Talk:Holozoa/GA1

GA Review
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Reviewer: Esculenta (talk · contribs) 20:27, 23 August 2023 (UTC)

Hi, I will review this article. Comments coming in a day or two. Esculenta (talk) 20:27, 23 August 2023 (UTC)

Initial thoughts:

Lead

The lead does not adequately summarize the contents of the article. In addition to what's already there, here are some things that should be addressed in the lead:
 * major subgroups: A quick mention of the primary subgroups or lineages within Holozoa, e.g. "Holozoa consists of various subgroups, including Filasterea, Choanoflagellata, and Metazoa (or animals)."
 * distinctive characteristics: If there are any unique or defining characteristics shared by members of this group, e.g. "Organisms in Holozoa typically share certain cellular characteristics, like a specific type of collar complex in choanoflagellates and some specific molecular markers."
 * relation to other groups: Any close relations or sister groups to Holozoa, e.g. "Holozoa, along with Fungi and some other groups, are part of the larger supergroup known as Opisthokonta."
 * current research or discoveries: Any mention of notable recent research, findings, or controversies, if they are highly relevant or have gained significant attention, e.g. "Recent genomic studies have shed light on the evolutionary relationships between the various Holozoan lineages, revealing insights into the origins of multicellularity."

The 3rd sentence addresses the significance of Holozoa in evolutionary biology (good), but it is a bit difficult to parse. Could it expressed more simply, such as "They play a crucial role in understanding the evolutionary steps leading to the emergence of multicellular animals from single-celled ancestors."

Definition and subdivisions
 * perhaps the original definition could be streamlined for clarity? Original: "Holozoa is the most inclusive clade containing Homo sapiens (a metazoan), but not Neurospora crassa (a fungus)." Suggested: "Holozoa is a clade that encompasses Homo sapiens (metazoans) and excludes fungi like Neurospora crassa."
 * suggest grouping ideas here for better flow? Original: "It is a clade with a branch-based definition: it contains all the closest relatives to animals that aren't fungi, as well as their common ancestor." Suggested: "Defined on a branch-based approach, it includes animals' closest relatives, barring fungi, and their common ancestor."
 * is this better? Original: "These mostly unicellular relatives are the protist lineages of choanoflagellates, filastereans, ichthyosporeans, and three independent genera Corallochytrium, Syssomonas and Tunicaraptor." Suggested: "Holozoa primarily comprises unicellular protist lineages such as choanoflagellates, filastereans, ichthyosporeans, and the distinct genera Corallochytrium, Syssomonas, and Tunicaraptor."
 * better? Original: "This taxon excludes the animals, which are descendants from the common ancestor of choanofilan protists. Therefore, it is a paraphyletic taxon, not a clade." Suggested: "This classification excludes animals, even though they descend from the same common ancestor as choanofilan protists, making it a paraphyletic group rather than a true clade."
 * more clarity on lineage: Original: "The clade was first discovered through phylogenetic analyses in 2002." Suggested: "The recognition of Holozoa as a distinct clade was established through phylogenetic analyses in 2002."
 * avoid repetition: Original: "This collar strongly resembles the collar cells of sponges; because of this, choanoflagellates were theorized to be related to sponges even in the 19th century." Suggested: "The collar of choanoflagellates closely resembles sponge collar cells, leading to theories since the 19th century about their relatedness to sponges."
 * maybe rephrase for better structure: Original: "Ichthyosporea or Mesomycetozoea (~40 species) are mostly parasites or commensals of a wide variety of animals, including humans, fish, and marine invertebrates." Suggested: "Ichthyosporea, also known as Mesomycetozoea and comprising around 40 species, largely consist of parasites or commensals. They interact with a diverse range of animals, from humans and fish to marine invertebrates."

Evolution Compare for example this with what's currently in the article:
 * The statement about the "two different hypotheses for the position of the Pluriformea clade" might benefit from a slightly more detailed explanation to enhance clarity. Are these different hypotheses from different research groups? Or two suggestions from 1 group about how to explain the observed data?
 * why are last metazoan common ancestor and unicellular metazoan common ancestor italicized?
 * The section on the "nature of the last metazoan common ancestor" is quite technical. Rewording or simplifying complex sentences might make it more accessible to general readers.

"The quest to elucidate the evolutionary origins of animals requires an examination of the pivotal transition from unicellular to multicellular organisms. In the absence of a comprehensive fossil record documenting this evolution, insights are gleaned from the analysis of shared genes and genetic pathways between contemporary animals and their most proximate unicellular counterparts.

Modern techniques in DNA sequencing have made it possible to delve deeper into the genetic content of ancient single-celled organisms related to animals. A significant discovery from this research is that many genetic characteristics we previously thought were unique to animals can also be found in these unicellular relatives. This suggests that the rise of multicellular animals did not happen solely because of the appearance of new genes. Instead, it seems that existing genes from their single-celled ancestors were adapted or utilized in new ways.

For more specific examples:


 * Adhesion Proteins: These are key in allowing cells to stick together, forming layers and tissues in animals. Some of the earliest unicellular organisms, like choanoflagellates, possess genes that encode for proteins involved in this cell-to-cell adhesion. While certain components, like β-catenin which regulates animal adhesions, seem to be found only in animals, others are observed in these unicellular relatives.
 * Cell-ECM Adhesion Systems: Filasterean organisms, like Capsaspora, possess a complete system similar to what is seen in animals, further bridging the gap between single-celled and multicellular organisms.
 * ECM-related Proteins: These proteins are involved in forming the cell's external matrix. Other ancient single-celled organisms, referred to as holozoans, have proteins connected to the extracellular matrix of animals, including components like laminins, collagens, and fibronectins."

This is just an example; I'm probably leaving out facts you might think are important, or getting other details wrong, but the idea is to try to present it more simply for the reader.

Ok, there's some stuff to think about! I'll be back after you've had time to digest and respond. Esculenta (talk) 22:43, 23 August 2023 (UTC)
 * The caption for the Bicellum brasieri image should provide a brief description or context. For instance: "A fossilized sample of Bicellum brasieri, a billion-year-old potential holozoan."
 * I think the section titled "Taxonomy" should be called "Classification". In biological sciences, taxonomy refers to the practice and science of classification, including the principles, rules, and procedures established by taxonomists to classify organisms. Taxonomy encompasses not just the classification of organisms but also their description, identification, nomenclature, and overall systematic arrangement. Classification, on the other hand, specifically pertains to the arrangement of organisms into groups based on similarities or differences. It's more about the hierarchical structure and categorization of organisms. The section provided is primarily focused on the hierarchical arrangement of Holozoa and related groups.
 * For a "true" taxonomy section, I think this sentence (from the Definition and subdivisions section) needs to be expanded in much more detail: "The clade was first discovered through phylogenetic analyses in 2002." Who did this work? Which institutions were they affiliated with? Knowing the researchers can also provide a backdrop against their previous works or the broader context of their research interests. Was there a particular reason or earlier finding that prompted them to investigate the Holozoa clade? Had there been previous, perhaps non-molecular, evidence suggesting such a group might exist? How many organisms were studied, and how diverse were these samples? Were they representative of a wide variety of groups, or were they more narrowly focused? What specific molecular techniques did they employ? Which genes or genetic markers did they analyze? Was their work reproduced and corroborated in later works? How did other experts in the field react to this new classification? Were there endorsements, criticisms, or debates? How was their work built upon by others in the field? Were their results reproduced, refined, or even challenged by later research?
 * Also, the etymology is given in the lead sentence (only), without a source. It needs to be also in the body of the article (perhaps in a revamped Taxonomy section?) with a source. Esculenta (talk) 23:12, 23 August 2023 (UTC)
 * might it be worth mentioning that the first sequenced unicellular Holozoan genome was that of Monosiga brevicolis? Then the major differences in the genomes (i.e., size, # of genes) between this species and different animals could be mentioned.
 * I think it would be useful to know about how many species are in each of the component groups, if this information is readily available? Missing from the article is a statement of how many taxa there are in the Holozoa.
 * Have you seen this paper, which describes uses environmental metagenomics on ocean water samples, finding 2000 unique sequences that are likely to represent unknown or uncharacterized unicellular Holozoans in the world’s oceans? I think that the mention of this group (MASHOL-Marine Small HOLozoa) would benefit the article. Esculenta (talk) 01:11, 24 August 2023 (UTC)
 * It would be good to mention both in the lead, and in the article body, the estimated time of divergence from its ancestor; I gather it's 1100 Mya from the cladogram, but this should be made explicit in the article text so it can also be specifically sourced. Esculenta (talk) 02:22, 24 August 2023 (UTC)
 * @Esculenta Hi, thank you so much for reviewing the article. I can tell you've put a lot of effort and work into this. I will be making the changes and updating you as soon as possible on each comment. The first one concerns the time divergence; I have had a hard time finding any source confirming the 1100 Mya (or any source that mentions a holozoan divergence time) but I have found one source that puts it at 1070 Mya instead, even though the study itself focuses on Amorphea as a whole. I will update the text accordingly. —Snoteleks 🦠  15:12, 24 August 2023 (UTC)
 * @Esculenta not sure if the ping works but I wanted to let you know I think I have applied all the changes that you suggested. Your advice was extremely useful and I found your suggested text to be very adecuate. I haven't been able to comment all of my changes individually but I would like you to review the state of the article as it is now. Let me know what you think and if there is anything else I can improve about it. —Snoteleks 🦠  10:24, 26 August 2023 (UTC)
 * The improvements look great! I will re-review the article over the next day or two against the GA criteria and get back soon. Esculenta (talk) 18:51, 26 August 2023 (UTC)


 * <--I've made several copyedits and added a bunch of links; please check and feel free to revert if you don't agree.
 * perhaps the Greek words/transcription is just a bit too much detail for the opening sentence of the lead (supposed to be easy-to-read for the layperson)? Of course the extra detail is welcome down below.
 * In the lead, I think it should be made clearer that Choanofila is a taxon name that was previously used as the name for a group similar in composition to Holozoa, but its usage is discouraged now. Right now, the significance of the word doesn't really make sense until later in the article.
 * "Pluriformea is a provisional name" would it be appropriate to link this term (the link would then redirect to undescribed taxon)
 * "Tunicaraptor unikontum is a recently discovered species" avoid using "recently" (see WP:RECENTLY) and give the year of discovery instead
 * "Holozoa diverged around 1070 million years ago (Mya)." I think a few more words of context are needed … "diverged from their ancestor around …" or something like that
 * "the Pluriformea clade receives more statistical support" link to Robust statistics?
 * have you seen the diagram on the right? RG347357480 Fig1.png Maybe worthy of inclusion in the "Unicellular ancestry of animals" subsection?
 * link morphology on its 1st occurrence
 * "It is currently an accepted clade by the International Society of Protistologists" suggest: "As of 2019, the clade has been accepted by the …"
 * current text: "Modern classifications of eukaryotes give preference to clades and strive away from the traditional ranks, which are seen as superfluous." Suggest: "Modern cladistic approaches to eukaryotic classification prioritise monophyletic groupings over traditional ranks, which are increasingly perceived as redundant."
 * I'm not sure how I feel about the parenthetical synonymy information in the Classification list. I suppose it's somewhat useful to be reminded that Metazoa is equivalent to Animalia and Eumetazoa, but the 9 synonyms of Choanoflagellata, for example, seems like detail that belongs on that page, not here. Also, it's not currently clear from what source(s) this synonymy information originates. Esculenta (talk) 01:35, 27 August 2023 (UTC)
 * @Esculenta All synonyms come from the Adl et al. (2019) publication, which I cite at the end of the paragraph of the Classification section. I agree it's not very relevant here. I might just delete that specific synonymy or perhaps leave only Choanoflagellatea since it's one of the most known currently.
 * The rest of the suggestions are very good, except the etymology one. But only because every other article I have seen does the etymology thing in the lead, right after the name. So I'm not sure if it's a good idea or not. I personally don't have an issue with erasing the etymology from the lead but it feels weird not to have it consistent with other articles. I don't even know if there is a policy regarding etymology. —Snoteleks 🦠  09:43, 27 August 2023 (UTC)
 * @Esculenta I forgot to mention, all of your copyedits and small changes were very positive, thank you for that. I didn't know there was a standardized quotation mark. —Snoteleks 🦠  10:13, 27 August 2023 (UTC)
 * @Esculenta Okay, I've made all the newly suggested changes except the etymology one. Let me know what you think! —Snoteleks 🦠  10:30, 27 August 2023 (UTC)
 * Changes look good; I am currently travelling and editing on iPad, but will see if I can wrap this up tonight. If not, will be back in a few days and will finish then. Esculenta (talk) 17:12, 30 August 2023 (UTC)
 * Alright, see you then. —Snoteleks 🦠  22:23, 30 August 2023 (UTC)

Thanks for your patience. Final thought about the new additions: the developmental processes image caption mentions the actomyosin network, which is information not directly presented in the article text; perhaps the caption should be cited to the original (open access) paper? Otherwise:
 * all images appear to be appropriately licensed and have suitable captions (this includes the 12 images comprising the Holozoan diversity collage in the taxobox, and the 9 images in the cladogram).
 * I spot-checked several statements; in all instances the checked text was supported by the citation.
 * I think the article is well-written, follows the MoS, is broad in its coverage, presents technical information in a way that's understandable for the layperson, and meets the other good article criteria. Promoting now. Esculenta (talk) 22:43, 7 September 2023 (UTC)