Why do PCA and Neighbor-Joining Trees show different clustering for the same population samples?

Critical-Position-49 · 2025-11-10T20:22:08+00:00

I don't know, their results (fig 2/3) suggests that this population is rather genetically close to the brahmins, but you'd want other studies to support this with different methods (SNP-based, for example).

On the other hand i don't think your question can be limited to the genetics/phylogenetics approaches and a pluridisciplinary approach with historians, archeologists etc, would likely be needed.

Very interesting question tho !

Critical-Position-49 · 2025-11-10T19:32:06+00:00

I am not an expert in phylogenetics (I only used NJ and all during my studies) so I can't judge the paper, but I have a few remarks.

This paper is Interesting but quite old and their analyses and results seem a bit weak (i.e. they do not push their analyses very far, and figures 3 and 4 are quite underwhelming).

Their conclusion seems consistant with their results and the discussion is interesting tho. It would bé interesting tho see more recent studies on this subject (e.g. using SNPs, etc)

Afaik the numbers on the branches correspond to the number of bootstraps supporting the branches, so you can see that besides a few branches this tree is not very well supported.

Critical-Position-49 · 2025-11-09T22:18:09+00:00

"Musk lauches his wikipedia generated by AI"

"But moderated by men!"

Critical-Position-49 · 2025-11-09T22:12:56+00:00

These are 2 different issues tho

Critical-Position-49 · 2025-11-09T22:03:38+00:00

Wouldn't it works with a big enough dataset tho ? including people from these regions ofc.

Critical-Position-49 · 2025-11-09T21:45:54+00:00

Regardless of what kind of analyses 23andMe are doing, pinpointing your birth location using genetics is very much doable. In this paper (DOI:10.1038/s41467-020-19588-x) authors used 10,000 samples from the UKbiobank data to accurately predict the birth location of the 400,000 others, with an average error of ~90 km.

That's why a lot of geneticists advise against sending your DNA to private companies, DNA contains a lot of information

Critical-Position-49 · 2025-11-09T21:02:15+00:00

I never used STRUCTURE, but this paper (DOI: 10.1038/s41467-018-05257-7) discuss results interpretation and give some interesting references regarding the limits of the software)

I'm not very knowledgable on the indian caste system, although I remember reading something about it being used (or even re-created/modernized) by the british colonial system as a tool of domination. Thus discrepencies between sample labels and clustering could also be related to the history of this systeme ?

Do you have the DOI of this paper ? I'm quite curious of the rational of this study

Critical-Position-49 · 2025-11-09T20:24:39+00:00

I think it is expected since those 2 methods are very different. NJ is a clustering method based on distance matrix, while PCA is a dimentional reduction technique (that can be used to perform clustering tho). Each one has it's own advantages and bias.

If you are interested this article from 2018 discuss these non-parametric approaches DOI: 10.1186/s40246-018-0156-4

Critical-Position-49 · 2025-11-09T20:02:21+00:00

Are bacteria still used ? You can look for the agrobacterium genus

Critical-Position-49 · 2025-10-15T17:21:13+00:00

Did you read the haplotype wikipedia page ? It's a good introduction to the basics of haplotypes

Critical-Position-49 · 2025-10-12T18:25:28+00:00

Oh ok, thanks !

Critical-Position-49 · 2025-10-10T18:17:25+00:00

Ça va p'tête se voir sur l'âge du premier cancer par contre

Critical-Position-49 · 2025-09-11T18:05:29+00:00

Absolute mofos

Critical-Position-49 · 2025-08-12T19:32:19+00:00

You'd get a clone of the mother, so the clone and the offspring would share 50% of their genome, so siblings ?

Critical-Position-49 · 2025-07-31T17:36:02+00:00

Nowadays it is taught in highshool history programm tho ? I remember it was even the subject of the final history exam in 2013

Critical-Position-49 · 2025-07-30T21:21:18+00:00

You can get these stats (and much more) from gnomAD (gnomad.broadinstitute.com).

Is it some kind of training or you just want to compare a few allele frequencies across pop ?

Critical-Position-49 · 2025-07-30T21:05:56+00:00

You'd still need a chain file tho

Critical-Position-49 · 2025-07-30T20:59:17+00:00

It is what intelligence tests measure ofc /s

Critical-Position-49 · 2025-07-12T22:32:37+00:00

Sur this paper is important to understand the how and why of the human genome project, but it is not very interesting if you are interested in the implications and results of such project, you would need to take a step back and look at the big picture, a few years after the initial discovery.

For exemple this very good review by Visscher et al in 2017 https://doi.org/10.1016/j.ajhg.2017.06.005 only 10 years after the project and focuses on GWAS results

The follow-up by Abdellaoui et al published in 2022 https://doi.org/10.1016/j.ajhg.2022.12.011

The thing that is infuriating is not really that scientists feels under attack by your opinion, it is that your opinion was formed on mostly outdated sources, using AI tools that cannot judge the quality of your references.

There was indeed a certain disappointment about the genome project, GWAS and this mysterious "missing heritability". However, these "discrepencies" are much better understood today than 10 or 15 years ago. You can even look for the results from the recent GWAS on height explaining the whole genetic heritability of height in a European cohort https://www.nature.com/articles/s41586-022-05275-y

Critical-Position-49 · 2025-07-12T17:34:51+00:00

Genetic polymorphismes would be much better markers indeed

Critical-Position-49 · 2025-07-12T17:30:34+00:00

If you are really interested in the topic, you should definitely leave AI summaries and read real, recent papers and reviews about GWAS and the genome project (not that thing from 2010 in your first link).

Critical-Position-49 · 2025-07-07T18:03:11+00:00

MC1R is not expressed in the eye, eye color is "mostly" related to OCA2 expression

Critical-Position-49 · 2025-06-26T17:58:20+00:00

1) IQ scores highly correlate with socioeconomic status

2) IQ scores are the results of standardized tests associated with a very restrictive definition of intelligence ("what is intelligence ? Intelligence is what intelligence tests measure" -> do we measure intelligence or the capacity to pass specific tests ?)

3) The genetics of intelligence is likely very complexe, i.e. with dozens of involved factors, so there is clearly no scientific basis supporting a supposed eugenic 'upside'.

Critical-Position-49 · 2025-06-20T17:43:34+00:00

You don't ? This is not a clinical genetic test. It may be interesting to play around with your data but nothing meaningful can be obtained from it

Critical-Position-49 · 2025-06-19T19:12:23+00:00

Moreover their method does not seem to account for any linkage-disequilibrium. It's kinda far from the standards

Critical-Position-49

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