View Full Version : Thread inspecting the low-recombination regions of the X-chromosome

05-06-2021, 07:58 PM
Essentially, these regions function as haplotypes like mitochondrial DNA or the Y chromosome. They only mutate.
Let's see which haplotypes people here fall in!

Check the supplementary tables and compare it to your X-chromosome. In theory, this should give you inherited haplotypes.

Human genetic diversity in Europe has been extensively studied using uniparentally-inherited sequences (mitochondrial DNA [mtDNA] and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap SNP data to identify segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as Phylogeographically informative Haplotypes on Autosomes and X chromosome (PHAXs). Three such sequences spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181 . PHAXs were confirmed to be essentially non-recombining across European samples. All three loci show highly homogeneous patterns across Europe and are highly differentiated from the African sample. Star-like structures of European-specific haplotypes in median-joining networks indicate past population expansions. Bayesian skyline plots and time-to-most-recent-common-ancestor estimates suggest expansions pre-dating the Neolithic transition, a finding that is more compatible with data on mtDNA than the Y chromosome, and with the female bias of X-chromosomal inheritance. This study demonstrates the potential of the use of X-chromosomal haplotype blocks, and the utility of the accurate ascertainment of rare variants for inferring human demographic history.

05-06-2021, 10:48 PM
PHAX 3115 Hungarian Orcadian YRI Spanish Irish Turkish CEU English Danish Palestinian Dutch Norwegian
Hungarian 0,000
Orcadian 0,019 0,000
YRI 0,045 0,074 0,000
Spanish 0,000 0,003 0,035 0,000
Irish 0,000 0,000 0,031 0,000 0,000
Turkish 0,000 0,109 0,064 0,000 0,000 0,000
CEU 0,000 0,000 0,043 0,000 0,000 0,009 0,000
English 0,000 0,000 0,055 0,000 0,000 0,043 0,000 0,000
Danish 0,000 0,045 0,049 0,000 0,000 0,000 0,000 0,018 0,000
Palestinian 0,000 0,086 0,021 0,002 0,005 0,001 0,031 0,021 0,016 0,000
Dutch 0,004 0,092 0,062 0,000 0,000 0,000 0,000 0,049 0,000 0,014 0,000
Norwegian 0,033 0,155 0,087 0,011 0,024 0,000 0,042 0,089 0,000 0,017 0,000 0,000

05-07-2021, 07:43 AM
Essentially, these regions function as haplotypes like mitochondrial DNA or the Y chromosome. They only mutate.
Let's see which haplotypes people here fall in!

How do you check that? What kind of raw data you need?

05-07-2021, 08:50 AM
There's an apparent dissonance with the study's results and my own inspection on NCBI

CHR_X: 39519963 39520046 39520428

3115_h1 A G G

HGDP00675 A G A

05-07-2021, 08:53 AM
How do you check that? What kind of raw data you need?

Go to the genetic test you may have purchased.
Take the raw data.
Make sure it is in hg19 format.
Inspect in a text editor to see which haplotype correlates the best with your own by comparing the positions and alleles.

Remember, these are very poorly studied regions, so the haplotypes are most likely to be different than what you have, but it will be closer to some of them.

05-07-2021, 07:16 PM
This sample may be a female, but I worked all evening on it so here's the results.

PHAX 3115
Match(x/33) %
PHAX 5574
Match (x/214) %
PHAX 8913
Match (x/50) %

(33/33) 100.00%
(212/214) 99.07%
(44/50) 88.00%

(33/33) 93.94%

Ancestral allele
(32/33) 96.97%

(48/50) 96.00%

(33/33) 100.00%
(210/214) 98.13%
Ancestral allele
(50/50) 100.00%

05-08-2021, 01:06 PM
Botai's seem to have some East Siberian lineage on PHAX 8913.

05-10-2021, 07:09 PM
This is the tree I got on R from PHAX 3115.

05-11-2021, 06:30 PM
I did this clustering on the much more detailed PHAX 5574, which I feel will be quite reliable as a marker. The obvious distance is between h31 and others, being deeply African.

Possible labels?

All D and C cluster haplotypes are African.

05-12-2021, 12:09 PM
Interesting! The Altai Neanderthal is seemingly closer to the C group than the D group is to any group. This would mean that Neanderthals have less mutated PHAX 5574.
Or perhaps D is super-archaic or super-bottlenecked. I recorded 10 new SNPs that differed from the previous dataset, and almost all variants that defied the reference genome were in correlation with the C group. So it might be that the Neanderthal had an ancestral haplotype to the C group.

05-12-2021, 02:50 PM
see https://anthrogenica.com/showthread.php?9619-Post-your-PHAX-haplotypes-here :-)

05-12-2021, 04:09 PM
see https://anthrogenica.com/showthread.php?9619-Post-your-PHAX-haplotypes-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?

05-12-2021, 07:00 PM
One of the Shum Laka individuals fits nicely in the C group.

05-13-2021, 06:35 PM
The Andamanese are interesting, seems that they are mostly h4. I reckon this is a founder effect.
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]

05-14-2021, 08:26 AM
Ust-Ishim: h4
Mota: h2'8'15'66-group/A3 -> singleton at 94551302
Wezmeh/WC1: h4

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.