G25 coordinates of non-human primates

[cass]

Not sure if this was already shared, but it’s funny.



Primate_Chimp.HO:Chimp_HO.HO,-0.686353,0.064994,0.035072,0.056525,0.016926,-0.006414,0.250756,-0.184146,-0.032315,0.047199,0.004872,-0.064892,-0.002379,0.003991,0.007736,-0.002652,0.019558,0.111359,-0.027276,-0.005628,-0.016596,0.006306,-0.001479,-0.004699,-0.018801
Chimp.REF,-0.676109,0.057885,0.02753,0.056525,0.009848,-0.00753,0.253106,-0.191992,-0.024134,0.040092,0.008444,-0.061595,-0.005203,0.00234,0.010722,-0.011933,0.015255,0.143792,-0.043869,-0.002501,-0.01435,0.000618,-0.000246,-0.004217,-0.009939
Gorilla.REF:Gorilla.REF,-0.670418,0.055854,0.025644,0.055879,0.007694,-0.008367,0.249346,-0.1883,-0.022702,0.042279,0.009256,-0.061295,-0.004757,0.001514,0.010043,-0.012729,0.013169,0.143285,-0.041103,-0.000375,-0.01672,0.000371,-0.002342,-0.002048,-0.009221
Bonobo_SAMN13935689_simulated_g25_scaled,-0.630267,0.047118,0.023308,0.04569,0.004497,-0.010584,0.259116,-0.200025,0.002095,0.027023,0.006407,-0.070165,-0.023447,0.008379,0.019256,-0.023548,0.035333,0.38415,-0.131672,0.008446,-0.050451,-0.004686,0.011635,-0.004286,0.002588



Target: cass
Distance: 88.5540% / 0.88554032
100.0 Gorilla.REF

Distance to: cass
0.88554032 Gorilla.REF:Gorilla.REF
0.89235959 Chimp.REF
0.89385825 Primate_Chimp.HO:Chimp_HO.HO
0.93838327 Bonobo_SAMN13935689_simulated_g25_scaled



+ Plus, as a control, hominids.

Denisova25:Denisova25__BC_198050__Cov_100.00%,-0.671556,0.053823,0.027153,0.072352,0.018465,-0.03514,0.260627,-0.195915,-0.034974,0.046652,0.008769,-0.060097,-0.001189,-0.000688,0.012758,-0.016309,0.014081,0.146452,-0.041983,-0.003001,-0.017344,0.000742,-0.000616,-0.006868,-0.013532
Altai_Neanderthal.DG:AltaiNeanderthal.DG__BC_10850 0__Cov_99.92%,-0.663589,0.050776,0.032055,0.068153,0.015695,-0.023706,0.265327,-0.204684,-0.028429,0.056311,0.009743,-0.063394,-0.007433,0.000688,0.011401,-0.015513,0.014473,0.148732,-0.040978,-0.000875,-0.016346,0.001237,-0.001725,-0.00735,-0.010658
Altai_Neanderthal.DG:AltaiNeanderthal_snpAD.DG__BC _108500__Cov_92.26%,-0.664727,0.051792,0.032055,0.067184,0.014772,-0.023985,0.264622,-0.203991,-0.028838,0.056129,0.009256,-0.061295,-0.006987,0.001514,0.010722,-0.015115,0.014212,0.148986,-0.041606,-0.001126,-0.017095,0.001237,-0.002342,-0.007832,-0.010298
DenisovaNeanderthalMix.SG:Denisova11.SG__BC_96750_ _Cov_74.15%,-0.667003,0.055854,0.03017,0.070414,0.018465,-0.025658,0.262037,-0.200992,-0.031292,0.049386,0.00747,-0.062644,-0.000743,0.002064,0.014794,-0.01432,0.014864,0.147719,-0.041229,0.001626,-0.019091,0.003833,0.001479,-0.003494,-0.016885
Mezmaiskaya3_Neanderthal:Mez3__BC_94750__Cov_11.04 %,-0.552042,0.053823,0.025267,0.052649,0.020004,-0.014502,0.196469,-0.169378,-0.026793,0.050662,0.014615,-0.066841,-0.0055,-0.000826,0.009908,-0.013259,0.014733,0.128209,-0.033436,0.003001,-0.009733,0.007296,-0.008997,-0.008796,0.003233
Neanderthal:Mezmaiskaya1_final_provisional__BC_630 50__Cov_56.66%,-0.631718,0.044683,0.030924,0.065246,0.015387,-0.016455,0.246526,-0.193146,-0.027815,0.050662,0.006658,-0.059347,-0.004311,0.004129,0.013708,-0.012861,0.008214,0.145565,-0.037081,0.007629,-0.012977,-0.000371,-0.006655,-0.003133,-0.008981
Denisova.DG:Denisova3.DG__BC_61950__Cov_99.89%,-0.672695,0.052808,0.024513,0.071706,0.019388,-0.035419,0.261567,-0.19753,-0.031906,0.04647,0.010393,-0.063394,-0.001933,-0.001789,0.01045,-0.016043,0.015646,0.145185,-0.040852,-0.001626,-0.019091,0.000247,-0.00037,-0.002771,-0.015448
Denisova.DG:Denisova3_snpAD.DG__BC_61950__Cov_92.2 4%,-0.674971,0.052808,0.024513,0.071706,0.018773,-0.03514,0.261332,-0.19753,-0.033133,0.046106,0.010555,-0.061595,-0.001933,-0.000826,0.010043,-0.01538,0.015646,0.145692,-0.042235,-0.002251,-0.019216,0.000866,0.000616,-0.003133,-0.015567
Denisova_light.SG:Denisova_light.SG__BC_61950__Cov _49.90%,-0.682939,0.058901,0.032809,0.071706,0.026159,-0.039045,0.260157,-0.190146,-0.041927,0.045559,0.011205,-0.063094,0.004906,0.002064,0.011672,-0.014983,0.011343,0.104011,-0.021369,0.0005,-0.00549,0.003215,-0.005423,-0.004097,-0.022872
Chagyrskaya_Neanderthal.DG:Chagyrskaya8_snpAD.DG__ BC_51450__Cov_92.25%,-0.663589,0.050776,0.032432,0.068799,0.01508,-0.023706,0.264387,-0.20353,-0.030065,0.057404,0.009581,-0.063244,-0.006838,0.000138,0.009908,-0.014054,0.012386,0.149746,-0.041732,0.001751,-0.017594,0.001484,-0.001109,-0.008073,-0.010658
GrotteMandrin_Neanderthal:Mandrin1600__BC_48525__C ov_59.10%,-0.645377,0.051792,0.031678,0.064923,0.019696,-0.016176,0.252871,-0.197069,-0.029656,0.053395,0.009581,-0.059197,-0.004757,-0.003853,0.013436,-0.014452,0.012256,0.147339,-0.038589,0.004502,-0.016845,0.002473,-0.003204,-0.006507,-0.011017


Target: cass
Distance: 75.8734% / 0.75873411
100.0 Mezmaiskaya3_Neanderthal


+
Germany_Ilsenhöhle_LRJ_UP:RNI087__BC_45245__Cov_64 .28%,-0.091058,-0.07718,-0.085606,0.05491,0.002154,-0.005299,-0.002585,-0.005077,0.032315,-0.004009,0.015265,-0.010191,0.001784,-0.002615,-0.001357,-0.00769,0.007693,0.005828,-0.004399,0.01038,0.009982,0.002226,-0.004683,-0.017352,-0.000239

Target: cass
Distance: 34.8336% / 0.34833635
100.0 Germany_Ilsenhöhle_LRJ_UP

[ecptr]

Bonobo is the genetically closest great ape to humans, followed by chimpanzee, followed by gorillas, and lastly by orangutans.

[cass]

Bonobo is the genetically closest great ape to humans, followed by chimpanzee, followed by gorillas, and lastly by orangutans.

It looks like it applies only to certain ones.

[celticdragongod]

Distance to: CDG_scaled
0.88822774 Gorilla.REF:Gorilla.REF
0.89517251 Chimp.REF
0.89690389 Primate_Chimp.HO:Chimp_HO.HO
0.94090588 Bonobo_SAMN13935689_simulated_g25_scaled

Target: CDG_scaled
Distance: 88.8228% / 0.88822774
100.0 Gorilla.REF:Gorilla.REF

[celticdragongod]

Distance to: CDG_scaled
0.76141882 Mezmaiskaya3_Neanderthal:Mez3__BC_94750__Cov_11.04 %
0.85523190 Neanderthal:Mezmaiskaya1_final_provisional__BC_630 50__Cov_56.66%
0.87016428 GrotteMandrin_Neanderthal:Mandrin1600__BC_48525__C ov_59.10%
0.89315668 Chagyrskaya_Neanderthal.DG:Chagyrskaya8_snpAD.DG__ BC_51450__Cov_92.25%
0.89341496 Altai_Neanderthal.DG:AltaiNeanderthal.DG__BC_10850 0__Cov_99.92%
0.89385737 DenisovaNeanderthalMix.SG:Denisova11.SG__BC_96750_ _Cov_74.15%
0.89393115 Altai_Neanderthal.DG:AltaiNeanderthal_snpAD.DG__BC _108500__Cov_92.26%
0.89694950 Denisova25:Denisova25__BC_198050__Cov_100.00%
0.89865174 Denisova.DG:Denisova3.DG__BC_61950__Cov_99.89%
0.89901911 Denisova_light.SG:Denisova_light.SG__BC_61950__Cov _49.90%
0.90069406 Denisova.DG:Denisova3_snpAD.DG__BC_61950__Cov_92.2 4%

Target: CDG_scaled
Distance: 76.1419% / 0.76141882
100.0 Mezmaiskaya3_Neanderthal:Mez3__BC_94750__Cov_11.04 %

[celticdragongod]

Distance to: CDG_scaled
0.35277939 Germany_Ilsenhöhle_LRJ_UP:RNI087__BC_45245__Cov_64 .28%

Target: CDG_scaled
Distance: 35.2779% / 0.35277939
100.0 Germany_Ilsenhöhle_LRJ_UP:RNI087__BC_45245__Cov_64 .28%

[Opie]

It just looks BS to me.

[Kowalski]

It just looks BS to me.

Why?

[Opie]

Why?

You could have asked this ChatGPT.


Global25 (G25) isn’t suitable for calculating genetic distance between humans and monkeys.

Why:

G25 is a human-focused PCA dataset built from human SNP genotyping panels. These SNPs are specifically selected because they are variable within humans.

Monkeys do not share the same SNP reference framework, and many of those SNPs either don’t exist, are not polymorphic, or cannot be directly matched across species.

PCA coordinates like G25 are relative positions built within a single, standardized dataset. They lose meaning once you step outside that dataset’s scope.

What should be used instead:
To compare humans and monkeys (or other primates), scientists typically use:

Whole-genome alignments

Orthologous gene comparisons

Measures like Fst, Nei’s genetic distance, or sequence divergence (% difference)

Phylogenomic tools to infer evolutionary distances across millions of years

Context:
Humans and Old World monkeys diverged ~25 million years ago; humans and chimpanzees diverged ~6–7 million years ago. That’s far beyond what G25, which is for relatively recent human population structure, was designed to analyze.

If you want, tell me:

Which monkeys (macaques? baboons? chimpanzees?),

What format of data you have (SNPs? genomes?),

And what you mean by “genetic distance” (evolutionary divergence, PCA space comparison, Fst, etc.),
and I can recommend appropriate tools or methods.

[gixajo]

We cannot compare ourselves to monkeys, so let's compare ourselves to Neanderthals, who did leave us part of our DNA.:)

Target: gixajo_scaled
Distance: 74.7647% / 0.74764734
100.0 Mezmaiskaya3_Neanderthal

And the one added by Cass later.

Target: gixajo_scaled
Distance: 34.6991% / 0.34699140
100.0 Germany_Ilsenhöhle_LRJ_UP


Distance to: gixajo_scaled
0.74764734 Mezmaiskaya3_Neanderthal:Mez3__BC_94750__Cov_11.04 %
0.84268812 Neanderthal:Mezmaiskaya1_final_provisional__BC_630 50__Cov_56.66%
0.85724049 GrotteMandrin_Neanderthal:Mandrin1600__BC_48525__C ov_59.10%
0.88010883 Chagyrskaya_Neanderthal.DG:Chagyrskaya8_snpAD.DG__ BC_51450__Cov_92.25%
0.88031184 Altai_Neanderthal.DG:AltaiNeanderthal.DG__BC_10850 0__Cov_99.92%
0.88073523 Altai_Neanderthal.DG:AltaiNeanderthal_snpAD.DG__BC _108500__Cov_92.26%
0.88107345 DenisovaNeanderthalMix.SG:Denisova11.SG__BC_96750_ _Cov_74.15%
0.88405012 Denisova25:Denisova25__BC_198050__Cov_100.00%
0.88569454 Denisova.DG:Denisova3.DG__BC_61950__Cov_99.89%
0.88641381 Denisova_light.SG:Denisova_light.SG__BC_61950__Cov _49.90%
0.88775351 Denisova.DG:Denisova3_snpAD.DG__BC_61950__Cov_92.2 4%

[Kowalski]

You could have asked this ChatGPT.

I'd rather not.