Talk:Bigyra

Improvements

This article needs big improvements. I'll get around to it if I have free time. For now, I can think of the following edits:

• Half of the lead makes no sense, it is weird that it mentions the subgroups in this vague incomplete manner.
• There needs to be a better phylogeny section.
• A section for characteristics or morphology or description or something like that would be nice.

☽ Snoteleks ☾ 06:57, 11 April 2023 (UTC)

Well, yes. The same applies to numerous other articles on clades, or shall I say supposed clades. Recent analyses break up the "Bigyra". Chiswick Chap (talk) 07:57, 11 April 2023 (UTC)

BTW: "Despite the power of large-scale phylogenomic analyses, the positions of the Opalozoa and Sagenista are not consistent among published analyses, and the phylogenetic validity of the Bigyra remains uncertain (Burki et al., 2016, Derelle et al., 2016, Noguchi et al., 2016)." Thakur et al, 2019

and in a 2020 preprint: "In the reconstructed phylogeny of Stramenopiles, Labyrinthula and other protist species in the phylum, Bigyra formed a paraphyletic group at the base of Stramenopile". Tan et al, 2020, which is at the least, suggestive.

Both the lead and the phylogeny section have been improved. ☽ Snoteleks ☾ 19:23, 11 April 2023 (UTC)

Very much improved, but the "possibly paraphyletic" remains very much the case! Chiswick Chap (talk) 19:26, 11 April 2023 (UTC)

Diversity

A section about bigyran diversity or ecology would be nice, since all the content right now is about the phylogeny. ☽ Snoteleks ☾ 19:22, 11 April 2023 (UTC)

GA Review

This review is transcluded from Talk:Bigyra/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Fritzmann2002 (talk · contribs) 00:34, 7 August 2023 (UTC)

Evening Snoteleks, I'll get started on this tonight. No rush for responses, take whatever time you need to make changes. Fritzmann (message me) 00:34, 7 August 2023 (UTC)

Lead

• Typically, leads don't have references (except for the Latin translation - that makes perfect sense). The rest of the lead should be a summary of the contents of the article; in other words, the references should be placed in the body of the article where the information is expounded upon.
• I'm not familiar with the terminology "lineage" with regards to the Stramenopiles, is that a technical term?
• Ideally, the lead would be lengthened quite a bit from its current state. As previously mentioned, it should provide a summary of the entire article. At the minimum, it should have a brief overview of the characteristics of the taxon, a quick word about its taxonomic status/history, and any unique ecological aspects that may be discussed.

Diversity and Ecology

• I think this should be two sections - or renamed to just diversity. It is difficult to pick out the ecology parts. It would be preferable to have a section devoted to the ecology of the clade. What is the range of niches that members occupy? Are there parasites in the clade (it seems there may be, though it just says they live in animal intestines) - or, in general, what are the organisms' relationships to their hosts? If it varies widely, say as much and maybe elaborate on the extremes.
• "The slime nets (known as Labyrinthulea, Labyrinthulomycetes, or Labyrinthulomycota) are fungus-like heterotrophic, colorless or yellowish protists that absorb nutrients in an osmotrophic or phagotrophic manner, either as free-living amoebae or as networks of anastomosing cytoplasmic threads that extend from a bothrosome. They are typically saprotrophic decomposers of the detrital food web" this whole part is... a lot. It is very difficult for even me to parse, and I have more exposure to these kinds of terms than most people are going to. Breaking this up into a few more sentences would be a good start, some simplification would be a nice entree, and brief explanation of the remaining jargon would make for a perfect dessert.
• Any reason proteromonads and opalinids are not linked in the first sentence instead of in there bullet point?
• Speaking of bullet points, I think that just having that information in prose makes more sense. Additionally, listing genera at a taxon this broad is a bit overkill; additionally, it is only done for a few of the subtaxa which does not help consistency.
• "Their (Bicosoecids) classification has changed multiple times over the years, and is still an unresolved issue." This definitely needs elaboration; the Bicosoecids are given much less time in the article than the other subtaxa and it appears there is great controversy over them from this statement, which is certainly warranted to include.
• To reiterate, I think that a dedicated ecology section is a good idea. At the very least, more on the ecology of the taxon is needed.

Origin

• Same note as for the first sentences of the slime nets section. This rapid-fire jargon is very difficult to digest. "double ciliary transition zone helix as its synapomorphy..." gesundheit
• "The common ancestor would have evolved from photosynthetic heterokonts, but would have secondarily lost its plastids, as opposed to the photosynthetic Ochrophyta which retain them." Okay, that makes sense after having read the Stramenopile article. However, any reason you refer to them as heterokonts? I understand that name has multiple meanings, am I correct in guessing that you are in fact referring to the Stramenopiles?
• "followed by", I'm not sure what this means. Temporally? In the tree of life? In time of description? Could use some clarification for dummies like me.
• This is extraordinarily nitpicky, but the color used for the Ochrophyta clade is exceptionally similar to the color that a widget gives to all disambiguation links; that's what I thought it was in the first place. Is there a particularly strong attraction to that color or could it be changed?

Taxonomic modifications

• Heterokonts used again here, same question applies.
• "Its monophyly was weakly supported" by whom? "weak support was thought to be caused by..." ah is this a computer model of some kind? What is the quantification of "weak support", if so?

Current phylogeny

• I don't have a great deal of notes for this section, but I can't help but feel like it is an inadequate summary. It would seem to me that the current phylogenetic status of the taxon is of great importance to the article, and should have at least a few paragraphs in content.

Other notes

• The characteristics of the taxon are briefly mentioned in the lead, but I found no elaboration on it? A characteristics or description section would certainly be welcome. What makes this taxon unique? What made someone set it apart? Perhaps there may not be enough to set it apart and authors have pointed that out - include that as well!
• More pictures are needed in my opinion! Images are the perfect way to get across the diversity of a high-level taxon, especially one that is paraphyletic. At a minimum, I would argue for the inclusion of an image of a species belonging to each of the three immediate subtaxa.

First summary

Overall, the article definitely needs some major work. I've not done reference checks or anything like that yet, just a content check. Even so, the article is difficult to broach due to exceedingly complex verbiage utilized in prompt succession, assembled in prolix sentences of ceaseless moribundity. Kind of like that one, for example. Additionally, it seems that there is more information that could be added across the sections. In particular, the characteristics, ecology, and current phylogeny need to be expanded. However, the writing clearly demonstrates an intimate and detailed understanding of the subject. The article is clear once the jargon is deciphered, and if elbow grease is applied it stands to be made into an exceptional example of biology content on Wikipedia. Once some of these preliminary concerns are addressed, I'll go back over for a second run-through which will (hopefully) result in a promotion shortly thereafter. Very Respectfully, Fritzmann (message me) 01:33, 7 August 2023 (UTC)

Hi Fritzmann, thank you for reviewing. I'll try to answer every point.

• Lead
  • I have taken out all the references from the lead, except for the translation.
  • The term 'lineage' is not technical at all, it's just a synonym for clade as far as I know. Well, maybe it is technical, but I have always thought of it as a more informal term.
  • I have lengthened the lead as much as I can for now.
• Diversity and Ecology
  • I'm afraid this part is the one I'm having the hardest time with. There is very little, if not nothing, to be said about Bigyra as a whole in terms of both diversity and ecological impact. Bigyra is just a phylogenetic taxon, but its components are all ecological taxa. Every piece of ecological information about Bigyra belongs to only one of its three main groups: labyrinthulomycetes, bicosoecids or opalines. That is why I'm struggling to find a way to separate the diversity talk from the ecology talk. I think "Diversity and ecology" (now better written) is the best I can hope for, for now. Please take a look at the section and let me know what you think now. I also erased the bullet points.
  • I think you'll find the labyrinthulomycetes paragraph better written now.
  • Proteromonads and opalinids were not linked in their first mentions because I prefer to link them when elaborating about them fully (but I know the first mention should be the first linked). Now I have simply ommitted their first mention, so it should be fixed.
  • I elaborated more on bicosoecids.
  • Again, if I could, I would definitely make an ecology section separate, but for now it's just too redundant. Any way I can change your mind?
• Origin
  • Simplified/clarified jargon. I struggled reading it too.
  • Yes that is correct, heterokont is a synonym for stramenopile. The only reason I refer to them as heterokonts is because the sources I use for that specific paragraph use heterokont and Heterokonta instead. But they are interchangeable.
  • Clarified the "followed by".
  • You're right, the font color is a bit too orange. The reason is that ochrophytes are named that way because a lot of them have an ochre color, so I went with that color for the font. It is changed now to be more deep brown.
• Taxonomic modifications
  • Yes, it is essentially because of computer models. But I erased all mentions of "weak support" because it is overly technical for a page this small. I think you'll find it easier to read now. I also erased other unnecessary parts of the section.
• Current phylogeny
  • It definitely was an inadequate summary. I moved all of that into a new "Evolution and systematics" section where I think it is more fitting.
• Other notes
  • The characteristics of this taxon is one of the most frustrating parts of it. There is no modern mention of the morphological characteristics that unify the taxon (the double helix definition is outdated, as mentioned in the "History" section). I inserted the current description of Bigyra as the first phrase in the "Ecological diversity" section, but there's not much else to be added other than "heterotrophic, mainly phagotrophic, no cell walls". Another way that Bigyra is defined is by mentioning all the groups included in it, so I think the lead is sufficient in that aspect.
  • I agree, more images is always better. I put some in the main cladogram and the "Ecological diversity" section. —Snoteleks 🦠 15:31, 7 August 2023 (UTC)

Changes response

All changes look very positive so far. My only concern is that there is still some important material in the sources that is not entirely represented by the article. I had a similar problem regarding scarcity of information when I nominated Hypericum sechmenii. However, with some more intensive research, the article was able to go from 650 words to almost 1700 words. I'm going to work on some other reviews and leave the article on hold for the time being, just to give some more time to find sourcing or expound upon the references already in the article. In-depth and complex biological topic absolutely belong in the article; they just need to be carefully written in order to be as approachable as possible. It is definitely close and certainly on the right track, but the content already in the article suggests that there is more to say on the subject. Fritzmann (message me) 19:04, 7 August 2023 (UTC)

@Snoteleks: any update on the article? There haven't been any major changes since the review, and the article has exited the typical seven day period for review fixes. In its current state, the article is not prepared for GA but if you have been working on expansions I wanted to give a chance for you to incorporate those. Fritzmann (message me) 20:37, 15 August 2023 (UTC)

@Fritzmann2002 To tell you the truth, for the past five days I have been preoccupied with personal stuff that I didn't foresee before nominating the article. I haven't had the time or internet connection to make any changes or at least do more research on Bigyra. Right now I've returned to normal but I understand that it's been too many days already. I've restarted the work on it today, but I have no expansions prepared. You can fail the GAN and I will nominate the article again when I think it's ready. Thank you anyway for giving me a chance. —Snoteleks 🦠 21:51, 15 August 2023 (UTC)

That sounds good to me, please feel free to drop me a ping once you're ready and I'll be happy to hop back on the review! Fritzmann (message me) 01:54, 16 August 2023 (UTC)