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reference: alternative nomenclatures and names
Topic Started: Jun 23 2005, 05:03:51 PM (441 Views)
ren
Advanced Member
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http://www.genome.org/cgi/content/full/12/2/339
http://hpgl.stanford.edu/publications/GR_2...12_p339-348.pdf

Buttler et al. 2003: Recent Developments in Y-Short Tandem Repeat and Y-Single Nucleotide Polymorphism Analysis
http://www.cstl.nist.gov/biotech/strbase/p...Butler2003b.pdf

http://ycc.biosci.arizona.edu/nomenclature_system/data.html

http://www.familytreedna.com/haplotree.html
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black man
The Right Hand
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ren
Jun 23 2005, 05:03 PM
system: alpha
Jobling and Tyler-Smith (2000), Kaladjieva et al. (2001), Weale et al. (2001)

hg1=

P*(92R7, P27, M45, M74)

P1 (M124)

Q* (P36, MEH2)
Q1 (M120)
Q2 (M25, M143)

R* (M207)
R1* (M173)
R1b* (P25)
R1b1 (M18)
R1b2 (M37)
R1b3 (M65)
R1b4 (M73)
R1b5 (M126)
R1b6 (M153)
R1b7 (M160)

In other words: the designation "hg1" is outdated, isn't it? Or am I becoming political again?

I only once witnessed a case in which someone stated "hg1" would be "Europoid". The other system seems to be more exact. But what is the background of the "alternative" nomenclatures? Results from new studies, awakened sense for "political correctness"...?
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ren
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It was just a case where different researchers used different naming systems for the same thing at the beginning stages of Y chromosome lineage studies.

I think there are several systems which use a name "Hg 1". Yeah, it's basically outdated. The main system used now are the big Roman alphabet letters on the left side: http://www.genome.org/content/vol12/issue2...-14f1_C4TT.jpeg
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black man
The Right Hand
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Regarding the YAP lineages, I found some haplogroups aren't clearly enough explained in the trees I previously used (e.g. http://www.genome.org/content/vol12/issue2...-14f1_C4TT.jpeg ):

they write "YAP - (below) M145 - (below) M203":

DE-M203, E2-M145 and YAP-M1.

Sources:
http://www.journals.uchicago.edu/AJHG/jour...02582.text.html
Quote:
 
DHPLC was used to type all biallelic markers, with the exception of YAP (also known as "M1"). Marker information such as primer sequences and PCR conditions for their amplification, whether alleles are ancestral or derived, as well as additional details for their typing conditions by DHPLC, have been provided by Underhill et al. (1997, 2000). YAP was assayed as described by Hammer and Horai (1995).


http://www.cstl.nist.gov/biotech/strbase/p...Butler2003b.pdf
Quote:
 
(...)markers discovered by other groups, such as Tat (M46), were given Stanford marker numbers and then later removed from the list. Some of these duplicates include YAP (M1), sY81 and SRY 2627 (M167).


--------

There is a new nomenclature of Hammer, Karafet et al.
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ren
Advanced Member
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ren
Jun 23 2005, 05:03:58 PM
system: alpha
Jobling and Tyler-Smith (2000), Kaladjieva et al. (2001), Weale et al. (2001)

hg1=

P*(92R7, P27, M45, M74)

P1 (M124)

Q* (P36, MEH2)
Q1 (M120)
Q2 (M25, M143)

R* (M207)
R1* (M173)
R1b* (P25)
R1b1 (M18)
R1b2 (M37)
R1b3 (M65)
R1b4 (M73)
R1b5 (M126)
R1b6 (M153)
R1b7 (M160)
P27 also is known as DYS257, which also defines O3a1.

In Hurles et al. 2002, they equated DYS257 with P/Hg1, which might've excluded O3a1 cases.

Y Chromosomal Evidence for the Origins of Oceanic-Speaking Peoples




Su et al. 1999/System Zeta
Hg 6, 7 (M7), 8 (M134) is O3.

update 2010-1-26
Hg 1 - A, B, C
Hg 4 - F, G, H, I, J
Hg 5 - K, L
Hg 14 - R(xP25, M17)




2010-10-30
Towards a complete sequence of the human Y chromosome
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138936/

Shows the different intron regions on which many SNPs are located. Helpful in referencing SNPs when they weren't defined by names in older studies.
Edited by ren, Oct 31 2010, 03:04:22 PM.
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black man
The Right Hand
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Hammer et al. 2001: Hierarchical Patterns of Global Human Y-Chromosome Diversity
p. 1192
Quote:
 
10 previously unpublished Y-specific polymorphisms were discovered: a C®T transition at position 20642 of 16E4; a G®A transition at position 905 of DYS190; a T®G transversion at position 922 of DYS190; a T®C transition at position 450 of DYS194; a T®C transition at position 1391 of DYS194; a C®A transversion at position 118453 of 486,O,2; a T®C transition and a T deletion at positions 71227 and 71228, respectively, of ARSEP; a C®T transition at position 108 of DYS7; a G®C transversion at position 83 of DYS265; and a G®A transition at position 162 of DYS257. Comparisons with the homologous sequences from one common chimpanzee, one bonobo, and one gorilla allowed us to infer the ancestral states at all of these sites except 16E420642 and 486,O,2118453, which only occurred in human-specific Alu elements.


according to the explanations on p. 1192 and in table 1 on p. 1190, "h" refers to figure 1 (not to any nomenclature outside of the immediate context of the paper):
"C®T transition at position 20642 of 16E4": "h4" (SSA)
"G®A transition at position 905 of DYS190": "h10" (Eurasian)
"T®G transversion at position 922 of DYS190": "h20" (SSA)
"T®C transition at position 450 of DYS194": "h8" (SSA)
"T®C transition at position 1391 of DYS194": "h17" (Oceanian)
"C®A transversion at position 118453 of 486,O,2": "ancestral haplotype 13", not in figure 1 (carrier/s?)
"T®C transition and a T deletion at positions 71227 and 71228, respectively, of ARSEP": "h29" (East Eurasian) = O2-P31
"C®T transition at position 108 of DYS7": "h3" (SSA)
"G®C transversion at position 83 of DYS265": "h7" (SSA)
"G®A transition at position 162 of DYS257": "h34" (Oceanian)




update

Hammer et al. 2003: Human Population Structure and Its Effects on Sampling Y Chromosome Sequence Variation
ARSDP 72636 - > T: YCC 25 Arizona Tohono => downstream to P36, not correlating with M3
ARSDP 72425a G > A: YCC 25 Arizona Tohono among others => probably within hg Q (P36?) since not shared by group R samples
ARSDP 71135 G > A: YCC 23 Arizona Navajo, one Taiwanese and one Buryat => probably within hg C
ARSDP 71227 T > C: YCC 69 Cambodia Khmer and one Japanese => probably within hg O since not shared by group N
ARSDP 67668a T > C: YCC 76 Japanese
ARSDP 67655 T > C: YCC 76 Japanese
ARSDP 60565 G > A: YCC 23 Arizona Navajo
ARSDP 57713 G > A: YCC 76 Japanese
3-1 1009 - > C: FN11 Forest Nenet => ?
3-8 474 A > G: YCC 76 Japanese
3-8 625 T > C: YCC 51 Yakut
3-8 1432 C > A: YCC 49 and YCC 50 both Yakuts
4-1 792 T > C: YCC 23, YCC 76, one Taiwanese, one Buryat, one Papuan, one Australian and most Africans => could be a recurrent mutation since it contradicts the currently acknowledged tree
486 290 T > C: YCC samples in Q and R groups => probably within hg P
16E4 268 G > A: FN 11 Forest Nenet and Khan 42 Khanty => ?

The Y chromosome consortium 2002: A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
YCC 23 Arizona Navajo C3b
YCC 25 Arizona Tohono O'odham Pima Q-P36*
YCC 49 and YCC 50 both Yakuts N-M178+, P21+
YCC 51 Yakut N-M178+, P21-
YCC 69 Cambodia Khmer O2a
YCC 76 Japanese D2a (2002 nomenclature)
Edited by black man, Nov 2 2010, 06:39:29 PM.
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