa and think it'll do you any good.

:Shyamal, and anyone else, if you want a copy of the papers w/o fulltext online (in addition to the Nature one), leave me a msg and I see what I can do. [[User:Dysmorodrepanis|Dysmorodrepanis]] ([[User talk:Dysmorodrepanis|talk]]) 18:52, 23 April 2008 (UTC)

::So...what is your opinion on which tree to present? [[User:Jefffire|Jefffire]] ([[User talk:Jefffire|talk]]) 19:06, 23 April 2008 (UTC)

:::I think here and in [[Lophotrochozoa]] and [[Coelomata]] (which both need a re-write in coordination with this article), both views should be presented as competing hypotheses. First the one that each article refers to, then the one of the alternate hypothesis. Perhaps smaller, if the code permits, and unlinked. That way, everybody is happy.
:::For an ecdysozoan tree, I have not had time to check the Nature paper (I'll do these days though), but I do suppose it's the one to use for the time being. Be prepared to change it at least once in the next 15 months or so.
:::Since you seem to be interested in the matter, I really advise you to monitor ''Mol. Biol. Evol.'' - that's the main "battlefield" and I expect more on the matter towards the last months of 2008. If some hard (as in "rock-hard", i.e. fossil) evidence turns up, it'll probably be published in ''Nature''/''Science''/''PNAS'', because it'll be too spectacular to go for the more specialist journals like ''J. Palaeontol.''. But I monitor that one, so if something turns up there I'll drop a note here. There might be some cladistic analyses in ''Mol. Phylogenet. Evol.'' or ''Cladistics'' which I also monitor, but it's unlikely. Reviews usually wind up in ''Current Biology'', and it may be that they'll have another one soon (like later this summer). I don't habitually check on that journal. [[User:Dysmorodrepanis|Dysmorodrepanis]] ([[User talk:Dysmorodrepanis|talk]]) 05:33, 24 April 2008 (UTC)

::::That sound really interesting. I'll definitely keep tabs on those journals. These sources you provided will definitely help improve the article, and I was expecting to have to make frequent updates to the tree. I'll also begin working on [[Coelomata]], even if it eventually becomes completely historical there is no reason not to have an article about the grouping. One last thing and that an FYI that wikipedia articles generally give weighting to ideas based on their prominence, rather than the equal weighting one might be used to in newspapers. Since Ecdysozoa appears to be more accepted than Coelomata the article does need to reflect that, but that doesn't mean that we can't give good coverage to both. [[User:Jefffire|Jefffire]] ([[User talk:Jefffire|talk]]) 07:25, 24 April 2008 (UTC)

:::::"wikipedia articles generally give weighting to ideas based on their prominence" - not sure, shouldn't it rather be "citeable support"? At least that's the way it's done in cases where the science becomes political, like those thorny human genetics-behavior issues.
:::::And there's another twist, and a serious one: all those molecular phylogenetics studies - or ''most'', anyway -are from people who are (forgive me for putting it so harshly, but it's really a problem - except in birds, where we've progressed past the stage of mutual ignorance last year. Phew!) boorishly ignorant of the fossil record. [[Thylacocephala]], [[Machaeridia]] and sundry others all want to go somewhere in the tree, and frankly I have learned to trus a well-assigned fossil more than a molecuzlar phylogeny, which after all is a statistical estimate based on certain preconditions that may or may not hold true. But there is little to cite. In such situations, OR has to be avoided; a way I found to work well is to cite up-to-date studies that ''lack'' the information and remark dryly that this-and-this information has not been integrated in that-and-that consideration as of yet. Make the ''lack'' of research a citeable fact, rather than speculate at length on the interpretation without reasonable backing.
:::::But [[Mikko's Phylogeny Archive|Mikko Haaramo]], who is usually pretty up-to-date and comprehensive on such things, has assembled an interesting tree, and he prefers this to the usual proposals, even though it is different:
:::::Both ecdysozoans and lophotrochopohorans are maintained. BUT: the nematode group is excluded from ''both''! I more or less happened over it, and I find it very fascinating - with a less close relationship between annelids and insects I have no problem; after all homeotic gene systems are more ancient than metazoans, so the molecular foundation of segmentation can well be older than metazoans too; and the idea that something ''morphologically'' not unlike an annelid gave rise to insects does not imply that that something was ''phylogenetically'' very close to modern annelids - for all we know, an awful lot of early Cambrian critters looked like but weren't "segmented worms". It's the presumed close relationship between nematodes and insects (or for the matter, of nematodes with anything else) that I have always found the drawback of the "traditional" ecdysozoans. See here: http://www.helsinki.fi/~mhaaramo/metazoa/protostoma/protostoma_1.html
:::::And speaking of fossils, [[Chancelloriida]] and [[Sachitida]] would seem to set the idea of a monophyletic Lophotrochozoa on a solid, material basis. I have no idea what they are though. [[Anabaritidae]] would also be something to ponder over.
:::::So the resultant phylogeny makes the "core" ecdysozoans (insects and stuff) an almost-sister to the mollusk-annelid clade - of which the annelids are very primitive morphologically, and the mollusks are very derived as adults, belying their affiliation only as larvae. And the entire group is only loosely related to the "weirder" protostomes, which include nematodes et al.
:::::Citations can be picked from Mikko's website. The Science paper {{doi|10.1126/science.1137187}} would need to be read (the supplement has nothing to say on the matter really, so I suppose the text has). [[User:Dysmorodrepanis|Dysmorodrepanis]] ([[User talk:Dysmorodrepanis|talk]]) 19:44, 27 April 2008 (UTC)

::::::As for the tree - a questionmark before the nematode et al lineage plus giving the citation as "based on Dunn ''et al.'' (2008) and the sources given in Haaramo (2008)" would do the trick. The present article would until further notice assume that nematodes ''are'' part of the Ecdysozoa, at least tentatively - although there is nor has ever been "hard" evidence to support this! It is still just a [[inference|statistical computer game]] that may or [[fallacy|may not]] be correct... [[User:Dysmorodrepanis|Dysmorodrepanis]] ([[User talk:Dysmorodrepanis|talk]]) 19:49, 27 April 2008 (UTC)

:::::::I'm quite busy at the moment IRL so it'll be a while till I've got a chance to read all this, but it is all extremely interesting material. I hope to have time to read it by this time next week. [[User:Jefffire|Jefffire]] ([[User talk:Jefffire|talk]]) 20:24, 27 April 2008 (UTC)

::::::::I'm not sure about adding a question mark over the nematodes, especially since only the tardigrades gave different results in the two models used by Dunn. My opinion was that this tree was simply an example of one working of the Ecdysozoa group, rather than a definitive one. As such it would be expected that quite a few of the groups would be wrongly placed. I agree that there is ample room to expand on this in the text though. [[User:Jefffire|Jefffire]] ([[User talk:Jefffire|talk]]) 08:08, 8 May 2008 (UTC)

:Does anybody else feel it's important to include a tree that includes the other animal phyla as well? Deuterostomes don't fit anywhere in the Animalia according to the current tree, which lists only the Lophotrochozoa as an outgroup.[[User:Dhicks3|Dhicks3]] ([[User talk:Dhicks3|talk]]) 23:35, 18 November 2009 (UTC)

I'd like to read more about the Coelomata hypothesis. At the moment [[Coelomata]] is just a redirect to [[body cavity]]. Where can I find a phylogeny of the metazoa under the Coelomata hypothesis? [[User:Evercat|Evercat]] ([[User talk:Evercat|talk]]) 22:33, 23 January 2010 (UTC)

== question: what are ''"mostly amoeboid sperm"''? ==

The article currently says: ''"The Ecdysozoans lack locomotory [[cilia]], produce mostly [[amoeboid]] sperm, and their embryos do not undergo [[spiral cleavage]] as in most other protostomes."''
'''So what are ''"mostly amoeboid sperm"''?'''

The article [[amoeboid]] says nothing about sperm.
It does say: ''"[[Myxomycotes]] use amoeboid gametes, as well."''  But we have no other articles that use the term ''"[[Myxomycotes]]"''.

I am going to wait, return here, and if no one has addressed this question I may change the link from [[amoeboid]] to a link to [[amoeboid sperm]].

Cheers!  [[User:Geo Swan|Geo Swan]] ([[User talk:Geo Swan|talk]]) 18:08, 1 October 2009 (UTC)

:[[Myxogastria]] has a section on ''"Myxomycota"'', which I think contradicts what this article says about ''"amoeboid sperm"''.  [[User:Geo Swan|Geo Swan]] ([[User talk:Geo Swan|talk]]) 18:34, 1 October 2009 (UTC)

== Perrier (1897) and Seurat (1920) ==

''Perrier in 1897 and Seurat in 1920'': I surmise that there are Wikipedia articles for this Perrier and this Seurat.  Can some editor more competent than I provide full names and wikilinks? Footnotes giving the book titles would be a generous and thoughtful gesture. That way we can all be included in the discourse.--[[User:Wetman|Wetman]] ([[User talk:Wetman|talk]]) 20:37, 28 November 2011 (UTC)

== External links modified ==

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