Talk:Chromalveolata

Phytophthora

The recent publication of the draft genome sequences of Phytophthora sojae and P. ramorum provides evidence that the oomycetes are decended from photosynthetic ancestors, and have lost chloroplasts they presumably once had. In light of this does this article need to be updated?

ref: Tyler,B.M.(2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science, 313, 1261-1266.—Preceding unsigned comment added by Inaflap (talk • contribs) 21:35, 16 September 2006

Chromalveolata colour

If Chromalveolate are ranked as a kingdom, the taxobox should have a different and specific colour. 83.45.216.23 18:01, 17 July 2007 (UTC)

This seems unnecessary for such a small and unsettled group. Better perhaps to class them under the Protist heading until the debate dies down? Otherwise we'll need a plethora of colours for each time someone calls their clade a kingdom... As I understand it, it's arguable that this forms a kingdom; it's fact that they are protists. Verisimilus T 21:12, 6 August 2007 (UTC)

Actually, it is a large and settled group, and it has been decided on Wikiproject: Tree of Life to classify it as a kingdom, with it's own color. Please check this page before reverting changes made. Werothegreat 13:48, 7 August 2007 (UTC)

Sorry: Wasn't aware this page existed. Will use in future. Verisimilus T 15:07, 7 August 2007 (UTC)

It might (or might not) have been a "settled group" in 2007 when Werothegreat wrote his comment, but as of 2010, most sources appear to agree that it is not a monophyletic group and have dismembered it. Sigh... Peter coxhead (talk) 11:25, 26 April 2010 (UTC)

Chromalveolate vs SAR vs whatever

There have been a few more edits ([1]) as papers continue to call into question Chromalveolate sensu Thomas Cavalier-Smith. But at least in my opinion it would be premature to embrace SAR with the same enthusiasm or confidence as wikipedia did in 2006 (or so) when we accepted Chromalveolate (for taxoboxes and taxobox colors, for example). My reasons for caution have been better articulated by Parfrey et al in the paper cited in this article. In short, throughout the last decade or so, many classifications have been proposed and few have lasted more than a year or two. This isn't to say we should ignore new research, just that we should be cautious about drawing any firm conclusions until they have stood a certain test of time and confirming evidence. There has been past discussion of this at places like Wikipedia talk:WikiProject Tree of life (if memory serves, although it would now be archived) and Talk:Eukaryote. Kingdon (talk) 19:54, 6 January 2009 (UTC)

Chromista and Alveolata

I've reverted this edit because it inserts the concept Chromista (it also introduces a source which is redundant to the papers we already have, which are primary sources and review articles, but that's not the main problem). The situation, as I understand it, is that Alveolata and Heterokontophyta are generally thought to each be monophyletic, but that Cryptophyta and Haptophyta are less studied and probably belong somewhere else entirely (closer to the Archaeplastida although that isn't really clear yet). Therefore, I think it is more clear to present a four-fold division, rather than include Chromista (which is already mentioned, but which is more of a historical/etymological note). I'm fine with adding the subgroups of the Alveolata, and I have done that. What do people think? It is always hard to be accurate, up to date, and not jump to conclusions when a field is not settled yet, so perhaps people have better ideas about how to represent a situation which is in flux. Kingdon (talk) 22:24, 17 January 2009 (UTC)

Revision of the "Groups and classification" section

I agree very much with Kingdon's preceding comments. The classification of the eukaryotes is currently very fluid. Wikipedia's adoption of one particular version which now appears to be discredited is already causing problems and inconsistencies in a range of articles. Changing to a new classification now isn't the answer. However, I do think that the article should make clear that there is no recent support for a group called 'Chromalveolata'. I've revised and combined two sections to this end. Views? Peter coxhead (talk) 13:04, 26 April 2010 (UTC)

The circumscription of Chromalveolata may be different than before 2007 (the SAR paper), but until the relationships are known a bit better, terminology is likely to be in flux. We generally try to walk a pretty fine line: being up to date while also not committing WP:OR/WP:SYN or giving undue weight to results which are still tentative. As for the position of the Hacrobia, we should treat it as unsettled and I'm not convinced by the relationship to Archaeplastida. See for example Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates (cited more fully at Hacrobia). Particularly read the paragraph starting "Altogether, the phylogenomic data presented here suggest that the chromalveolate assemblage should be expanded" which discusses the possible relationships, reviews most of the papers we are discussing, and also (implicitly at least) gives insight into terminology. Kingdon (talk) 14:30, 3 May 2010 (UTC)

It's interesting that Cavalier-Smith is a co-author of this paper, because he's often been outside the main consensus (which doesn't of course mean that he won't turn out to be right, although if he's right that the Woese two domain model for prokaryotes is wrong, a lot of articles will need to be changed). What seems clear is that no source after the SAR paper supports the circumscription of the chromalveolates given in the Adl et al. 2005 classification (i.e. alveolates + strameopiles + Hacrobia). All recent sources support the SAR group. The position of the Hacrobia varies. If it is finally agreed that it goes with the SAR group, as per the paper under discussion, then there is an expanded chromalveolate group (the original + Rhizaria + some small groups), and this could be discussed in the Chromalveolata article. Judging from the author list, it would be reasonable to assume that this paper replaces Burki, Shalchian-Tabrizi, Kamran & Pawlowski (2008), which is the paper which puts the Hacrobia as sister to the Archaeplastida. But there's still the Kim & Graham 2008 paper (cited in the eukaryote article) which nests the Hacrobia inside the Archaeplastida, which can't, I think, be ignored yet without WP:OR/WP:SYN. However, my starting point was the problems caused by the fact that the 2005 classification of eukaryotes is embedded in many Wikipedia articles (and even more in Wikispecies), yet is now clearly not in accord with the evidence. This has surely to be addressed, even though we don't know what to put in its place yet. Peter coxhead (talk) 11:08, 4 May 2010 (UTC)

The paragraph I mentioned from Burki2009 dicusses Burki2008 but does not dismiss ("replace") it; it just presents these as two contradictory results which need to be resolved. As for Kim and Graham 2008, I'd give it less weight than Burki2008 as it is a single-gene analysis (I note Sakaguchi 2009 discusses elongation factors in Hacrobia but it appears to be a different gene and I've only seen the abstract, not the article). But as interesting as this is, we don't really need to worry about it too hard to write wikipedia articles; we merely need to note the lack of scientific consensus. This is more or less like WP:NPOV although I would note the (subtle/fuzzy) difference between controversy among opinions versus weighing of facts/evidence. As for any articles which assume Adl2005, I agree those need to be cleaned up (I think I, and perhaps others, fixed the worst of it a year or a few ago, but there is surely some left). Don't get me started on wikispecies :-). Kingdon (talk) 12:22, 4 May 2010 (UTC)

Famine vs Blight

It would be much more precise (and much less offensive) to say that water molds caused the Irish Potato Blight (as opposed to causing the Famine). Socio-political factors enabled the Potato Blight (which only killed potatoes) to lead to the Great Irish Famine (which killed Irish). — Preceding unsigned comment added by 159.53.78.143 (talk) 20:09, 18 February 2013 (UTC)