make money online Mapping the Genome: The isolation of the Afghan mitochondrial gene pool

Thursday, September 2, 2010

The isolation of the Afghan mitochondrial gene pool

From the article The mtDNA composition of Uzbekistan: a microcosm
of Central Asian patterns “Of the seven population samples, Afghanistan and
Kazakhstan appear to be the least and most genetically
diverse, respectively. Kazakhstan had a large number of
unique haplotypes and thus a low random-match probability
(0.13%). Afghanistan, on the other hand, had the fewest total
number of haplotypes relative to population size and the
highest random-match probability, at 5.5%. mtDNA haplotype
diversities for all populations ranged from 0.946 to
0.999.” Quite interesting aspects of this sample of Afghan Uzbeks include its relatively high frequencies of western Eurasian mtDNA  (about 81%) as well as its relatively high regional frequencies of haplogroups K and H (both around 25%) .
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Afghan mitochondrial haplotypes
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H6    AFG002    Afghanistan    16111T 16362C 16482G    239C 263G 309.1C 315.1C
M    AFG003    Afghanistan    16184T 16186T 16223T 16234T 16519C    73G 195G 263G 315.1C 489C 523- 524-
M    AFG004    Afghanistan    16184T 16186T 16223T 16234T 16519C    73G 152Y 195G 263G 315.1C 489C 523- 524-
U2e1    AFG005    Afghanistan    16051G 16129C 16189C 16362C 16391A 16519C    73G 152C 217C 263G 309.1C 315.1C 340T 508G
H1f    AFG006    Afghanistan    16041G 16189C 16286T    263G 309.1C 315.1C
M3    AFG007    Afghanistan    16126C 16223T 16519C    73G 143A 146C 189G 204C 215G 263G 309.1C 315.1C 482C 489C
H    AFG008    Afghanistan    16320T    263G 309.1C 315.1C
G3a1    AFG009    Afghanistan    16215G 16223T 16225T 16274A    16T 73G 143A 150T 263G 309.1C 315.1C 489C 523- 524-
T2    AFG010    Afghanistan    16126C 16179T 16274A 16294T 16296T 16519C    73G 152C 263G 309.1C 309.2C 315.1C
Z    AFG011    Afghanistan    16223T 16260T 16298C    73G 143A 152C 204C 249- 263G 309.1C 315.1C 489C 523- 524-
U4    AFG012    Afghanistan    16325C 16356C    73G 195C 263G 315.1C 499A
G1a2'3    AFG013    Afghanistan    16184T 16223T 16362C 16519C    73G 263G 309.1C 315.1C 489C
T2    AFG014    Afghanistan    16126C 16179T 16274A 16294T 16296T 16519C    73G 152C 263G 309.1C 309.2C 315.1C
K1a1a    AFG015    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
D4k    AFG016    Afghanistan    16192T 16223T    73G 195C 263G 309.1C 315.1C 489C
C4a1    AFG017    Afghanistan    16093C 16129A 16223T 16298C 16327T 16519C    73G 195C 249- 263G 309.1C 315.1C 489C
T2    AFG018    Afghanistan    16126C 16179T 16274A 16294T 16296T 16519C    73G 152C 263G 309.1C 309.2C 315.1C
K1a    AFG019    Afghanistan    16224C 16311C 16519C    73G 152C 263G 309.1C 315.1C 497T
N1b    AFG020    Afghanistan    16145A 16176G 16223T 16390A 16519C    73G 152C 263G 315.1C 523- 524-
U7    AFG021    Afghanistan    16069T 16260T 16274A 16318T 16519C    73G 151T 152C 263G 315.1C 523- 524-
U7    AFG022    Afghanistan    16069T 16260T 16274A 16318T 16519C    73G 151T 152C 263G 315.1C 523- 524-
H    AFG023    Afghanistan    16189C 16193.1C 16193.2C 16519C    263G 309.1C 309.2C 315.1C
K1a    AFG024    Afghanistan    16224C 16311C 16519C    73G 152C 263G 309.1C 315.1C 497T
K1a    AFG025    Afghanistan    16224C 16311C 16519C    73G 152C 263G 309.1C 315.1C 497T
K1a1a    AFG026    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
K1a    AFG027    Afghanistan    16224C 16311C 16519C    73G 152C 263G 309.1C 315.1C 497T
K1a1a    AFG028    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
U7    AFG029    Afghanistan    16129A 16146G 16318T 16519C    73G 151T 152C 263G 309.1C 315.1C 523- 524-
K1a1a    AFG030    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
K1a    AFG031    Afghanistan    16093Y 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
Z    AFG032    Afghanistan    16223T 16260T 16298C    73G 143A 152C 204C 249- 263G 309.1C 315.1C 489C 523- 524-
U3a    AFG033    Afghanistan    16343G 16390A 16519C    73G 146C 150T 263G 315.1C
U1a'c    AFG034    Afghanistan    16182C 16183C 16189C 16249C 16319A 16519C 16527T    73G 195C 263G 285T 309.1C 309.2C 315.1C
U7    AFG035    Afghanistan    16309G 16318C 16519C    73G 151T 152C 263G 309.1C 315.1C 523- 524-
K1a1a    AFG036    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
K1a    AFG037    Afghanistan    16093Y 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
K1a1a    AFG039    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
K1a    AFG040    Afghanistan    16224C 16311C 16519C    73G 152C 263G 309.1C 315.1C 497T
K1a1a    AFG041    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
H11a1    AFG042    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
K1a1a    AFG043    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
M3    AFG044    Afghanistan    16126C 16223T 16519C    73G 146C 263G 315.1C 482C 489C
H6    AFG045    Afghanistan    16111T 16362C 16482G    239C 263G 309.1C 315.1C
H11a1    AFG046    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
K1a    AFG047    Afghanistan    16093Y 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
N9b    AFG048    Afghanistan    16086C 16172C 16187T 16189C 16217C 16223T    73G 146C 210G 263G 309.1C 315.1C 338T 571T
K1a1a    AFG049    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
H11a1    AFG050    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
K1a    AFG051    Afghanistan    16224C 16311C 16519C    73G 152C 263G 309.1C 315.1C 497T
K1a    AFG052    Afghanistan    16093Y 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
U2e1    AFG053    Afghanistan    16051G 16129C 16189C 16362C 16391A 16519C    73G 150Y 152C 217C 263G 309.1C 315.1C 340T 508G
U2e1    AFG054    Afghanistan    16051G 16129C 16189C 16362C 16391A 16519C    73G 150Y 152C 217C 263G 309.1C 315.1C 340T 508G 524.1A 524.2C
K1a1a    AFG055    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
M    AFG056    Afghanistan    16223T 16311C 16335G 16519C    73G 143A 152C 189G 199C 204C 263G 315.1C 489C
A    AFG057    Afghanistan    16111T 16223T 16290T 16293C 16319A 16519C    73G 151T 152C 235G 263G 309.1C 309.2C 315.1C 523- 524-
K1a    AFG058    Afghanistan    16093Y 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
H11a1    AFG059    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
H11a1    AFG060    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
H11a1    AFG061    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
U1a'c    AFG062    Afghanistan    16182C 16183C 16189C 16249C 16319A 16519C 16527T    73G 152Y 195C 263G 285T 309.1C 309.2C 315.1C
H    AFG063    Afghanistan    16519C    263G 309.1C 309.2C 315.1C
K1a1a    AFG064    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
H11a1    AFG065    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
J1    AFG066    Afghanistan    16069T 16126C 16193T 16519C    73G 152C 263G 295T 315.1C 462T 489C
H11a1    AFG067    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
H    AFG069    Afghanistan    16519C    263G 315.1C
H    AFG070    Afghanistan    16519C    263G 315.1C
U7    AFG071    Afghanistan    16069T 16189C 16227G 16318T 16359C 16519C    73G 151T 152C 263G 315.1C 368.1A 368.2G 368.3A 368.4A 523- 524-
U7    AFG072    Afghanistan    16069T 16189C 16227G 16318T 16359C 16519C    73G 151T 152C 263G 315.1C 368.1A 368.2G 368.3A 368.4A 523- 524-
T2    AFG073    Afghanistan    16126C 16179T 16274A 16294T 16296T 16519C    73G 152C 263G 309.1C 309.2C 315.1C
U4    AFG074    Afghanistan    16325C 16356C    73G 195C 263G 315.1C 499A
M30    AFG075    Afghanistan    16223T 16234T 16519C    73G 109A 195A 263G 309.1C 315.1C 489C 523- 524-
U4    AFG076    Afghanistan    16325C 16356C    73G 195C 263G 315.1C 499A
C4a1    AFG077    Afghanistan    16129A 16223T 16298C 16327T 16519C    73G 195C 249- 255A 263G 315.1C 489C
M3    AFG078    Afghanistan    16126C 16185T 16209C 16223T 16519C    73G 195C 198T 263G 315.1C 482C 489C
U4    AFG079    Afghanistan    16325C 16356C    73G 195C 263G 315.1C 499A
U4    AFG080    Afghanistan    16325C 16356C    73G 195C 263G 315.1C 499A
T    AFG081    Afghanistan    16126C 16294T 16519C    73G 152C 194T 263G 309.1C 315.1C
U1a'c    AFG082    Afghanistan    16183C 16189C 16193.1C 16242T 16249C 16256T 16294T 16519C    73G 263G 285T 309.1C 309.2C 315.1C 523- 524-
H5    AFG083    Afghanistan    16294T 16301T 16304C 16311C    263G 309.1C 315.1C 456T 523- 524-
D4    AFG084    Afghanistan    16223T 16362C    73G 152C 195C 263G 309.1C 309.2C 315.1C 489C
HV1    AFG085    Afghanistan    16067T 16242A 16311C    263G 309.1C 309.2C 315.1C 523- 524-
H    AFG086    Afghanistan    16519C    263G 315.1C
K1a1a    AFG087    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
U2e1    AFG088    Afghanistan    16051G 16093C 16129C 16182C 16183C 16189C 16290Y 16362C 16519C    73G 152C 217C 263G 309.1C 309.2C 315.1C 340T 508G 524.1A 524.2C
H11a1    AFG089    Afghanistan    16278T 16311C    152C 263G 309.1C 315.1C
B4    AFG090    Afghanistan    16092C 16182C 16183C 16189C 16217C 16519C 16527T    73G 263G 315.1C
U3a    AFG091    Afghanistan    16343G 16390A 16519C    73G 146C 150T 263G 315.1C
U3a    AFG092    Afghanistan    16343G 16390A 16519C    73G 146C 150T 263G 315.1C
U1a'c    AFG093    Afghanistan    16182C 16183C 16189C 16249C 16319A 16519C 16527T    73G 152Y 195C 263G 285T 309.1C 309.2C 315.1C
K1a1a    AFG094    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
K1a1a    AFG095    Afghanistan    16093C 16129A 16224C 16311C 16519C    16T 73G 150T 199C 263G 315.1C 497T
U3a    AFG096    Afghanistan    16343G 16390A 16519C    73G 146C 150T 263G 315.1C
A    AFG097    Afghanistan    16111T 16223T 16290T 16293C 16319A 16519C    73G 151T 152C 235G 263G 309.1C 309.2C 315.1C 523- 524-
A    AFG098    Afghanistan    16111T 16223T 16290T 16293C 16319A 16519C    73G 151T 152C 235G 263G 309.1C 309.2C 315.1C 523- 524-
H    AFG099    Afghanistan    16311C    93G 152C 263G 309.1C 315.1C
M30b    AFG100    Afghanistan    16169Y 16189C 16191.1C 16192T 16223T 16278T    73G 152C 195A 263G 315.1C 489C 523- 524-
Posted by clusteredmaps at 6:49 PM
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2 comments:

princenuadha said...

How about some cluster maps of Europe and Asia? Also I'd like to see genetic distances of populations from aborigines.

September 3, 2010 at 9:26 AM
Maju said...

Very interesting, thanks. I counted the haplogroups and I see the following:

There was a massive founder effect, possibly in Neolithic, involving K1a (and specifically K1a1a and maybe another clade hidden under the K1a* label). K1a alone accounts for 32% of all Afghan (Uzbekistan Afghan - whatever this means) mtDNA lineages and 44% of those that can be clearly described as West Eurasian. The smaller presence of haplogroup T (T2 in particular) may be associated to this impressive Neolithic(?) founder effect.

I think all the rest of West Eurasian mtDNA (72% of Afghan in my hand account) is Central Asian or at most from West Asia or Eastern Europe (and this only in less important cases). Of the WEA mtDNA, besides K1a, it is noticeable H11a1, a small Central Asian haplogroup if my memory doesn't fail and H*, maybe again a hidden local haplogroup.

It may be also noticeable the relatively high apportion of rare haplogroup U1 (U1a'c specifically), which is found between SE Europe and India. Also U4 which instead is generally related to NE Europe and the Eurasian steppes.

Is this a new blog? If so I'm really glad I stumble upon it. Keep it up!

September 15, 2010 at 4:49 AM

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