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alvaroabascal
02-16-2018, 09:42 PM
I belong to haplogroup DF17 (waiting for the Big-Y results to go deeper in the tree).
I'm interested in many questions, the first one of which is the following:
Where can I find what defines haplogroups? For example: what defines exactly haplogroup DF27? Is it a SNP? Is it a Y-STR? Is it a combination on both?
Where can I find that/those locus/loci in the chromosome? Is there any way of seeing a real full y-genome and identifying it (with blast or any other tool)?
Thanks in advance.

breckenheimer
02-17-2018, 12:30 PM
I belong to haplogroup DF17 (waiting for the Big-Y results to go deeper in the tree).
I'm interested in many questions, the first one of which is the following:
Where can I find what defines haplogroups? For example: what defines exactly haplogroup DF27? Is it a SNP? Is it a Y-STR? Is it a combination on both?
Where can I find that/those locus/loci in the chromosome? Is there any way of seeing a real full y-genome and identifying it (with blast or any other tool)?
Thanks in advance.

Welcome! You're asking for a resources for information, so you might start here: https://isogg.org/wiki/Beginners'_guides_to_genetic_genealogy

ArmandoR1b
02-17-2018, 01:24 PM
I belong to haplogroup DF17 (waiting for the Big-Y results to go deeper in the tree).
I'm interested in many questions, the first one of which is the following:
Where can I find what defines haplogroups? For example: what defines exactly haplogroup DF27? Is it a SNP? Is it a Y-STR? Is it a combination on both?
Where can I find that/those locus/loci in the chromosome? Is there any way of seeing a real full y-genome and identifying it (with blast or any other tool)?
Thanks in advance.

Haplogroups are defined by SNPs which are defined by a mutation in a specific position in the Y-chromosome. You can find the position and mutation at http://www.ytree.net/SNPIndex.php and at http://ybrowse.org/gb2/gbrowse/chrY/?

For instance DF27 is the mutation of G to A at hg38 position 19,218,314 noted as 19218314-G-A at http://www.ytree.net/BlockInfo.php?blockID=29

The first 12 STRs correlate with major haplogroups most of the time but sometimes even for that SNP testing is needed.

alvaroabascal
02-18-2018, 07:25 AM
Thank you for your answer.
I'm CTS7768+, so in The Big Tree that corresponds with BY907=DF17 haplogroup. I'm also S1306+, S1319+ and S11695+ but have not tested for the other markers associated with the haplogroup. I guess that the fact that there are so many SNPs associated with BY907=DF17 means that there is not a very clear idea of the structure of the group yet. A haplogroup should be defined by an unique SNP, not by many, right?

ArmandoR1b
02-18-2018, 01:56 PM
Thank you for your answer.
I'm CTS7768+, so in The Big Tree that corresponds with BY907=DF17 haplogroup. I'm also S1306+, S1319+ and S11695+ but have not tested for the other markers associated with the haplogroup. I guess that the fact that there are so many SNPs associated with BY907=DF17 means that there is not a very clear idea of the structure of the group yet.
Correct. It will take someone with a BigY, or similar test, that tests negative for some of the SNPs that are currently in the block that contains BY907 and DF17 in order for some to be shown as a downstream branch.


A haplogroup should be defined by an unique SNP, not by many, right?
Some haplogroups might always have multiple SNPs defining the group. That will happen if no one ever tests negative for any of the phylogenetic equivalents. For example, M269 might always have 96 equivalents if no one ever tests negative for any of them. That happens when there is only lineage that survived over hundreds of years. I doubt that BY907 will always have all of the phylogenetic equivalents it has now.

alvaroabascal
02-18-2018, 04:30 PM
Correct. It will take someone with a BigY, or similar test, that tests negative for some of the SNPs that are currently in the block that contains BY907 and DF17 in order for some to be shown as a downstream branch.
My BigY will be up in April. Let's see if it sheds some light on DF17 ...


haplogroups might always have multiple SNPs defining the group. That will happen if no one ever tests negative for any of the phylogenetic equivalents. For example, M269 might always have 96 equivalents if no one ever tests negative for any of them. That happens when there is only lineage that survived over hundreds of years. I doubt that BY907 will always have all of the phylogenetic equivalents it has now.
So I guess at least 95 haplogroups were lost in the way ...

ArmandoR1b
02-18-2018, 05:16 PM
So I guess at least 95 haplogroups were lost in the way ...
96. There are 96 SNPs apart from M269, so 97 in total, that define the haplogroup but each of those SNPs would have also created a lot of other branches downstream so there would have been a much larger number of haplogroups if all of the lineages had survived until now.

alvaroabascal
02-18-2018, 08:17 PM
Thanks for the info and the insights Armando.