Talk:Human genetic clustering

This article was nominated for deletion on October 29, 2020. The result of the discussion was delete.

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Article recreated following deletion

This is just a note to say that this article was created, largely from scratch but incorporating some pre-deletion segments, following its deletion in October 2020. Many in the deletion discussion recommended WP:TNT as a solution. As a Wiki Education instructor, I supervised a student Millager who wrote the article. I invite those concerned with the problems of the old article, including Citing, XOR'easter, Vanamonde93 to improve the new article.--Carwil (talk) 15:20, 4 May 2021 (UTC)[reply]

I think this is a great start, thank you and Millager for doing the legwork.Citing (talk) 15:34, 4 May 2021 (UTC)[reply]

I am concerned about the framing of the final section, "genetic clustering and race". The views discussed in the second paragraph represent the mainstream view among biologists today; that genetic clustering correlates with ancestry, but that they both have a tenuous link at best to socially constructed race. Those are the sources that need to be used to frame the section; the view in the first paragraph are historical and/or based on a complete misunderstanding of race, and need to be treated as such. The final paragraph is well-written, and is a model for how the first ought to be framed. Vanamonde (Talk) 19:13, 4 May 2021 (UTC)[reply]

I rewrote the first paragraph to better reflect what the main sources actually said (at no point did Rosenberg's study suggest humans be split into five populations, rather that they found six clusters with five corresponding to geographic regions). I'm hoping it clears up some confusion about why clusters are not race but why people might think they are, but I'm open to anything.Citing (talk) 21:21, 4 May 2021 (UTC)[reply]

Comments on this draft

Opening conceptual comment: I'm not sure whether you should say that "clustering" refers to the pattern of relative genetic similarity among human individuals and populations, as well as the tools to study this phenomenon, but I think that would be a good idea. It does require re-writing the opening a little, though.

Your lead section offers a great and detailed conceptual summary. Be sure to cite claims like "Humans tend to cluster together by geographic ancestry…" The sentence afterward might also be cited to Kalinowski et al. (see below). The only thing missing from the lead, I think, is summaries of other non-global and therefore non-race-focused studies of genetic clustering. Read on for my suggestions for things that might be covered.

Things that could be added to this article:

Many techniques are "model-based," but you don't explain the model. STRUCTURE and ADMIXTURE, in particular, imagine distinct ancestral populations that combined and formed the current populations. Tell that story so that the "clusters" are put in context.
The applications section currently only considers studies of global human population, but there are significant other studies, most notably on…
- Ancestry inference: Such as this one that claims "Analyzing a Puerto Rican dataset (192 individuals, 7,257 SNPs), we show that PCA-correlated SNPs can be used to successfully predict structure and ancestry proportions." You should probably reference the American Society of Human Genetics (ASHG) Ancestry and Ancestry Testing Task Force white paper on this issue.
- Describing admixed populations, such as [1] [2] [3]
- So-called fine structure studies of regional populations, like this one
A more detailed summary of the critical literature on the uses and limits of STRUCTURE. A quick bibliography:
- Pritchard, Jonathan K; Stephens, Matthew; Donnelly, Peter (2000-06-01). "Inference of Population Structure Using Multilocus Genotype Data". Genetics. 155 (2): 945–959. doi:10.1093/genetics/155.2.945. ISSN 1943-2631. Retrieved 2021-02-16.
- Novembre, John (2016-10-01). "Pritchard, Stephens, and Donnelly on Population Structure". Genetics. 204 (2): 391–393. doi:10.1534/genetics.116.195164. ISSN 1943-2631. Retrieved 2021-02-16.
- Kalinowski, S. T. (2011-04). "The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure". Heredity. 106 (4): 625–632. doi:10.1038/hdy.2010.95. ISSN 1365-2540. Retrieved 2021-02-11. {{cite journal}}: Check date values in: |date= (help)
- And maybe… Lawson, Daniel J.; van Dorp, Lucy; Falush, Daniel (2018-08-14). "A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots". Nature Communications. 9. doi:10.1038/s41467-018-05257-7. ISSN 2041-1723. PMC 6092366. PMID 30108219. Retrieved 2018-09-10.{{cite journal}}: CS1 maint: PMC format (link)

Good luck with this; you're off to a great start!--Carwil (talk) 22:52, 22 April 2021 (UTC)[reply]

Genetic clustering vs human genetic clustering

The methods discussed in this article are used in a variety of species (e.g. mosquitos, rhinos), but at the moment there is no article on genetic clustering. Are there any thoughts on moving this article there and having it be dedicated to mostly humans (since that's where a lot of the research is) and having a section to applications to non-humans (as with genome wide association study and polygenic score)?Citing (talk) 21:46, 4 May 2021 (UTC)[reply]