IBS Kurdish distances

[Zoro]

The more pressing question is why Europe being slightly closer to SSA (it's very slight) than E.Asian is a problem? I think it's well documented it's the case, again the difference is anecdotical and in both cases the distances are still very large.

ps: i think the formating of the table screws up the whole page

I was told that the reason is that DNA companies use alot of SNPs that are fixed ancestral in both Africans and Eurasians or that have high allele frequencies in both. If they captured positions that were variable in Africans then Neanderthals would not score like 90% African because in fact Neanderthals are more related to Eurasians than Africans.

As far as I know Eurasian DNA's SAPDA software is the only one that doesn't show Neanderthal as 90% African. Unlike Admixture calculators SAPDA actually correctly shows Neanderthal more related to Eurasians than Africans ( fig 1 and 2 https://eurasiandna.com/sapda-admixt...tes-revisions/

This diagram shows S African pygmies split from Eurasian and other African ancestors around 270,000 years ago compared to only around 40,000 years ago for W. Eurasian-E. Eurasian split. So Europeans are much much more related to E. Asians than African pygmies

[IMG][/IMG]

[Mingle]

Honestly I must zoom Firefox to 130% to read properly. Only you on this forum use smallest fonts.

I'm not sure its cause he uses small fonts. Maybe it has to do with the input method of the table. I notice that in posts that include his tables, the text is tiny. But in other posts, the text is normal.

[Zoro]

I went back and rechecked the genotype rate (how many samples have missing SNPs) and found it to be 99% for the majority of samples. Although this is good I wanted to push it to 100% such that all samples are perfectly overlapping in ALL positions and NO sample has ANY missing genotype.

This is the result I got for the Kurmanji sample (100% Kurdish relative from Iraq). Although IBS distance is useful I really like the IBD feature of Plink because it's informative on more recent geneflows.

For example the Plink IBS program perfectly showed that the ALL EURASIANS ( including E. Asians and American Indians) are closer to the Kurdish sample than Africans. This is a good result because we know that overall ALL EURASIANS are more related to each other than they are to SSA Africans. You would think all calculators should show this but don't assume that because I showed that on Vahuado all Admixture calculators showed some SSA Africans closer to Europeans than some E. Asians to Europeans.

Now to Plink's IBD feature. It shows if there have been some more recent admixtures. So in this table you'll see that not all SSA Africans are on the bottom of the table. In fact you'll see that some E. Africans are higher up the table than Karitiana and other E. Eurasians. This is fine. All it indicates is that after the time American-Indians split from Siberians this individual received some African admixture of the E. African type most likely from neighboring Arab populations via some Kurdish ancestor.

Sorted by PPC binomial test

FID1	FID2	IID2	Z0	Z1	Z2	PI_HAT	DST	PPC	RATIO
Kurd-Kurmanji-Iraq-WGS	Kurd_Kurmanji	Kurd_Kurmanji	0.001	0.947	0.053	0.526	0.89204	1.000	3,262.00
Kurd-Kurmanji-Iraq-WGS	Kurd_Kurmanji	Kurd_Kurmanji	0.003	0.968	0.030	0.513	0.88920	1.000	1,068.33
Kurd-Kurmanji-Iraq-WGS	Iranian	S_Iranian-1	0.929	0.052	0.020	0.046	0.81077	0.877	2.09
Kurd-Kurmanji-Iraq-WGS	Lezgin	S_Lezgin-1	0.931	0.000	0.070	0.070	0.81269	0.731	2.05
Kurd-Kurmanji-Iraq-WGS	Adygei	S_Adygei-1	0.942	0.000	0.058	0.058	0.81171	0.490	2.00
Kurd-Kurmanji-Iraq-WGS	Turkish	Turkish	0.925	0.000	0.075	0.075	0.81242	0.455	1.99
Kurd-Kurmanji-Iraq-WGS	Georgian	S_Georgian-1	1.000	0.000	0.000	0.000	0.81201	0.391	1.98
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	0.942	0.000	0.059	0.059	0.81215	0.387	1.98
Kurd-Kurmanji-Iraq-WGS	Iranian	Iranian	0.946	0.000	0.055	0.055	0.80922	0.372	1.98
Kurd-Kurmanji-Iraq-WGS	Armenian	S_Armenian-1	0.934	0.000	0.066	0.066	0.81212	0.357	1.97
Kurd-Kurmanji-Iraq-WGS	Pashtun_Pak	Pashtun_Pak	0.960	0.003	0.038	0.039	0.81019	0.319	1.96
Kurd-Kurmanji-Iraq-WGS	Georgian	S_Georgian-2	1.000	0.000	0.000	0.000	0.81060	0.281	1.96
Kurd-Kurmanji-Iraq-WGS	Punjabi_Pak	Punjabi_Pak	1.000	0.000	0.000	0.000	0.80874	0.238	1.95
Kurd-Kurmanji-Iraq-WGS	Pashtun_Pak	S_Pathan-1	1.000	0.000	0.000	0.000	0.80888	0.210	1.94
Kurd-Kurmanji-Iraq-WGS	Assyrian	Assyrian	0.925	0.000	0.075	0.075	0.81202	0.207	1.94
Kurd-Kurmanji-Iraq-WGS	Pashtun_Afg	Pashtun_Afg	0.957	0.016	0.027	0.035	0.80919	0.197	1.94
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	0.937	0.000	0.063	0.063	0.81131	0.181	1.93
Kurd-Kurmanji-Iraq-WGS	Kurd_Turkey	Kurd_Turkey	0.927	0.000	0.073	0.073	0.81419	0.178	1.93
Kurd-Kurmanji-Iraq-WGS	Turkish	S_Turkish-1	0.956	0.002	0.042	0.043	0.81102	0.178	1.93
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	0.926	0.000	0.074	0.074	0.81257	0.174	1.93
Kurd-Kurmanji-Iraq-WGS	Iranian	Iranian	0.962	0.000	0.038	0.038	0.80997	0.141	1.92
Kurd-Kurmanji-Iraq-WGS	N-Ossetian	S_North_Ossetian-1	0.952	0.006	0.043	0.046	0.81144	0.135	1.92
Kurd-Kurmanji-Iraq-WGS	Pashtun_Pak	Pashtun_Pak	0.952	0.000	0.048	0.048	0.80922	0.132	1.92
Kurd-Kurmanji-Iraq-WGS	English	S_English-2	1.000	0.000	0.000	0.000	0.80855	0.120	1.91
Kurd-Kurmanji-Iraq-WGS	Adygei	S_Adygei-2	0.959	0.000	0.041	0.041	0.81037	0.120	1.91
Kurd-Kurmanji-Iraq-WGS	Makrani	S_Makrani-1	1.000	0.000	0.000	0.000	0.80928	0.121	1.91
Kurd-Kurmanji-Iraq-WGS	Sindhi	S_Sindhi-2	0.956	0.000	0.045	0.045	0.80919	0.084	1.90
Kurd-Kurmanji-Iraq-WGS	Spanish	S_Spanish-2	1.000	0.000	0.000	0.000	0.80866	0.071	1.89
Kurd-Kurmanji-Iraq-WGS	Pashtun_Afg	Pashtun_Afg	1.000	0.000	0.000	0.000	0.80873	0.051	1.88
Kurd-Kurmanji-Iraq-WGS	Armenian	S_Armenian-2	0.930	0.000	0.070	0.070	0.81191	0.045	1.88
Kurd-Kurmanji-Iraq-WGS	Finnish	S_Finnish-1	1.000	0.000	0.000	0.000	0.80720	0.046	1.88
Kurd-Kurmanji-Iraq-WGS	Punjabi_Arain	Punjabi_Arain	1.000	0.000	0.000	0.000	0.80835	0.033	1.87
Kurd-Kurmanji-Iraq-WGS	Basque	S_Basque-1	1.000	0.000	0.000	0.000	0.80893	0.026	1.86
Kurd-Kurmanji-Iraq-WGS	Pashtun_Pak	S_Pathan-2	0.952	0.000	0.048	0.048	0.80858	0.025	1.86
Kurd-Kurmanji-Iraq-WGS	Punjabi	S_Punjabi-4	0.958	0.000	0.042	0.042	0.80871	0.025	1.86
Kurd-Kurmanji-Iraq-WGS	Iranian	S_Iranian-2	1.000	0.000	0.000	0.000	0.80974	0.023	1.86
Kurd-Kurmanji-Iraq-WGS	Turkish	S_Turkish-2	1.000	0.000	0.000	0.000	0.81158	0.019	1.85
Kurd-Kurmanji-Iraq-WGS	Spanish	S_Spanish-1	1.000	0.000	0.000	0.000	0.80880	0.014	1.84
Kurd-Kurmanji-Iraq-WGS	Lezgin	S_Lezgin-2	1.000	0.000	0.000	0.000	0.81146	0.013	1.84
Kurd-Kurmanji-Iraq-WGS	Finnish	S_Finnish-3	1.000	0.000	0.000	0.000	0.80831	0.011	1.84
Kurd-Kurmanji-Iraq-WGS	Brahui	S_Brahui-1	1.000	0.000	0.000	0.000	0.80887	0.011	1.84
Kurd-Kurmanji-Iraq-WGS	Punjabi_Pak	Punjabi_Pak	1.000	0.000	0.000	0.000	0.80758	0.011	1.83
Kurd-Kurmanji-Iraq-WGS	Sardinian	S_Sardinian-2	1.000	0.000	0.000	0.000	0.80943	0.007	1.82
Kurd-Kurmanji-Iraq-WGS	Hungarian	S_Hungarian-2	1.000	0.000	0.000	0.000	0.80742	0.003	1.81
Kurd-Kurmanji-Iraq-WGS	Estonian	S_Estonian-1	1.000	0.000	0.000	0.000	0.80722	0.002	1.80
Kurd-Kurmanji-Iraq-WGS	English	S_English-1	1.000	0.000	0.000	0.000	0.80811	0.002	1.80
Kurd-Kurmanji-Iraq-WGS	Hungarian	S_Hungarian-1	1.000	0.000	0.000	0.000	0.80898	0.002	1.79
Kurd-Kurmanji-Iraq-WGS	BedouinB	S_BedouinB-2	1.000	0.000	0.000	0.000	0.80839	0.001	1.78
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	1.000	0.000	0.000	0.000	0.81135	0.001	1.78
Kurd-Kurmanji-Iraq-WGS	Assyrian	Assyrian	1.000	0.000	0.000	0.000	0.81133	0.001	1.78
Kurd-Kurmanji-Iraq-WGS	Uyghur	S_Uygur-2	1.000	0.000	0.000	0.000	0.80651	0.001	1.77
Kurd-Kurmanji-Iraq-WGS	Punjabi_India	Punjabi_India	0.951	0.000	0.049	0.049	0.80906	0.000	1.76
Kurd-Kurmanji-Iraq-WGS	Punjabi_Pak	Punjabi_Pak	0.970	0.000	0.030	0.030	0.80851	0.000	1.76
Kurd-Kurmanji-Iraq-WGS	Tajik	S_Tajik-2	0.946	0.000	0.054	0.054	0.80969	0.000	1.75
Kurd-Kurmanji-Iraq-WGS	Estonian	S_Estonian-2	1.000	0.000	0.000	0.000	0.80863	0.000	1.74
Kurd-Kurmanji-Iraq-WGS	Basque	S_Basque-2	1.000	0.000	0.000	0.000	0.80907	0.000	1.72
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	1.000	0.000	0.000	0.000	0.81021	0.000	1.70
Kurd-Kurmanji-Iraq-WGS	Sardinian	S_Sardinian-1	1.000	0.000	0.000	0.000	0.80677	0.000	1.68
Kurd-Kurmanji-Iraq-WGS	Uyghur	S_Uygur-1	1.000	0.000	0.000	0.000	0.80522	0.000	1.68
Kurd-Kurmanji-Iraq-WGS	Punjabi_Gujjar	Punjabi_Gujjar	1.000	0.000	0.000	0.000	0.80893	0.000	1.68
Kurd-Kurmanji-Iraq-WGS	Tajik_Tajikistan	Tajik_Tajikistan	1.000	0.000	0.000	0.000	0.80634	0.000	1.68
Kurd-Kurmanji-Iraq-WGS	Finnish	S_Finnish-2	1.000	0.000	0.000	0.000	0.80701	0.000	1.66
Kurd-Kurmanji-Iraq-WGS	Balochi	S_Balochi-2	1.000	0.000	0.000	0.000	0.80795	0.000	1.65
Kurd-Kurmanji-Iraq-WGS	Stuttgart-EEF	Stuttgart_published	1.000	0.000	0.000	0.000	0.80833	0.000	1.65
Kurd-Kurmanji-Iraq-WGS	Kalash	S_Kalash-2	1.000	0.000	0.000	0.000	0.80901	0.000	1.64
Kurd-Kurmanji-Iraq-WGS	Baloch_IR	Baloch_IR	1.000	0.000	0.000	0.000	0.80721	0.000	1.62
Kurd-Kurmanji-Iraq-WGS	Punjabi	S_Punjabi-3	1.000	0.000	0.000	0.000	0.80536	0.000	1.62
Kurd-Kurmanji-Iraq-WGS	Punjabi	S_Punjabi-2	1.000	0.000	0.000	0.000	0.80634	0.000	1.61
Kurd-Kurmanji-Iraq-WGS	Sardinian	B_Sardinian-3	1.000	0.000	0.000	0.000	0.80623	0.000	1.61
Kurd-Kurmanji-Iraq-WGS	Kapu	S_Kapu-1	1.000	0.000	0.000	0.000	0.80474	0.000	1.61
Kurd-Kurmanji-Iraq-WGS	Punjabi	S_Punjabi-1	1.000	0.000	0.000	0.000	0.80493	0.000	1.60
Kurd-Kurmanji-Iraq-WGS	Sindhi	S_Sindhi-1	1.000	0.000	0.000	0.000	0.80605	0.000	1.54
Kurd-Kurmanji-Iraq-WGS	Kapu	S_Kapu-2	1.000	0.000	0.000	0.000	0.80466	0.000	1.54
Kurd-Kurmanji-Iraq-WGS	Balochi	S_Balochi-1	1.000	0.000	0.000	0.000	0.80658	0.000	1.49
Kurd-Kurmanji-Iraq-WGS	BedouinB	S_BedouinB-1	1.000	0.000	0.000	0.000	0.80574	0.000	1.44
Kurd-Kurmanji-Iraq-WGS	Tajik	S_Tajik-1	1.000	0.000	0.000	0.000	0.80589	0.000	1.44
Kurd-Kurmanji-Iraq-WGS	Kalash	S_Kalash-1	1.000	0.000	0.000	0.000	0.80695	0.000	1.43
Kurd-Kurmanji-Iraq-WGS	Makrani	S_Makrani-2	1.000	0.000	0.000	0.000	0.80602	0.000	1.40
Kurd-Kurmanji-Iraq-WGS	Brahui	S_Brahui-2	1.000	0.000	0.000	0.000	0.80602	0.000	1.37
Kurd-Kurmanji-Iraq-WGS	Baloch_IR	Baloch_IR	1.000	0.000	0.000	0.000	0.80535	0.000	1.29
Kurd-Kurmanji-Iraq-WGS	Yakut	S_Yakut-2	1.000	0.000	0.000	0.000	0.79993	0.000	1.18
Kurd-Kurmanji-Iraq-WGS	Masai	S_Masai-1	1.000	0.000	0.000	0.000	0.77087	0.000	1.17
Kurd-Kurmanji-Iraq-WGS	Mongola	S_Mongola-1	1.000	0.000	0.000	0.000	0.80119	0.000	1.16
Kurd-Kurmanji-Iraq-WGS	Masai	S_Masai-2	1.000	0.000	0.000	0.000	0.77156	0.000	1.14
Kurd-Kurmanji-Iraq-WGS	Mongola	S_Mongola-2	1.000	0.000	0.000	0.000	0.80061	0.000	1.13
Kurd-Kurmanji-Iraq-WGS	Yakut	S_Yakut-1	1.000	0.000	0.000	0.000	0.79923	0.000	1.13
Kurd-Kurmanji-Iraq-WGS	Han	S_Han-2	1.000	0.000	0.000	0.000	0.79882	0.000	1.13
Kurd-Kurmanji-Iraq-WGS	Han	S_Han-1	1.000	0.000	0.000	0.000	0.79980	0.000	1.11
Kurd-Kurmanji-Iraq-WGS	Somali	S_Somali-1	1.000	0.000	0.000	0.000	0.77769	0.000	1.11
Kurd-Kurmanji-Iraq-WGS	Dai	S_Dai-2	1.000	0.000	0.000	0.000	0.79656	0.000	1.09
Kurd-Kurmanji-Iraq-WGS	China_Lahu	S_Lahu-1	1.000	0.000	0.000	0.000	0.79834	0.000	1.09
Kurd-Kurmanji-Iraq-WGS	Japanese	S_Japanese-3	1.000	0.000	0.000	0.000	0.79852	0.000	1.09
Kurd-Kurmanji-Iraq-WGS	Dai	A_Dai-5	1.000	0.000	0.000	0.000	0.79719	0.000	1.09
Kurd-Kurmanji-Iraq-WGS	Han	B_Han-3	1.000	0.000	0.000	0.000	0.79757	0.000	1.08
Kurd-Kurmanji-Iraq-WGS	Japanese	S_Japanese-1	1.000	0.000	0.000	0.000	0.79856	0.000	1.08
Kurd-Kurmanji-Iraq-WGS	Dai	S_Dai-1	1.000	0.000	0.000	0.000	0.79887	0.000	1.07
Kurd-Kurmanji-Iraq-WGS	Dai	B_Dai-4	1.000	0.000	0.000	0.000	0.79973	0.000	1.07
Kurd-Kurmanji-Iraq-WGS	Japanese	S_Japanese-2	1.000	0.000	0.000	0.000	0.79736	0.000	1.07
Kurd-Kurmanji-Iraq-WGS	China_Lahu	S_Lahu-2	1.000	0.000	0.000	0.000	0.79720	0.000	1.03
Kurd-Kurmanji-Iraq-WGS	Luhya	S_Luhya-2	1.000	0.000	0.000	0.000	0.75814	0.000	0.90
Kurd-Kurmanji-Iraq-WGS	Luhya	S_Luhya-1	1.000	0.000	0.000	0.000	0.75619	0.000	0.88
Kurd-Kurmanji-Iraq-WGS	Yoruba	B_Yoruba-3	1.000	0.000	0.000	0.000	0.75526	0.000	0.85
Kurd-Kurmanji-Iraq-WGS	Loschbour-WHG	Loschbour_snpAD	1.000	0.000	0.000	0.000	0.79529	0.000	0.83
Kurd-Kurmanji-Iraq-WGS	Yoruba	S_Yoruba-2	1.000	0.000	0.000	0.000	0.75499	0.000	0.81
Kurd-Kurmanji-Iraq-WGS	Yoruba	S_Yoruba-1	1.000	0.000	0.000	0.000	0.75639	0.000	0.81
Kurd-Kurmanji-Iraq-WGS	Karitiana	B_Karitiana-3	1.000	0.000	0.000	0.000	0.79407	0.000	0.65
Kurd-Kurmanji-Iraq-WGS	Karitiana	S_Karitiana-2	1.000	0.000	0.000	0.000	0.79534	0.000	0.63
Kurd-Kurmanji-Iraq-WGS	Mbuti	S_Mbuti-3	1.000	0.000	0.000	0.000	0.75232	0.000	0.63
Kurd-Kurmanji-Iraq-WGS	Karitiana	S_Karitiana-1	1.000	0.000	0.000	0.000	0.79442	0.000	0.63
Kurd-Kurmanji-Iraq-WGS	Mbuti	S_Mbuti-2	1.000	0.000	0.000	0.000	0.75147	0.000	0.60

[Zoro]

These results are from a different smaller dataset. Since no IBD was indicated I simply sorted by distance.

FID1	FID2	IID2	DST
Kurd-Kurmanji-Iraq-WGS	Tajik	Tadjik	0.78435
Kurd-Kurmanji-Iraq-WGS	Turkmen	Turkmens2	0.78397
Kurd-Kurmanji-Iraq-WGS	Kazakh	Kazakhs2	0.78348
Kurd-Kurmanji-Iraq-WGS	Tatar_Volga	VolgaTatars1	0.78317
Kurd-Kurmanji-Iraq-WGS	Karakalpak	Karakalpaks3	0.78302
Kurd-Kurmanji-Iraq-WGS	Karakalpak	Karakalpaks2	0.78277
Kurd-Kurmanji-Iraq-WGS	Tajik	Tajiks1	0.78275
Kurd-Kurmanji-Iraq-WGS	Uzbek	Uzbeks3	0.78267
Kurd-Kurmanji-Iraq-WGS	Bashkir	Bashkirs3	0.78247
Kurd-Kurmanji-Iraq-WGS	Bashkir	Bashkirs1	0.78244
Kurd-Kurmanji-Iraq-WGS	Uzbek	Uzbeks1	0.78239
Kurd-Kurmanji-Iraq-WGS	Tajik	Tajiks3	0.78201
Kurd-Kurmanji-Iraq-WGS	Tatar_Volga	VolgaTatars2	0.78165
Kurd-Kurmanji-Iraq-WGS	Kazakh	Kazkahs1	0.78164
Kurd-Kurmanji-Iraq-WGS	Bashkir	Bashkirs2	0.78156
Kurd-Kurmanji-Iraq-WGS	Tatar_Tomsk	TomskTatars2	0.78154
Kurd-Kurmanji-Iraq-WGS	Uzbek	Uzbeks2	0.78138
Kurd-Kurmanji-Iraq-WGS	Uyghur	Uyghurs3	0.78133
Kurd-Kurmanji-Iraq-WGS	Tatar_Tomsk	TomskTatars1	0.78132
Kurd-Kurmanji-Iraq-WGS	Uyghur	Uyghurs1	0.78125
Kurd-Kurmanji-Iraq-WGS	Kalmyk	Kalmyks1	0.78119
Kurd-Kurmanji-Iraq-WGS	Turkmen	Turkmens1	0.78093
Kurd-Kurmanji-Iraq-WGS	Karakalpak	Karakalpaks1	0.78084
Kurd-Kurmanji-Iraq-WGS	Buryat	Buryats2	0.78057
Kurd-Kurmanji-Iraq-WGS	Uyghur	Uyghurs2	0.78057
Kurd-Kurmanji-Iraq-WGS	Kazakh	Kazakhs3	0.78036
Kurd-Kurmanji-Iraq-WGS	Kalmyk	Kalmyks2	0.77946
Kurd-Kurmanji-Iraq-WGS	Buryat	Buryats1	0.77881

[Zoro]

This is the table with the strongest evidence of recent admixture Pi-Hat which is equal to Proportion IBD, i.e. P(IBD=2) + 0.5*P(IBD=1). The reason the 2 Kurmanji numbers are so much higher is because they are close relatives of the subject.

FID1	FID2	IID2	Z0	Z1	Z2	PI_HAT	DST	PPC	RATIO
Kurd-Kurmanji-Iraq-WGS	Kurd_Kurmanji	Kurd_Kurmanji	0.001	0.947	0.053	0.526	0.89204	1.000	3,262.00
Kurd-Kurmanji-Iraq-WGS	Kurd_Kurmanji	Kurd_Kurmanji	0.003	0.968	0.030	0.513	0.88920	1.000	1,068.33
Kurd-Kurmanji-Iraq-WGS	Turkish	Turkish	0.925	0.000	0.075	0.075	0.81242	0.455	1.99
Kurd-Kurmanji-Iraq-WGS	Assyrian	Assyrian	0.925	0.000	0.075	0.075	0.81202	0.207	1.94
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	0.926	0.000	0.074	0.074	0.81257	0.174	1.93
Kurd-Kurmanji-Iraq-WGS	Kurd_Turkey	Kurd_Turkey	0.927	0.000	0.073	0.073	0.81419	0.178	1.93
Kurd-Kurmanji-Iraq-WGS	Armenian	S_Armenian-2	0.930	0.000	0.070	0.070	0.81191	0.045	1.88
Kurd-Kurmanji-Iraq-WGS	Lezgin	S_Lezgin-1	0.931	0.000	0.070	0.070	0.81269	0.731	2.05
Kurd-Kurmanji-Iraq-WGS	Armenian	S_Armenian-1	0.934	0.000	0.066	0.066	0.81212	0.357	1.97
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	0.937	0.000	0.063	0.063	0.81131	0.181	1.93
Kurd-Kurmanji-Iraq-WGS	Kurd_Feyli	Kurd_Feyli	0.942	0.000	0.059	0.059	0.81215	0.387	1.98
Kurd-Kurmanji-Iraq-WGS	Adygei	S_Adygei-1	0.942	0.000	0.058	0.058	0.81171	0.490	2.00
Kurd-Kurmanji-Iraq-WGS	Iranian	Iranian	0.946	0.000	0.055	0.055	0.80922	0.372	1.98
Kurd-Kurmanji-Iraq-WGS	Tajik	S_Tajik-2	0.946	0.000	0.054	0.054	0.80969	0.000	1.75
Kurd-Kurmanji-Iraq-WGS	Punjabi_India	Punjabi_India	0.951	0.000	0.049	0.049	0.80906	0.000	1.76
Kurd-Kurmanji-Iraq-WGS	Pashtun_Pak	Pashtun_Pak	0.952	0.000	0.048	0.048	0.80922	0.132	1.92
Kurd-Kurmanji-Iraq-WGS	Pashtun_Pak	S_Pathan-2	0.952	0.000	0.048	0.048	0.80858	0.025	1.86
Kurd-Kurmanji-Iraq-WGS	Iranian	S_Iranian-1	0.929	0.052	0.020	0.046	0.81077	0.877	2.09
Kurd-Kurmanji-Iraq-WGS	N-Ossetian	S_North_Ossetian-1	0.952	0.006	0.043	0.046	0.81144	0.135	1.92
Kurd-Kurmanji-Iraq-WGS	Sindhi	S_Sindhi-2	0.956	0.000	0.045	0.045	0.80919	0.084	1.90
Kurd-Kurmanji-Iraq-WGS	Turkish	S_Turkish-1	0.956	0.002	0.042	0.043	0.81102	0.178	1.93
Kurd-Kurmanji-Iraq-WGS	Punjabi	S_Punjabi-4	0.958	0.000	0.042	0.042	0.80871	0.025	1.86
Kurd-Kurmanji-Iraq-WGS	Adygei	S_Adygei-2	0.959	0.000	0.041	0.041	0.81037	0.120	1.91
Kurd-Kurmanji-Iraq-WGS	Pashtun_Pak	Pashtun_Pak	0.960	0.003	0.038	0.039	0.81019	0.319	1.96
Kurd-Kurmanji-Iraq-WGS	Iranian	Iranian	0.962	0.000	0.038	0.038	0.80997	0.141	1.92
Kurd-Kurmanji-Iraq-WGS	Pashtun_Afg	Pashtun_Afg	0.957	0.016	0.027	0.035	0.80919	0.197	1.94
Kurd-Kurmanji-Iraq-WGS	Punjabi_Pak	Punjabi_Pak	0.970	0.000	0.030	0.030	0.80851	0.000	1.76

[Avicenna]

Zoro man do you mind explaining what these results mean for us folks who don't get it please

[Zoro]

Zoro man do you mind explaining what these results mean for us folks who don't get it please

Ok I'm going to try. Let's say there's a 50% Tajik, 50% British person from your hometown and you ask 2 people who you are related to more; your Homie or a random Kurd.

One says your Homie, the other says the Kurd. Who is correct? Well they sort of both are in their own way. On the one hand you'll share more recent ancestry with your Homie, but on the other hand if you look at your genome SNP by SNP you'll have more matching SNPs with the Kurd and the Kurd will cluster closer to you on PCA than your Homie. But on the other hand you'll share larger DNA chunks with your Homie.

So if we look at straight IBS your distance will be closer to the Kurd because you're made of roughly similar ancient proportions as him but if we look at recent admixture or IBD (Pi-Hat) you'll be closer to your Homie.

I think this paper will help you a little https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178600/

It is an assumption of large, population-based datasets that samples are annotated accurately whether they correspond to known relationships or unrelated individuals. These annotations are key for a broad range of genetics applications. While many methods are available to assess relatedness that involve estimates of identity-by-descent (IBD) and/or identity-by-state (IBS) allele-sharing proportions, we developed a novel approach that estimates IBD0, 1, and 2 based on observed IBS within windows. When combined with genome-wide IBS information, it provides an intuitive and practical graphical approach with the capacity to analyze datasets with thousands of samples without prior information about relatedness between individuals or haplotypes. We applied the method to a commonly used Human Variation Panel consisting of 400 nominally unrelated individuals. Surprisingly, we identified identical, parent-child, and full-sibling relationships and reconstructed pedigrees. In two instances non-sibling pairs of individuals in these pedigrees had unexpected IBD2 levels, as well as multiple regions of homozygosity, implying inbreeding. This combined method allowed us to distinguish related individuals from those having atypical heterozygosity rates and determine which individuals were outliers with respect to their designated population. Additionally, it becomes increasingly difficult to identify distant relatedness using genome-wide IBS methods alone. However, our IBD method further identified distant relatedness between individuals within populations, supported by the presence of megabase-scale regions lacking IBS0 across individual chromosomes. We benchmarked our approach against the hidden Markov model of a leading software package (PLINK), showing improved calling of distantly related individuals, and we validated it using a known pedigree from a clinical study. The application of this approach could improve genome-wide association, linkage, heterozygosity, and other population genomics studies that rely on SNP genotype data.

For any given pair of individuals with genotype information, identity-by-state (IBS) can be observed at a given locus with three possible outcomes: the individuals have two different alleles (IBS0) or they share one (IBS1) or two (IBS2) alleles in common. For example, a pair of individuals with genotypes AA and BB are IBS0 at this locus whereas a pair with AA and AB are IBS1. Two individuals who share 1 or 2 alleles IBS at a given locus may have inherited the shared allele(s) from a recent common ancestor, in which these allele(s) are identical-by-descent (IBD). IBD approaches have been applied to linkage mapping [2] in which segments of IBD are detected with informative SNPs. IBD regions tend to be small between pairs of individuals derived from a given population that are not closely related, primarily because their last common ancestor was many generations ago. As such, GWAS are predicated upon the detection of regions of IBD when stratifying by phenotype.

[Avicenna]

Ok I'm going to try. Let's say there's a 50% Tajik, 50% British person from your hometown and you ask 2 people who you are related to more; your Homie or a random Kurd.

One says your Homie, the other says the Kurd. Who is correct? Well they sort of both are in their own way. On the one hand you'll share more recent ancestry with your Homie, but on the other hand if you look at your genome SNP by SNP you'll have more matching SNPs with the Kurd and the Kurd will cluster closer to you on PCA than your Homie. But on the other hand you'll share larger DNA chunks with your Homie.

So if we look at straight IBS your distance will be closer to the Kurd because you're made of roughly similar ancient proportions as him but if we look at recent admixture or IBD (Pi-Hat) you'll be closer to your Homie.

I think this paper will help you a little https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178600/

Very easily explained homie haha . But I generally meant the list ? How can a kurd have a non Kurd as closer than a kurd?

[Zoro]

Very easily explained homie haha . But I generally meant the list ? How can a kurd have a non Kurd as closer than a kurd?

Because populations are not homogeneous especially when talking about a population that spans such a geographical area and borders various types of ethnicities. Heck even the various kurdish languages are quite different from each other reflecting different genetic inputs. Kurmanji and Sorani are not 80% mutually intelligible. Then you have Feyli and Gorani.

Even with more homogeneous smaller ethnic groups they only share a certain amount of DNA but by no means all DNA. That’s why calculators have to make haplotypes out of the small number of shared alleles between a bunch of individuals from the same population. That’s also why you can’t use one individual as a population average you have to make the average out of a bunch of individuals

[Avicenna]

Because populations are not homogeneous especially when talking about a population that spans such a geographical area and borders various types of ethnicities. Heck even the various kurdish languages are quite different from each other reflecting different genetic inputs. Kurmanji and Sorani are not 80% mutually intelligible. Then you have Feyli and Gorani.

Even with more homogeneous smaller ethnic groups they only share a certain amount of DNA but by no means all DNA. That’s why calculators have to make haplotypes out of the small number of shared alleles between a bunch of individuals from the same population. That’s also why you can’t use one individual as a population average you have to make the average out of a bunch of individuals

But the kurd is closer to a Punjabi than another fellow Kurd? Could you do one with a more homogenous population to compare please?