PHAX5574 discussion
#1
This thread is dedicated for discussing PHAX5574. This region of the X-chromosome rarely recombines and can be used for population genetic analyses like mtDNA or y-DNA. I have done some additional analysis of samples that this study has done and given some labels for the various clades in PHAX5574 I have discovered.
https://www.nature.com/articles/ejhg2016207
   

The tree in Newick format
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You can view the tree here: https://phylo.io/#
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#2
Code:
Sample    Population    Haplotype    Haplogroup
N2    Norwegian    h1    B
N3    Norwegian    h4    B
N7    Norwegian    h73    C
N8    Norwegian    h1    B
N9    Norwegian    h74    C
N13    Norwegian    h75    B
N14    Norwegian    h76    B
N15    Norwegian    h4    B
N16    Norwegian    h1    B
N17    Norwegian    h7    E
N18    Norwegian    h7    E
N20    Norwegian    h11    C
N21    Norwegian    h77    C
N23    Norwegian    h3    B
N25    Norwegian    h1    B
N28    Norwegian    h78    E
N29    Norwegian    h1    B
N24    Norwegian    h3    B
N26    Norwegian    h5    F
N27    Norwegian    h6    A1
DA8283    Danish    h1    B
DA150    Danish    h1    B
DA152    Danish    h1    B
DA157    Danish    h8    A1
DA158    Danish    h1    B
DA176    Danish    h61    B
DA183    Danish    h33    C
DA186    Danish    h62    C
DA189    Danish    h1    B
DA190    Danish    h8    A1
DA191    Danish    h1    B
DA192    Danish    h50    B
DA207    Danish    h1    B
DAsn    Danish    h1    B
DA34    Danish    h63    F
DA30    Danish    h1    B
DA36    Danish    h3    B
DA104    Danish    h1    B
DA50/51    Danish    h4    B
DA113    Danish    h4    B
D1312    Dutch    h67    C
D1309    Dutch    h1    B
D1311    Dutch    h3    B
D1313    Dutch    h1    B
D1317    Dutch    h68    E
D1319    Dutch    h2    C
D1320    Dutch    h69    C
D1324    Dutch    h2    C
D1325    Dutch    h1    B
D1329    Dutch    h3    B
D1516    Dutch    h70    F
D1718    Dutch    h71    F
D1722    Dutch    h1    B
D1725    Dutch    h72    F
D1784    Dutch    h1    B
D1788    Dutch    h1    B
D1937    Dutch    h3    B
D1938    Dutch    h4    B
D1048    Dutch    h16    C
D1087    Dutch    h5    F
S0052    Irish    h2    C
S0053    Irish    h44    B
S0059    Irish    h2    C
S0068    Irish    h8    A1
S0078    Irish    h45    B
S0095    Irish    h2    C
S0100    Irish    h46    B
S0109    Irish    h2    C
S0116    Irish    h1    B
S0120    Irish    h1    B
S0136    Irish    h1    B
S0114    Irish    h10    B
S55    Irish    h2    C
S74    Irish    h4    B
S94    Irish    h47    B
S112    Irish    h1    B
S132    Irish    h48    B
S0093    Irish    h45    B
S0130    Irish    h2    C
S0107    Irish    h43    B
OXF063    English    h5    F
WOR020    English    h1    B
OXF036    English    h1    B
FOD006    English    h3    B
GLO009    English    h1    B
HER038    English    h5    F
FOD058    English    h1    B
WOR017    English    h1    B
WOR011    English    h6    A1
OXF023    English    h57    C
OXF069    English    h1    B
OXF045    English    h2    C
WOR013    English    h1    B
OXF093    English    h1    B
OXF015    English    h16    C
NTH005    English        
OXF109    English    h60    H
OXF044    English    h1    B
FOD002    English    h1    B
HER018    English    h1    B
ORK573    Orcadian    h7    E
ORK571    Orcadian    h2    C
ORK010    Orcadian    h2    C
ORK564    Orcadian    h2    C
ORK579    Orcadian    h1    B
ORK007    Orcadian    h12    B
ORK583    Orcadian    h1    B
ORK577    Orcadian    h6    A1
ORK525    Orcadian    h2    C
ORK575    Orcadian    h1    B
ORK565    Orcadian    h9    C
ORK584    Orcadian    h14    C
ORK585    Orcadian    h8    A1
ORK552    Orcadian    h16    C
ORK567    Orcadian    h6    A1
ORK008    Orcadian    h17    B
ORK004    Orcadian    h8    A1
ORK022    Orcadian    h11    C
ORK026    Orcadian    h8    A1
ORK036    Orcadian    h19    B
NA12814    CEU    h8    A1
NA12872    CEU    h1    B
NA12874    CEU    h1    B
NA12707    CEU    h55    B
NA06994    CEU    h56    B
NA07048    CEU    h57    C
NA07357    CEU    h9    C
NA10851    CEU    h1    B
NA11829    CEU    h58    B
NA11831    CEU    h1    B
NA11992    CEU    h1    B
NA11994    CEU    h56    B
NA12003    CEU    h7    E
NA12043    CEU    h7    E
NA12144    CEU    h1    B
NA12154    CEU    h1    B
NA12155    CEU    h59    A1
NA12716    CEU    h10    B
NA12750    CEU    h2    C
NA12812    CEU    h11    C
SP28    Spanish    h4    B
SP30    Spanish    h2    C
SP34    Spanish    h1    B
SP36    Spanish    h1    B
SP51    Spanish    h1    B
SP52    Spanish    h3    B
SP53    Spanish    h38    B
SP54    Spanish    h2    C
SP58    Spanish    h9    C
SP60    Spanish    h39    B
SP74    Spanish    h1    B
SP87    Spanish    h5    F
SP96    Spanish    h1    B
SP99    Spanish    h41    A1
SP15    Spanish        
SP15_il    Spanish    h42    A1
SP20    Spanish    h3    B
SP37    Spanish    h1    B
SP47    Spanish    h40    B
SP63    Spanish    h43    B
TK1    Turkish    h1    B
TK10    Turkish    h49    A1
TK11    Turkish    h50    B
TK12    Turkish    h51    C
TK13    Turkish    h1    B
TK14    Turkish    h1    B
TK15    Turkish    h52    E
TK16    Turkish    h1    B
TK17    Turkish    h5    F
TK18    Turkish    h49    A1
TK19    Turkish    h1    B
TK2    Turkish    h2    C
TK21    Turkish    h53    E
TK3    Turkish    h1    B
TK4    Turkish    h6    A1
TK5    Turkish    h1    B
TK6    Turkish    h54    E
TK7    Turkish    h2    C
TK8    Turkish    h1    B
TK9    Turkish    h1    B
4918    Palestinian    h1    B
4919    Palestinian    h1    B
4921    Palestinian    h1    B
4941    Palestinian    h1    B
4942    Palestinian    h1    B
4943    Palestinian    h2    C
5047    Palestinian    h1    B
5048    Palestinian    h64    A1
5225    Palestinian    h2    C
5232    Palestinian    h5    F
5257    Palestinian    h65    A1
5341    Palestinian    h1    B
5365    Palestinian    h2    C
5366    Palestinian    h1    B
5370    Palestinian    h1    B
5420    Palestinian    h7    E
HGDP00675    Palestinian    h66    A1
HGDP00676    Palestinian    h1    B
HGDP00677    Palestinian    h64    A1
HGDP00678    Palestinian    h7    E
HU5    Hungarian    h10    B
HU1    Hungarian    h2    C
HU2    Hungarian    h4    B
HU25    Hungarian    h1    B
HU26    Hungarian    h15    C
HU27    Hungarian    h18    B
HU28    Hungarian    h37    F
HU29    Hungarian    h1    B
HU33    Hungarian    h6    A1
HU34    Hungarian    h1    B
HU35    Hungarian    h40    B
HU39    Hungarian    h13    B
HU40    Hungarian    h2    C
HU9    Hungarian    h2    C
HU3    Hungarian    h1    B
HU38    Hungarian    h1    B
HU47    Hungarian    h6    A1
HU37    Hungarian    h1    B
HU43    Hungarian    h2    C
HU46    Hungarian    h1    B
NA19098    YRI    h20    A1
NA19119    YRI    h1    B
NA19138    YRI    h21    A1
NA19160    YRI    h22    G
NA19171    YRI    h23    G
NA19200    YRI    h24    A4
NA19207    YRI    h25    A2
NA19223    YRI    h26    A1
NA19130    YRI    h1    B
NA19153    YRI    h26    A1
NA19144    YRI    h27    G
NA19203    YRI    h28    A3
NA18501    YRI    h29    G
NA18504    YRI    h30    A4
NA18507    YRI    h31    D
NA18516    YRI    h32    A2
NA18522    YRI    h33    C
NA18853    YRI    h34    A4
NA18856    YRI    h35    A2
NA18871    YRI    h36    A2
HG02923    Esan    Luhya:NA19350    A1
HG02938    Esan    Esan:HG02938    G
HG02941    Esan    h32    A2
HG02944    Esan    h27    G
HG02947    Esan    h34    A4
HG02953    Esan    Esan:HG02938    G
HG02968    Esan    Esan:HG02938    G
HG02971    Esan    Esan:HG02971    A2
HG02973    Esan    Esan:HG02973    G
HG02977    Esan    Esan:HG02973    G
HG02981    Esan    h28    A3
HG03100    Esan    h27    G
HG03103    Esan    Esan:HG03103    A2
HG03109    Esan    Esan:HG03109    A2
HG03112    Esan    Esan:HG03112    C
HG03115    Esan    h22    G
HG03118    Esan    h22    G
HG03120    Esan    Esan:HG03120    G
HG03124    Esan    Esan:HG03124    G
HG03127    Esan    h22    G
HG03130    Esan    h27    G
HG03133    Esan    Esan:HG03133    A1
HG03139    Esan    Esan:HG03139    G
HG03157    Esan    h36    A2
HG03160    Esan    Esan:HG03103    A2
HG03163    Esan    Esan:HG03124    G
HG03166    Esan    h27    G
HG03169    Esan    Esan:HG03169    A2
HG03172    Esan    Esan:HG03172    A1
HG03175    Esan    h21    A1
HG03190    Esan    h27    G
HG03193    Esan    Esan:HG03193    A1
HG03196    Esan    h25    A2
HG03199    Esan    h22    G
HG03202    Esan    Esan:HG03202    A2
HG03265    Esan    Esan:HG03103    A2
HG03268    Esan    h36    A2
HG03271    Esan    Esan:HG03271    A1
HG03280    Esan    Esan:HG02971    A2
HG03295    Esan    h21    A1
HG03298    Esan    Esan:HG03271    A1
HG03301    Esan    h35    A2
HG03304    Esan    h1    B
HG03311    Esan    Esan:HG03311    A2
HG03313    Esan    Esan:HG03313    G
HG03343    Esan    h30    A4
HG03352    Esan    Esan:HG03352    G
HG03367    Esan    Esan:HG03367    A1
HG03370    Esan    h30    A4
HG03515    Esan    Esan:HG03172    A1
HG03518    Esan    Esan:HG03103    A2
HG03521    Esan    Esan:HG03103    A2
HG03644    TamilSriLanka    TamilSriLanka:HG03644    H
HG03646    TamilSriLanka    TamilSriLanka:HG03644    H
HG03672    TamilSriLanka    h1    B
HG03679    TamilSriLanka    h1    B
HG03680    TamilSriLanka    h1    B
HG03681    TamilSriLanka    h1    B
HG03685    TamilSriLanka    h1    B
HG03686    TamilSriLanka    TamilSriLanka:HG03686    B
HG03687    TamilSriLanka    TamilSriLanka:HG03687    H
HG03691    TamilSriLanka    TamilSriLanka:HG03691    B
HG03693    TamilSriLanka    TamilSriLanka:HG03693    B
HG03694    TamilSriLanka    TamilSriLanka:HG03694    A2
HG03695    TamilSriLanka    TamilSriLanka:HG03695    B
HG03696    TamilSriLanka    h1    B
HG03697    TamilSriLanka    TamilSriLanka:HG03697    A2
HG03711    TamilSriLanka    TamilSriLanka:HG03711    A2
HG03738    TamilSriLanka    TamilSriLanka:HG03644    H
HG03740    TamilSriLanka    TamilSriLanka:HG03740    B
HG03743    TamilSriLanka    TamilSriLanka:HG03743    H
HG03744    TamilSriLanka    h1    B
HG03745    TamilSriLanka    h45    B
HG03746    TamilSriLanka    h1    B
HG03750    TamilSriLanka    h1    B
HG03753    TamilSriLanka    TamilSriLanka:HG03753    B
HG03755    TamilSriLanka    h1    B
HG03837    TamilSriLanka    h1    B
HG03844    TamilSriLanka    h11    C
HG03846    TamilSriLanka    TamilSriLanka:HG03846    F
HG03848    TamilSriLanka    h1    B
HG03850    TamilSriLanka    h60    H
HG03851    TamilSriLanka    TamilSriLanka:HG03851    B
HG03854    TamilSriLanka    h1    B
HG03856    TamilSriLanka    h1    B
HG03885    TamilSriLanka    TamilSriLanka:HG03885    B
HG03887    TamilSriLanka    TamilSriLanka:HG03887    B
HG03890    TamilSriLanka    h8    A1
HG03896    TamilSriLanka    h1    B
HG03899    TamilSriLanka    h1    B
HG03900    TamilSriLanka    TamilSriLanka:HG03711    A2
HG03943    TamilSriLanka    h1    B
HG03950    TamilSriLanka    TamilSriLanka:HG03950    B
HG03953    TamilSriLanka    h1    B
HG03985    TamilSriLanka    h60    H
HG03990    TamilSriLanka    h1    B
HG03991    TamilSriLanka    TamilSriLanka:HG03991    B
HG03998    TamilSriLanka    TamilSriLanka:HG03887    B
HG03999    TamilSriLanka    h1    B
HG04003    TamilSriLanka    h53    E
HG04006    TamilSriLanka    TamilSriLanka:HG04006    H
HG04033    TamilSriLanka    TamilSriLanka:HG04033    B
HG04039    TamilSriLanka    h7    E
HG04100    TamilSriLanka    h37    F
HG04107    TamilSriLanka    h1    B
HG04210    TamilSriLanka    TamilSriLanka:HG03697    A2
HG04229    TamilSriLanka    h1    B
JAR-27    Jarawa    h1    B
JAR-32    Jarawa    h1    B
JAR-54    Jarawa    Jarawa:JAR-54    A2
JAR-61    Jarawa    Jarawa:JAR-61    B
ONG-12    Onge    Onge:ONG-12    B
ONG-14    Onge    Onge:ONG-12    B
ONG-1    Onge    Onge:ONG-12    B
ONG-4    Onge    h1    B
ONG-8    Onge    Onge:ONG-12    B
ONG-9    Onge    Onge:ONG-12    B
HG01596    Kinh    h1    B
HG01840    Kinh    Kinh:HG01840    B
HG01842    Kinh    h1    B
HG01844    Kinh    Kinh:HG01840    B
HG01846    Kinh    h1    B
HG01849    Kinh    Kinh:HG01840    B
HG01852    Kinh    Kinh:HG01852    H
HG01860    Kinh    TamilSriLanka:HG03697    A2
HG01861    Kinh    h1    B
HG01864    Kinh    Kinh:HG01864    B
HG01865    Kinh    Kinh:HG01864    B
HG01866    Kinh    TamilSriLanka:HG03697    A2
HG01867    Kinh    Kinh:HG01867    B
HG01872    Kinh    Kinh:HG01872    H
HG01873    Kinh    h1    B
HG02017    Kinh    Kinh:HG02017    B
HG02020    Kinh    h1    B
HG02023    Kinh    h1    B
HG02026    Kinh    h1    B
HG02029    Kinh    Kinh:HG02029    H
HG02032    Kinh    Kinh:HG02032    B
HG02035    Kinh    Jarawa:JAR-54    A2
HG02040    Kinh    Kinh:HG02040    B
HG02047    Kinh    Kinh:HG02047    B
HG02050    Kinh    Kinh:HG02050    H
HG02058    Kinh    Kinh:HG02058    B
HG02061    Kinh    h1    B
HG02064    Kinh    h60    H
HG02067    Kinh    Kinh:HG02067    A2
HG02070    Kinh    h1    B
HG02073    Kinh    h60    H
HG02076    Kinh    h60    H
HG02079    Kinh    Kinh:HG02079    B
HG02082    Kinh    Kinh:HG01864    B
HG02085    Kinh    h1    B
HG02088    Kinh    Kinh:HG02088    B
HG02116    Kinh    Kinh:HG02116    B
HG02122    Kinh    Kinh:HG02122    B
HG02128    Kinh    Kinh:HG02088    B
HG02131    Kinh    Kinh:HG02058    B
HG02134    Kinh    h60    H
HG02137    Kinh    Kinh:HG02088    B
HG02138    Kinh    Kinh:HG01864    B
HG02141    Kinh    h60    H
HG02512    Kinh    Kinh:HG02512    B
HG02521    Kinh    Kinh:HG02088    B
NA19350    Luhya    Luhya:NA19350    A1
NA19020    Luhya    Esan:HG03172    A1
NA19025    Luhya    Luhya:NA19025    A2
NA19026    Luhya    Luhya:NA19026    A2
NA19027    Luhya    Luhya:NA19025    A2
NA19028    Luhya    h1    B
NA19031    Luhya    Gambian:HG02461    A1
NA19035    Luhya    Esan:HG03124    G
NA19041    Luhya    Luhya:NA19041    G
NA19043    Luhya    Esan:HG03172    A1
NA19307    Luhya    Luhya:NA19307    A2
NA19308    Luhya    Esan:HG03311    A2
NA19309    Luhya    Gambian:HG02461    A1
NA19312    Luhya    Luhya:NA19312    B
NA19317    Luhya    h27    G
NA19318    Luhya    Luhya:NA19318    A2
NA19319    Luhya    Luhya:NA19319    A1
NA19331    Luhya    Esan:HG03311    A2
NA19334    Luhya    Luhya:NA19334    A2
NA19346    Luhya    Esan:HG03172    A1
NA19347    Luhya    Esan:HG03311    A2
NA19360    Luhya    Esan:HG03311    A2
NA19372    Luhya    Luhya:NA19372    A2
NA19374    Luhya    Esan:HG03311    A2
NA19375    Luhya    h30    A4
NA19376    Luhya    Gambian:HG02461    A1
NA19380    Luhya    Esan:HG03311    A2
NA19383    Luhya    Luhya:NA19383    A1
NA19384    Luhya    h25    A2
NA19385    Luhya    h1    B
NA19393    Luhya    h64    A1
NA19394    Luhya    Gambian:HG02461    A1
NA19397    Luhya    Luhya:NA19025    A2
NA19428    Luhya    Luhya:NA19428    F
NA19429    Luhya    Luhya:NA19429    D
NA19430    Luhya    Gambian:HG02461    A1
NA19443    Luhya    Luhya:NA19372    A2
NA19448    Luhya    Luhya:NA19448    G
NA19451    Luhya    h1    B
NA19452    Luhya    h2    C
NA19454    Luhya    Luhya:NA19454    A2
NA19455    Luhya    Gambian:HG02461    A1
NA19461    Luhya    Luhya:NA19461    G
NA19466    Luhya    Luhya:NA19025    A2
HG02461    Gambian    Gambian:HG02461    A1
HG02464    Gambian    h27    G
HG02561    Gambian    Gambian:HG02561    A1
HG02570    Gambian    Gambian:HG02570    A5
HG02573    Gambian    Esan:HG03169    A2
HG02582    Gambian    Gambian:HG02582    G
HG02585    Gambian    Esan:HG03193    A1
HG02588    Gambian    Gambian:HG02588    A2
HG02594    Gambian    Gambian:HG02594    A2
HG02610    Gambian    Gambian:HG02610    G
HG02613    Gambian    h21    A1
HG02623    Gambian    h30    A4
HG02628    Gambian    Gambian:HG02628    A2
HG02634    Gambian    Esan:HG03271    A1
HG02642    Gambian    Gambian:HG02642    A1
HG02645    Gambian    Gambian:HG02645    A5
HG02666    Gambian    Gambian:HG02666    C
HG02675    Gambian    Gambian:HG02675    G
HG02678    Gambian    h1    B
HG02702    Gambian    h1    B
HG02715    Gambian    h27    G
HG02721    Gambian    Gambian:HG02721    A2
HG02756    Gambian    h1    B
HG02759    Gambian    Gambian:HG02594    A2
HG02768    Gambian    Gambian:HG02645    A5
HG02771    Gambian    Gambian:HG02771    A3
HG02798    Gambian    Gambian:HG02798    A1
HG02804    Gambian    h21    A1
HG02807    Gambian    Gambian:HG02807    A2
HG02810    Gambian    Gambian:HG02810    A2
HG02813    Gambian    h21    A1
HG02816    Gambian    h1    B
HG02819    Gambian    Gambian:HG02588    A2
HG02836    Gambian    Gambian:HG02836    C
HG02839    Gambian    Gambian:HG02839    B
HG02851    Gambian    Gambian:HG02771    A3
HG02854    Gambian    Esan:HG02971    A2
HG02860    Gambian    Gambian:HG02860    G
HG02878    Gambian    h27    G
HG02881    Gambian    Gambian:HG02881    G
HG02881    Gambian    h27    G
HG02887    Gambian    Gambian:HG02887    G
HG02890    Gambian    h27    G
HG02982    Gambian    h1    B
HG03024    Gambian    Gambian:HG03024    C
HG03027    Gambian    Gambian:HG03027    A2
HG03039    Gambian    h1    B
HG03045    Gambian    Gambian:HG03045    B
HG03048    Gambian    h32    A2
HG03240    Gambian    Gambian:HG02588    A2
HG03246    Gambian    h21    A1
HG03258    Gambian    Esan:HG03271    A1
HG03538    Gambian    Gambian:HG02645    A5
NA18940    Japanese    Japanese:NA18940    B
NA18943    Japanese    Japanese:NA18943    B
NA18944    Japanese    h1    B
NA18945    Japanese    Esan:HG03271    A1
NA18948    Japanese    h1    B
NA18952    Japanese    h1    B
NA18953    Japanese    Japanese:NA18953    B
NA18959    Japanese    Kinh:HG01872    H
NA18960    Japanese    Japanese:NA18960    B
NA18961    Japanese    Japanese:NA18961    C
NA18962    Japanese    Japanese:NA18962    B
NA18965    Japanese    Japanese:NA18965    C
NA18966    Japanese    Japanese:NA18966    H
NA18967    Japanese    h1    B
NA18970    Japanese    Japanese:NA18953    B
NA18971    Japanese    Japanese:NA18971    B
NA18974    Japanese    Japanese:NA18974    H
NA18977    Japanese    Japanese:NA18977    B
NA18982    Japanese    Kinh:HG01872    H
NA18983    Japanese    Kinh:HG02088    B
NA18984    Japanese    Japanese:NA18984    B
NA18985    Japanese    h1    B
NA18986    Japanese    Japanese:NA18986    H
NA18988    Japanese    Japanese:NA18953    B
NA18989    Japanese    h60    H
NA18990    Japanese    Japanese:NA18990    B
NA18994    Japanese    Kinh:HG01872    H
NA18995    Japanese    h1    B
NA19000    Japanese    h60    H
NA19004    Japanese    Japanese:NA18960    B
NA19005    Japanese    h2    C
NA19006    Japanese    h1    B
NA19007    Japanese    Japanese:NA19007    B
NA19009    Japanese    h1    B
NA19012    Japanese    Japanese:NA19012    H
NA19055    Japanese    TamilSriLanka:HG03697    A2
NA19056    Japanese    h1    B
NA19058    Japanese    Japanese:NA19058    B
NA19060    Japanese    h1    B
NA19062    Japanese    h1    B
NA19063    Japanese    Japanese:NA18943    B
NA19066    Japanese    h60    H
NA19067    Japanese    Japanese:NA19067    B
NA19068    Japanese    Kinh:HG02088    B
NA19070    Japanese    Japanese:NA19070    B
NA19072    Japanese    h60    H
NA19075    Japanese    Japanese:NA19075    B
NA19076    Japanese    Japanese:NA19076    H
NA19079    Japanese    h1    B
NA19082    Japanese    Japanese:NA19082    B
NA19083    Japanese    Japanese:NA19083    B
NA19085    Japanese    Japanese:NA19012    H
NA19086    Japanese    h1    B
NA19088    Japanese    h1    B
NA19089    Japanese    Japanese:NA18965    C
NA19091    Japanese    Japanese:NA19091    H
HG03713    Telugu    h1    B
HG03716    Telugu    h1    B
HG03718    Telugu    Telugu:HG03718    B
HG03720    Telugu    h1    B
HG03727    Telugu    TamilSriLanka:HG03644    H
HG03729    Telugu    h8    A1
HG03771    Telugu    Telugu:HG03771    B
HG03773    Telugu    h1    B
HG03775    Telugu    h7    E
HG03777    Telugu    h1    B
HG03778    Telugu    h1    B
HG03779    Telugu    Telugu:HG03779    B
HG03785    Telugu    h1    B
HG03786    Telugu    h1    B
HG03788    Telugu    Jarawa:JAR-61    B
HG03790    Telugu    Telugu:HG03790    B
HG03792    Telugu    h1    B
HG03864    Telugu    Telugu:HG03864    C
HG03866    Telugu    Telugu:HG03866    C
HG03867    Telugu    TamilSriLanka:HG03711    A2
HG03869    Telugu    Telugu:HG03869    B
HG03870    Telugu    Telugu:HG03870    C
HG03871    Telugu    h1    B
HG03872    Telugu    h1    B
HG03875    Telugu    TamilSriLanka:HG03887    B
HG03960    Telugu    h1    B
HG03963    Telugu    h1    B
HG03965    Telugu    h1    B
HG03967    Telugu    h1    B
HG03969    Telugu    Telugu:HG03969    C
HG03976    Telugu    Telugu:HG03976    A2
HG03978    Telugu    TamilSriLanka:HG03644    H
HG04002    Telugu    h1    B
HG04015    Telugu    h1    B
HG04017    Telugu    TamilSriLanka:HG03950    B
HG04019    Telugu    h2    C
HG04020    Telugu    h1    B
HG04022    Telugu    Telugu:HG04022    A2
HG04023    Telugu    h1    B
HG04056    Telugu    Telugu:HG04056    B
HG04060    Telugu    Telugu:HG04060    C
HG04061    Telugu    h1    B
HG04080    Telugu    Telugu:HG04080    B
HG04093    Telugu    h1    B
HG04094    Telugu    Telugu:HG04094    A2
HG04096    Telugu    h1    B
HG04098    Telugu    h1    B
HG04198    Telugu    h1    B
HG04206    Telugu    h1    B
HG04211    Telugu    h1    B
HG04219    Telugu    h1    B
HG04222    Telugu    h1    B
HG04225    Telugu    h1    B
HG04235    Telugu    Telugu:HG04235    B
HG04238    Telugu    h2    C
HG04239    Telugu    Telugu:HG04239    B
HG00844    Dai    Dai:HG00844    B
HG00881    Dai    Dai:HG00881    B
HG00982    Dai    h1    B
HG01028    Dai    Dai:HG01028    H
HG01031    Dai    Japanese:NA18961    C
HG01810    Dai    Kinh:HG01872    H
HG01811    Dai    Japanese:NA18961    C
HG01816    Dai    h60    H
HG02250    Dai    h60    H
HG02351    Dai    h1    B
HG02353    Dai    Dai:HG02353    B
HG02355    Dai    Dai:HG02355    B
HG02356    Dai    Kinh:HG02067    A2
HG02360    Dai    h60    H
HG02364    Dai    Dai:HG02364    C
HG02367    Dai    h1    B
HG02371    Dai    Dai:HG02371    B
HG02373    Dai    Kinh:HG01840    B
HG02374    Dai    Kinh:HG02058    B
HG02375    Dai    h60    H
HG02379    Dai    Dai:HG02355    B
HG02380    Dai    Dai:HG02380    A2
HG02382    Dai    h60    H
HG02383    Dai    Dai:HG02383    B
HG02384    Dai    h60    H
HG02385    Dai    h60    H
HG02386    Dai    Dai:HG02386    B
HG02389    Dai    h60    H
HG02390    Dai    Dai:HG02355    B
HG02391    Dai    Dai:HG02391    B
HG02392    Dai    h1    B
HG02394    Dai    h1    B
HG02395    Dai    h1    B
HG02396    Dai    Dai:HG02383    B
HG02397    Dai    Dai:HG02397    B
HG02398    Dai    h1    B
HG02399    Dai    Kinh:HG02067    A2
HG02401    Dai    Dai:HG02401    B
HG02402    Dai    h60    H
HG02406    Dai    Dai:HG02406    B
HG02407    Dai    Kinh:HG01840    B
HG02408    Dai    h50    B
HG02409    Dai    Dai:HG02409    B
HG02410    Dai    Jarawa:JAR-54    A2
HG03054    Mende    h34    A4
HG03057    Mende    Esan:HG03169    A2
HG03060    Mende    Mende:HG03060    A2
HG03063    Mende    Mende:HG03063    A1
HG03066    Mende    h1    B
HG03069    Mende    Luhya:NA19025    A2
HG03072    Mende    Mende:HG03072    A2
HG03074    Mende    h25    A2
HG03077    Mende    Gambian:HG02771    A3
HG03078    Mende    h22    G
HG03081    Mende    Mende:HG03081    A2
HG03084    Mende    h22    G
HG03096    Mende    Gambian:HG02588    A2
HG03209    Mende    h33    C
HG03224    Mende    h1    B
HG03225    Mende    Mende:HG03225    B
HG03376    Mende    Mende:HG03376    A2
HG03382    Mende    Mende:HG03382    A1
HG03385    Mende    h28    A3
HG03388    Mende    Mende:HG03388    A5
HG03391    Mende    Gambian:HG02645    A5
HG03394    Mende    Mende:HG03394    A1
HG03397    Mende    h21    A1
HG03432    Mende    h32    A2
HG03433    Mende    h34    A4
HG03436    Mende    Esan:HG03139    G
HG03439    Mende    Mende:HG03439    G
HG03442    Mende    h21    A1
HG03445    Mende    Mende:HG03445    A4
HG03451    Mende    h22    G
HG03457    Mende    Mende:HG03457    D
HG03460    Mende    Mende:HG03460    A2
HG03469    Mende    h21    A1
HG03472    Mende    Esan:HG03172    A1
HG03478    Mende    Mende:HG03063    A1
HG03547    Mende    h1    B
HG03556    Mende    h34    A4
HG03559    Mende    h30    A4
HG03565    Mende    Mende:HG03565    A3
HG03571    Mende    Esan:HG03193    A1
HG03577    Mende    h31    D
HGDP00540    Papuan    h1    B
HGDP00541    Papuan    h1    B
HGDP00543    Papuan    Papuan:HGDP00543    B
HGDP00545    Papuan    h1    B
HGDP00546    Papuan    h1    B
HGDP00547    Papuan    Papuan:HGDP00547    B
HGDP00548    Papuan    h1    B
HGDP00549    Papuan    h1    B
HGDP00551    Papuan    h1    B
HGDP00553    Papuan    h1    B
HGDP00555    Papuan    h1    B
HGDP00556    Papuan    h1    B
DGMQ-31036    QatarAfrican    Esan:HG03120    G
DGMQ-31244    QatarAfrican    QatarAfrican:DGMQ-31244    A2
DGMQ-31406    QatarAfrican    Esan:HG03124    G
DGMQ-31489    QatarAfrican    h1    B
DGMQ-31583    QatarAfrican    h2    C
DGMQ-32044    QatarAfrican    QatarAfrican:DGMQ-32044    A2
DGMQ-32160    QatarAfrican    QatarAfrican:DGMQ-32160    A2
DGMQ-32220    QatarAfrican    h2    C
DGMQ-32251    QatarAfrican    h1    B
DGMQ-32371    QatarAfrican    h50    B
DGMQ-31005    QatarBedouin    h1    B
DGMQ-31029    QatarBedouin    QatarBedouin:DGMQ-31029    C
DGMQ-31105    QatarBedouin    h1    B
DGMQ-31123    QatarBedouin    h1    B
DGMQ-31237    QatarBedouin    Luhya:NA19312    B
DGMQ-31282    QatarBedouin    QatarBedouin:DGMQ-31029    C
DGMQ-31416    QatarBedouin    h1    B
DGMQ-31433    QatarBedouin    h1    B
DGMQ-31444    QatarBedouin    h1    B
DGMQ-31449    QatarBedouin    h1    B
DGMQ-31516    QatarBedouin    h2    C
DGMQ-31606    QatarBedouin    h1    B
DGMQ-31607    QatarBedouin    h1    B
DGMQ-31623    QatarBedouin    h5    F
DGMQ-31645    QatarBedouin    h1    B
DGMQ-31650    QatarBedouin    Luhya:NA19428    F
DGMQ-31711    QatarBedouin    h1    B
DGMQ-31724    QatarBedouin    h1    B
DGMQ-31725    QatarBedouin    QatarBedouin:DGMQ-31725    E
DGMQ-32064    QatarBedouin    h66    A1
DGMQ-32118    QatarBedouin    QatarBedouin:DGMQ-31029    C
DGMQ-32121    QatarBedouin    h54    E
DGMQ-32148    QatarBedouin    h1    B
DGMQ-32167    QatarBedouin    h43    B
DGMQ-32180    QatarBedouin    h1    B
DGMQ-32215    QatarBedouin    h64    A1
DGMQ-32219    QatarBedouin    QatarBedouin:DGMQ-32219    F
DGMQ-32224    QatarBedouin    Telugu:HG03969    C
DGMQ-32287    QatarBedouin    QatarBedouin:DGMQ-32287    B
DGMQ-32302    QatarBedouin    Mende:HG03565    A3
DGMQ-31108    QatarPersian-SouthAsian    QatarPersian-SouthAsian:DGMQ-31108    C
DGMQ-31226    QatarPersian-SouthAsian    h2    C
DGMQ-31529    QatarPersian-SouthAsian    h1    B
DGMQ-31582    QatarPersian-SouthAsian    QatarPersian-SouthAsian:DGMQ-31582    B
DGMQ-31601    QatarPersian-SouthAsian    h8    A1
DGMQ-31872    QatarPersian-SouthAsian    QatarPersian-SouthAsian:DGMQ-31872    C
DGMQ-32145    QatarPersian-SouthAsian    QatarPersian-SouthAsian:DGMQ-32145    A1
DGMQ-32368    QatarPersian-SouthAsian    h1    B
DGMQ-32977    QatarPersian-SouthAsian    h1    B
DQMQ-31514    QatarPersian-SouthAsian    TamilSriLanka:HG04033    B
HG00181    Finnish    h1    B
HG00182    Finnish    h1    B
HG00183    Finnish    h2    C
HG00185    Finnish    h1    B
HG00186    Finnish    h2    C
HG00187    Finnish    h2    C
HG00188    Finnish    h6    A1
HG00189    Finnish    h1    B
HG00190    Finnish    h1    B
HG00267    Finnish    h2    C
HG00271    Finnish    Finnish:HG00271    B
HG00273    Finnish    h48    B
HG00277    Finnish    Finnish:HG00277    F
HG00278    Finnish    h11    C
HG00280    Finnish    Finnish:HG00280    C
HG00284    Finnish    h10    B
HG00290    Finnish    h3    B
HG00308    Finnish    h1    B
HG00310    Finnish    h43    B
HG00311    Finnish    Finnish:HG00311    E
HG00321    Finnish    h1    B
HG00325    Finnish    h8    A1
HG00329    Finnish    h4    B
HG00335    Finnish    h57    C
HG00336    Finnish    h1    B
HG00338    Finnish    h1    B
HG00341    Finnish    Finnish:HG00341    B
HG00342    Finnish    Finnish:HG00342    H
HG00345    Finnish    Finnish:HG00345    B
HG00351    Finnish    Finnish:HG00351    B
HG00358    Finnish    h1    B
HG00360    Finnish    h3    B
HG00366    Finnish    h8    A1
HG00369    Finnish    Finnish:HG00369    B
HG00371    Finnish    h1    B
HG00372    Finnish    h60    H
HG00375    Finnish    h1    B
HG00376    Finnish    h8    A1
Reply
#3
PHAX5574 table of Haplotypes 31.10.2024:
.xlsx   PHAX5574 haplotypes.xlsx (Size: 792.31 KB / Downloads: 12)
Reply
#4
If you have any suggestions for new haplogroup labels, want to do your own research or figure out your own haplotype I can help with that.
Reply
#5
The most interesting features of PHAX5574 are in my opinion the following:
  • B seems to have existed ever since the Upper Paleolithic, since Ust Ishim has it as well.
  • A2b seems to be the first and only case of a haplotype intrusion from Neanderthals to Humans ever observed directly. Several South and East Asian samples have haplotypes that are nested within Neanderthal haplotypes of PHAX5574.
  • The mutation rate is very low as evidenced by the fact that most subclades of B only differ from B by one mutation from it.
  • Thus D seems to have split very long ago, on the order of millions of years ago. The region of genome has either maintained diversity for much longer than the y-DNA or mtDNA or there has been a population that preserved D before an intrusion into humans.
  • B dominates Eurasians.
  • C is broadly West Eurasian.
  • H is broadly East Eurasian.
  • A1 has haplotypes mostly in Eurasia but haplotypes unique to Africa also exist, hard to tell if it's back migration or A1 emerged before Eurasians became their own population.
  • Sub-Saharan Africans have a lot more diversity of haplogroups than Eurasians do as expected.
  • Very little recurrent mutation in comparison to mtDNA, but this may be due to lower mutation rate overall reducing the amount of recurrence observed so far.
  • A2a dominates Sub-Saharan Africa, especially G.
  • Denisovans somehow are closer to Sub-Saharan African A2 subclades than Neanderthals are, having their haplotype within A2a2b, indicating that the haplotype formed before Denisovans and Humans split from one another or there was geneflow between the two.
Reply
#6
This paper should be of interest to you if you haven't already seen it-


Extraordinary selection on the human X chromosome associated with archaic admixture
https://www.cell.com/cell-genomics/fullt...23)00034-4

Are there any known protein-coding genes in this region? What's interesting about this paper is not only is Neanderthal ancestry depleted in long regions of the X chromosome of Eurasians but also older "African" ancestry is too - the Eurasian X has disproportionately lower variation relative to the autosomes then what is expected even given the inheritance pattern of the X (African X variation is about 75% of the autosomal, Eurasians are lower in the 40-60% range). John Hawks had a really interesting write up about this on his blog when the paper came out.

Quote:Michael Hammer and coworkers showed in 2010 that the ratio of X chromosome variation to autosomal variation covaries directly with distance to coding regions. Parts of the X chromosome near genes have lower diversity, parts far from genes have diversity more similar to the autosomes. Such a correlation of diversity and functional genome content means that natural selection must be part of the explanation. In other words, not only Neandertal and Denisovan ancestry but also ancestral African variation was diminished in X chromosomes of peoples outside Africa today. That means that Neandertal and Denisovan mixture were not the causes of this selection, but they may have been casualties of it

Explaining the X chromosome hole in Neandertal ancestry
Reply
#7
ENSG00000307552 seems to overlap with this region a lot. It is a Long non-coding RNA, so it doesn't code for a protein.
https://www.ensembl.org/Homo_sapiens/Gen...0000827048
Reply
#8
Fixed a problem with A1 and A2 grouping into a clade separate from the rest of A.
   

Show Content
Reply
#9
(10-31-2024, 12:59 AM)Norfern-Ostrobothnian Wrote: This thread is dedicated for discussing PHAX5574. This region of the X-chromosome rarely recombines and can be used for population genetic analyses like mtDNA or y-DNA. I have done some additional analysis of samples that this study has done and given some labels for the various clades in PHAX5574 I have discovered.
https://www.nature.com/articles/ejhg2016207
Quote:Signatures of human European Palaeolithic expansion shown by resequencing of non-recombining X-chromosome segments
Maisano Delser et al 2017
... to identify genome-wide 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 on the X chromosome spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181×. These 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.
Interesting. Newer saw this and wonder why none since 2017 has investigated further regarding phylogeny.
May I ask
Does PHAX5574 describe the three segments on the X spanning a total of ~49 kb?
Since mtDNA has 16,569 base pairs does that mean PHAX5574 allows a ca. 3x times more accurate phylogeny?
Reply
#10
(10-31-2024, 05:04 PM)ChrisR Wrote:
(10-31-2024, 12:59 AM)Norfern-Ostrobothnian Wrote: This thread is dedicated for discussing PHAX5574. This region of the X-chromosome rarely recombines and can be used for population genetic analyses like mtDNA or y-DNA. I have done some additional analysis of samples that this study has done and given some labels for the various clades in PHAX5574 I have discovered.
https://www.nature.com/articles/ejhg2016207
Quote:Signatures of human European Palaeolithic expansion shown by resequencing of non-recombining X-chromosome segments
Maisano Delser et al 2017
... to identify genome-wide 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 on the X chromosome spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181×. These 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.
Interesting. Newer saw this and wonder why none since 2017 has investigated further regarding phylogeny.
May I ask
Does PHAX5574 describe the three segments on the X spanning a total of ~49 kb?
Since mtDNA has 16,569 base pairs does that mean PHAX5574 allows a ca. 3x times more accurate phylogeny?

PHAX5574 is the longest PHAX and one of three that were analyzed further in the study it was discovered in. It's length is 38100 base pairs.
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#11
Very cool, are there any snps covered in typical commercial tests that would allow us to gain some insight into our own PHAX5774 'haplogroups'?
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#12
C
rs12557363
B
rs3131400
H
rs148852196
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#13
I'm thinking about this:
- extracting the PHAX5774 sequence from WGS data (maybe to include in tools like WGS Extract)
- creation of a PHAX5774 sequence repository with automatic phylogeny determination and phylotree addition
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Main Projects
: Tyrol DNA, Alpine DNA, J2-M172, J2a-M67, J2a-PF5197, ISOGG Wiki, GenWiki;
Focus on Y-DNA: J2a-M67-L210, J2a-PF5197-PF5169, R1a-M17, R1b-U106-Z372
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#14
Very interesting, thanks! I tried it on my family's WGS data. Unfortunately, there seems to be much less diversity and subbranches in haplogroups than on the Y chromosome and mitochondria (because of the very low mutation rate).

[Image: yZyUcJE.png]

[Image: 41431_2017_Article_BFejhg2016207_Fig3_HTML.jpg]
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#15
^^^
just to clarify: I can not code, so this is more a wish ;-)

Also I realized (please notify if I'm wrong):
- Men have one PHAX5774 (inherited from the mother)
- Women have two PHAX5774 (inherited from the mother and the father)
- X-Hg's can't be associated to a certain ancestral line so the value knowing the Hg is of limited value for the single individual, more interesting is to maybe to compare the mtDNA prevalence with PHAX5774 prevalence in a certain population, both modern and ancient.
---
Main Projects
: Tyrol DNA, Alpine DNA, J2-M172, J2a-M67, J2a-PF5197, ISOGG Wiki, GenWiki;
Focus on Y-DNA: J2a-M67-L210, J2a-PF5197-PF5169, R1a-M17, R1b-U106-Z372
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