Talk:Human genetic clustering

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 {{u|Millager}} who wrote the article. I invite those concerned with the problems of the old article, including {{u|Citing}}, {{u|XOR'easter}}, {{u|Vanamonde93}} to improve the new article.--Carwil (talk) 15:20, 4 May 2021 (UTC)

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

::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)

:::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)

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 [https://journals-plos-org.proxy.library.vanderbilt.edu/plosgenetics/article?id=10.1371/journal.pgen.0030160 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 [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869013/ white paper on this issue].
• Describing admixed populations, such as [https://www.nature.com/articles/ncomms14238] [https://www.nature.com/articles/ncomms14238] [https://pubmed.ncbi.nlm.nih.gov/31545791/]
• So-called fine structure studies of regional populations, like [https://www.nature.com/articles/nature14230 this one]
• A more detailed summary of the critical literature on the uses and limits of STRUCTURE. A quick bibliography:
• {{Cite journal| doi = 10.1093/genetics/155.2.945| issn = 1943-2631| volume = 155| issue = 2| pages = 945–959| last1 = Pritchard| first1 = Jonathan K| last2 = Stephens| first2 = Matthew| last3 = Donnelly| first3 = Peter| title = Inference of Population Structure Using Multilocus Genotype Data| journal = Genetics| accessdate = 2021-02-16| date = 2000-06-01| url = https://doi.org/10.1093/genetics/155.2.945}}
• {{Cite journal| doi = 10.1534/genetics.116.195164| issn = 1943-2631| volume = 204| issue = 2| pages = 391–393| last = Novembre| first = John| title = Pritchard, Stephens, and Donnelly on Population Structure| journal = Genetics| accessdate = 2021-02-16| date = 2016-10-01| url = https://doi.org/10.1534/genetics.116.195164}}
• {{Cite journal| doi = 10.1038/hdy.2010.95| issn = 1365-2540| volume = 106| issue = 4| pages = 625–632| last = Kalinowski| first = S. T.| title = The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure| journal = Heredity| accessdate = 2021-02-11| date = 2011-04| url = https://www.nature.com/articles/hdy201095}}
• And maybe… {{Cite journal| doi = 10.1038/s41467-018-05257-7| issn = 2041-1723| volume = 9| last1 = Lawson| first1 = Daniel J.| last2 = van Dorp| first2 = Lucy| last3 = Falush| first3 = Daniel| title = A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots| journal = Nature Communications| accessdate = 2018-09-10| date = 2018-08-14| url = https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092366/| pmid = 30108219| pmc = PMC6092366}}

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

The methods discussed in this article are used in a variety of species (e.g. [https://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-020-04278-w mosquitos], [https://www.nature.com/articles/srep41417 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)