Thread inspecting the low-recombination regions of the X-chromosome

**MacUalraig** · 05-12-2021, 02:50 PM

see https://anthrogenica.com/showthread....aplotypes-here :-)

**Norfern-Ostrobothnian** · 05-12-2021, 04:09 PM

Originally Posted by MacUalraig

see https://anthrogenica.com/showthread....aplotypes-here :-)

Nice that there was a discussion thread prior. I guess that thread could be revived if people want to post results of theirs.

As a side note, Loschbour's PHAX 5574 is h37 with no discrepancies, Stuggart's is h2. Meanwhile Kolyma1 has it's own singleton differing by one from the h4 haplotype cluster.
Indeed h4 seems to be at an ancestral position to multiple haplotypes of the 'A' cluster, and could maybe mark the Eurasian dispersal?
H2 is ancestral to most haplotypes in the A cluster after h4. Could it be so that these were some pioneering West Eurasians?

**Norfern-Ostrobothnian** · 05-12-2021, 07:00 PM

updated PHAX 5574 mcquitty.png
One of the Shum Laka individuals fits nicely in the C group.

**Norfern-Ostrobothnian** · 05-13-2021, 06:35 PM

The Andamanese are interesting, seems that they are mostly h4. I reckon this is a founder effect.
https://www.ebi.ac.uk/ena/browser/view/PRJEB11455
JAR-27: h4
JAR-32: h4
JAR-54: Denisovan haplotype? (C group, Differs from the Neanderthal haplotype by 22 nucleotides, 27 from the ancestral allele.)
JAR-61: h4->singleton [94574432]
ONG-12: h4->singleton [94573323]
ONG-14: h4->singleton [94573323]
ONG-1: h4->singleton [94573323]
ONG-4: h4
ONG-8: h4 and? h4->singleton [94573323] (female?)
ONG-9: h4->singleton [94573323]
PHAX 5574 updated mcquitty.png

**Norfern-Ostrobothnian** · 05-14-2021, 08:26 AM

Ust-Ishim: h4
Mota: h2'8'15'66-group/A3 -> singleton at 94551302
Wezmeh/WC1: h4

**Norfern-Ostrobothnian** · 05-15-2021, 12:18 PM

Finnish:HG00188: h8
Mbuti:HGDP00462: h25
Mozabite:HGDP01262: h4-> singleton at 94572379 + 3 African C group alleles, might be caused by slight recombination, but considering that the sample is 14% SSA it's still pretty low.

**Norfern-Ostrobothnian** · 10-07-2022, 08:21 AM

An incomplete tree of PHAX 5574
phyloPng.png

Code:

(
	((
		((((((((((
			(
			A1a1-h41:1,
			A1a2-h65:1
			):0.0001,
		A1a-h6:0.0001
		):1,
		(
			(
			A1b1-h49:1,
			A1b2-h59:1
			):0.0001,
		A1b-h8:0.0001
		):1
		):0.0001,
		A1c-h20:2
		):0.0001,
		A1d-h21:2
		):0.0001,
		A1e-h26:1
		):0.0001,
		A1f-h60:1
		):0.0001,
		A1g-h64:1
		):0.0001,
		(
			(((((((((((((((((
			B1-h3:1,
			B2-h4:1
			):0.0001,
			(
				B3a-h44:1,
			B3-h10:0.0001
			):1
			):0.0001,
			B4-h13:1
			):0.0001,
			B5-h17:1
			):0.0001,
			B6-h18:1
			):0.0001,
			B7-h19:1
			):0.0001,
			B8-h38:1
			):0.0001,
			B9-h39:1
			):0.0001,
			(
				B10a-h75:1,
			B10-h43:0.0001
			):1
			):0.0001,
			B11-h45:1
			):0.0001,
			B12-h46:1
			):0.0001,
			B13-h47:1
			):0.0001,
			(
				B14a-h40:1,
			B14-h48:0.0001
			):1
			):0.0001,
			B15-h50:1
			):0.0001,
			B16-h61:3
			):0.0001,
			(
				B17a-h12:1,
			B17-h76:0.0001
			):1
			):0.0001,
			(
				(((
				E1-h52:1,
				(
					E2a-h53:1,
				E2-h54:0.0001
				):1
				):0.0001,
				E3-h68:1
				):0.0001,
				E4-h78:1
				):0.0001,
			E-h7:0.0001
			):1
			):0.0001,
		B-h1:0.0001
		):1
		):0.0001,
		(
			((((((((
			(
				((
				C1a-h15:2,
				C1b-h73:1
				):0.0001,
				C1c-h74:1
				):0.0001,
			C1-h11:0.0001
			):1,
			C2-h14:1
			):0.0001,
			(
				C3a-h72:2,
			C3-h16:0.0001
			):2
			):0.0001,
			C4-h33:1
			):0.0001,
			C5-h51:1
			):0.0001,
			(
				C6a-h67:1,
			C6-h57:0.0001
			):1
			):0.0001,
			C7-h62:1
			):0.0001,
			C8-h69:1
			):0.0001,
			(
				(((
					F1a-h71:1,
				F1-h37:0.0001
				):1,
				F2-h63:1
				):0.0001,
				(
					F3a-h72:1,
				F3-h70:0.0001
				):1
				):0.0001,
			F-h5:0.0001
			):2
			):0.0001,
		C-h2:0.0001
		):1
		):0.0001,
		(
		(((
			(
				(
				D1a:2,
				D1b:2
				):0.0001,
			D1:0.0001
			):3,
			D2-h28:8
			):0.0001,
			D3-h31:58
			):0.0001,
			(
				(
				D4a-h24:1,
				D4b-h30:1
				):0.0001,
			D4-h34:0.0001
			):13
			):0.0001
		,D:0.0001
		):7
		):0.0001,
	A1:0.0001
	):1,
	A2-h66:1
	):3,
Ancestral_allele:0.0001
);

**Norfern-Ostrobothnian** · 10-08-2022, 03:44 PM

This is the definitive tree of the PHAX 5574 with all it's reported haplotypes. I will be adding more ancient DNA and modern samples to this phylogeny. I welcome any discussion regarding the naming scheme and haplogroup designations, as they are based on reported haplotypes.
PHAX5574_tree.png
I made this with phyloPNG.

Code:

(
	((
		((((((((((
			(
			A1a1-h41:1,
			A1a2-h65:1
			):0.0001,
		A1a-h6:0.0001
		):1,
		(
			(
			A1b1-h49:1,
			A1b2-h59:1
			):0.0001,
		A1b-h8:0.0001
		):1
		):0.0001,
		A1c-h20:2
		):0.0001,
		A1d-h21:2
		):0.0001,
		A1e-h26:1
		):0.0001,
		A1f-h60:1
		):0.0001,
		A1g-h64:1
		):0.0001,
		(
			(((((((((((((((((((((
			B1-h3:1,
			B2-h4:1
			):0.0001,
			(
				B3a-h44:1,
			B3-h10:0.0001
			):1
			):0.0001,
			B4-h13:1
			):0.0001,
			B5-h17:1
			):0.0001,
			B6-h18:1
			):0.0001,
			B7-h19:1
			):0.0001,
			B8-h38:1
			):0.0001,
			B9-h39:1
			):0.0001,
			B10-h42:1
			):0.0001,
			(
				B11a-h75:1,
			B11-h43:0.0001
			):1
			):0.0001,
			B12-h45:1
			):0.0001,
			B13-h46:1
			):0.0001,
			B14-h47:1
			):0.0001,
			(
				B15a-h40:1,
			B15-h48:0.0001
			):1
			):0.0001,
			B16-h50:1
			):0.0001,
			B17-h55:2
			):0.0001,
			B18-h56:1
			):0.0001,
			B19-h58:2
			):0.0001,
			B20-h61:3
			):0.0001,
			(
				B21a-h12:1,
			B21-h76:0.0001
			):1
			):0.0001,
			(
				(((
				E1-h52:1,
				(
					E2a-h53:1,
				E2-h54:0.0001
				):1
				):0.0001,
				E3-h68:1
				):0.0001,
				E4-h78:1
				):0.0001,
			E-h7:0.0001
			):1
			):0.0001,
		B-h1:0.0001
		):1
		):0.0001,
		(
			(((((((((
			C1-h9:3,
			(
				((
				C2a-h15:2,
				C2b-h73:1
				):0.0001,
				C2c-h74:1
				):0.0001,
			C2-h11:0.0001
			):1
			):0.0001,
			C3-h14:1
			):0.0001,
			(
				C4a-h77:1,
			C4-h16:0.0001
			):2
			):0.0001,
			C5-h33:1
			):0.0001,
			C6-h51:1
			):0.0001,
			(
				C7a-h67:1,
			C7-h57:0.0001
			):1
			):0.0001,
			C8-h62:1
			):0.0001,
			C9-h69:1
			):0.0001,
			(
				(((
					F1a-h71:1,
				F1-h37:0.0001
				):1,
				F2-h63:1
				):0.0001,
				(
					F3a-h72:1,
				F3-h70:0.0001
				):1
				):0.0001,
			F-h5:0.0001
			):2
			):0.0001,
		C-h2:0.0001
		):1
		):0.0001,
		(
		(((
			(
				((
					((
						((
							D1a1a1-h22:1,
						D1a1a-h29:0.0001
						):4,
						(
							D1a1b1-h23:1,
						D1a1b-h27:0.0001
						):4
						):0.0001,
					D1a1:0.0001
					):4,
					D1a2-h32:7
					):0.0001,
				D1a:0.0001
				):2,
				(
					(
					D1b1-h25:6,
					(
						(
						D1b2a-h35:3,
						D1b2b-h36:9
						):0.0001,
					D1b2:0.0001
					):2
					):0.0001,
				D1b:0.0001
				):2
				):0.0001,
			D1:0.0001
			):3,
			D2-h28:8
			):0.0001,
			D3-h31:58
			):0.0001,
			(
				(
				D4a-h24:1,
				D4b-h30:1
				):0.0001,
			D4-h34:0.0001
			):13
			):0.0001,
		D:0.0001
		):7
		):0.0001,
	A1:0.0001
	):1,
	A2-h66:1
	):3,
Ancestral_allele:0.0001
);

**Norfern-Ostrobothnian** · 01-07-2023, 09:04 AM

phylotree.png

I found a new haplotype A3 that is present exclusively among people of African descent. The haplotype is defined by a mutation at 94581024.
A2 is represented by a single sample from Palestinians. The African sample is Luhya.

Code:

(
	(((
		((((((((((
			(
			A1a1-h41:1,
			A1a2-h65:1
			):0.0001,
		A1a-h6:0.0001
		):1,
		(
			(
			A1b1-h49:1,
			A1b2-h59:1
			):0.0001,
		A1b-h8:0.0001
		):1
		):0.0001,
		A1c-h20:2
		):0.0001,
		A1d-h21:2
		):0.0001,
		A1e-h26:1
		):0.0001,
		A1f-h60:1
		):0.0001,
		A1g-h64:1
		):0.0001,
		(
			(((((((((((((((((((((
			B1-h3:1,
			B2-h4:1
			):0.0001,
			(
				B3a-h44:1,
			B3-h10:0.0001
			):1
			):0.0001,
			B4-h13:1
			):0.0001,
			B5-h17:1
			):0.0001,
			B6-h18:1
			):0.0001,
			B7-h19:1
			):0.0001,
			B8-h38:1
			):0.0001,
			B9-h39:1
			):0.0001,
			B10-h42:1
			):0.0001,
			(
				B11a-h75:1,
			B11-h43:0.0001
			):1
			):0.0001,
			B12-h45:1
			):0.0001,
			B13-h46:1
			):0.0001,
			B14-h47:1
			):0.0001,
			(
				B15a-h40:1,
			B15-h48:0.0001
			):1
			):0.0001,
			B16-h50:1
			):0.0001,
			B17-h55:2
			):0.0001,
			B18-h56:1
			):0.0001,
			B19-h58:2
			):0.0001,
			B20-h61:3
			):0.0001,
			(
				B21a-h12:1,
			B21-h76:0.0001
			):1
			):0.0001,
			(
				(((
				E1-h52:1,
				(
					E2a-h53:1,
				E2-h54:0.0001
				):1
				):0.0001,
				E3-h68:1
				):0.0001,
				E4-h78:1
				):0.0001,
			E-h7:0.0001
			):1
			):0.0001,
		B-h1:0.0001
		):1
		):0.0001,
		(
			(((((((((
			C1-h9:3,
			(
				((
				C2a-h15:2,
				C2b-h73:1
				):0.0001,
				C2c-h74:1
				):0.0001,
			C2-h11:0.0001
			):1
			):0.0001,
			C3-h14:1
			):0.0001,
			(
				C4a-h77:1,
			C4-h16:0.0001
			):2
			):0.0001,
			C5-h33:1
			):0.0001,
			C6-h51:1
			):0.0001,
			(
				C7a-h67:1,
			C7-h57:0.0001
			):1
			):0.0001,
			C8-h62:1
			):0.0001,
			C9-h69:1
			):0.0001,
			(
				(((
					F1a-h71:1,
				F1-h37:0.0001
				):1,
				F2-h63:1
				):0.0001,
				(
					F3a-h72:1,
				F3-h70:0.0001
				):1
				):0.0001,
			F-h5:0.0001
			):2
			):0.0001,
		C-h2:0.0001
		):1
		):0.0001,
		(
		(((
			(
				((
					((
						((
							D1a1a1-h22:1,
						D1a1a-h29:0.0001
						):4,
						(
							D1a1b1-h23:1,
						D1a1b-h27:0.0001
						):4
						):0.0001,
					D1a1:0.0001
					):4,
					D1a2-h32:7
					):0.0001,
				D1a:0.0001
				):2,
				(
					(
					D1b1-h25:6,
					(
						(
						D1b2a-h35:3,
						D1b2b-h36:9
						):0.0001,
					D1b2:0.0001
					):2
					):0.0001,
				D1b:0.0001
				):2
				):0.0001,
			D1:0.0001
			):3,
			D2-h28:8
			):0.0001,
			D3-h31:58
			):0.0001,
			(
				(
				D4a-h24:1,
				D4b-h30:1
				):0.0001,
			D4-h34:0.0001
			):13
			):0.0001,
		D:0.0001
		):7
		):0.0001,
	A1:0.0001
	):1,
	A2-h66:1
	):0.0001,
	A3-NA19350:1
	):3,
Ancestral_allele:0.0001
);

**Norfern-Ostrobothnian** · 02-16-2023, 01:10 PM

This is is the current form of the tree:

phylogram.png

I studied the Esan, Tamil, Kinh and Luhya people and partially the Gambian people from 1000 genomes project and some other populations like Onge, Jarawa and JuHoan.

The largest changes are the diversity found in D, and the introduction of it's subclade G. The haplogroup also has a new subclade D5 found in a Gambian sample. I also discovered a new subclade of D3.
D1b found among Tamil, Kinh and Jarawa was a bit of a surprise, but I guess that means it was present among East Eurasian ancestors' when they left Africa. It could also be from some obscure archaic population.
H is a haplogroup that seems to be really solidly East Eurasian related, but also shows up among some European samples.
There are now a total 162 haplotypes in PHAX5574. Any and all contributions to research into it are welcome be it from public modern data, ancient DNA or personal genomes.

Code:

(
	((
		(
			A1a1-h41:1,
			A1a2-h65:1,
		A1a-h6:0
		):1,
		(
			(
			A1b1-h49:1,
			A1b2-h59:1
			):0,
		A1b-h8:0
		):1,
		A1c-h20:2,
		A1d-h21:2,
		A1e-h26:1,
		A1f-h64:1,
		(
			A1g1-HG03133:1,
			A1g2-NA19383:2,
		A1g-HG02461:0
		):1,
		(
			A1h1-NA19319:1,
		A1h-HG03172:0
		):1,
		A1i-HG02561:1,
		(
			B1-h3:1,
			(
				B2a-NA19312:1,
			B2-h4:0
			):1,
			(
				B3a-h44:1,
			B3-h10:0
			):1,
			B4-h13:1,
			B5-h17:1,
			B6-h18:1,
			B7-h19:1,
			B8-h38:1,
			B9-h39:1,
			B10-h42:1,
			(
				(
				B11a-h75:1,
				B11b-HG03991:1
				):0,
			B11-h43:0
			):1,
			B12-h45:1,
			B13-h46:1,
			B14-h47:1,
			(
				B15a-h40:1,
			B15-h48:0
			):1,
			(
				B16-HG04033:1,
			B16-h50:0
			):1,
			B17-h55:2,
			B18-h56:1,
			B19-h58:2,
			B20-h61:3,
			(
				B21a-h12:1,
			B21-h76:0
			):1,
			B22-HG03686:1,
			B23-HG03691:1,
			B24-HG03693:2,
			B25-JAR-61:1,
			B26-ONG-12:1,
			B27-HG03695:2,
			B28-HG03749:2,
			B29-HG03753:1,
			B30-HG03851:1,
			B31-HG03885:1,
			B32-HG03887:2,
			B33-HG03950:1,
			B34-HG01840:3,
			(
				B35a-HG01867:1,
				B35b-HG02047:1,
			B35-HG02088:0
			):3,
			B36-HG02017:1,
			B37-HG02032:1,
			B38-HG02040:1,
			(
				B39a-HG02512:1,
			B39-HG02058:0
			):2,
			B40-HG02079:1,
			B41-HG02116:1,
			B42-HG02122:1,
			(
				E1-h52:1,
				(
					E2a-h53:1,
				E2-h54:0
				):1,
				E3-h68:1,
				E4-h78:1,
			E-h7:0
			):1,
		B-h1:0
		):1,
		(
			C1-h9:3,
			(
				C2a-h15:2,
				C2b-h73:1,
				C2c-h74:1,
			C2-h11:0
			):1,
			C3-h14:1,
			(
				C4a-h77:1,
			C4-h16:0
			):2,
			C5-h33:1,
			C6-h51:1,
			(
				C7a-h67:1,
			C7-h57:0
			):1,
			C8-h62:1,
			C9-h69:1,
			C10-HG03112:1,
			(
				(
					F1a-h71:1,
					F1b-HG03846:1,
				F1-h37:0
				):1,
				F2-h63:1,
				F3-h70:1,
				(
					F4a-h72:1,
				F4-NA19428:0
				):2,
			F-h5:0
			):2,
		C-h2:0
		):1,
		(
			(
				(
					(
						(
							(
								D1a1a1a-h32:1,
								(
									D1a1a1b1-NA19318:1,
								D1a1a1b-NA19025:0
								):1,
							D1a1a1-NA19307:0
							):1,
							(
								D1a1a2a-HG03103:1,
							D1a1a2-HG02971:0
							):1,
							D1a1a3-NA19454:3,
						D1a1a:0
						):5,
						(
							(
								(
									G1a1-h22:1,
								G1a-h29:0
								):3,
								G1b-NA19448:2,
							G1:0
							):1,
							(
								(
									G2a1-h23:1,
									G2a2-HG02938:1,
									G2a3-HG02973:1,
									G2a4-HG03313:1,
								G2a-h27:0
								):3,
								G2b-HG02582:2,
							G2-HG02610:0
							):1,
							G3-HG03120:1,
							G4-HG03124:3,
							G5-HG03352:1,
							G6-NA19041:3,
							G7-NA19461:2,
						G-HG03139:0
						):4,
					D1a1:0
					):2,
					(
						(
							(
								D1a2a1a-HG03109:2,
								D1a2a1b-NA19026:1,
								D1a2a1c-NA19334:1,
							D1a2a1-HG02588:0
							):1,
							D1a2a2-HG02594:1,
						D1a2a-h25:0
						):6,
						(
							(
								(
									(
										D1a2b1a1a-HG03311:1,
									D1a2b1a1-HG03169:0
									):1,
								D1a2b1a-h35:0
								):1,
								D1a2b1b-HGDP01036:10,
							D1a2b1:0
							):2,
							(
								D1a2b2a-NA19372:1,
							D1a2b2-h36:0
							):9,
						D1a2b:0
						):2,
					D1a2:0
					):2,
				D1a:0
				):2,
				(
					(
						D1b1a-JAR-54:1,
						D1b1b-HG03694:2,
					D1b1-HG03697:0
					):1,
					D1b2-HG03711:1,
				D1b-HG02067:0
				):13,
			D1:0
			):1,
			D2-h28:8,
			(
				D3a-h31:4,
				D3b-NA19429:6,
			D3:0
			):54,
			(
				D4a-h24:1,
				D4b-h30:1,
			D4-h34:0
			):13,
			D5-HG02570:12,
		D:0
		):7,
		(
			(
				H1a-HG03687:1,
				H1b-HG03743:1,
			H1-HG03644:0
			):2,
			H2-HG04006:1,
			H3-HG01852:2,
			H4-HG01872:1,
			H5-HG02029:1,
			H6-HG02050:1,
		H-h60:0
		):1,
	A1-HG03271:0
	):1,
	A2-h66:1,
	(
		A3a-HG03367:1,
	A3-NA19350:0
	):1,
	A-HG03193:0
	):3,
Ancestral_allele:0
);

Thread: Thread inspecting the low-recombination regions of the X-chromosome

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