Comments on: Her identity by descent made flesh http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/ Fri, 24 May 2013 15:27:00 +0000 hourly 1 http://wordpress.org/?v=3.4.2 By: Douglas Knight http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42343 Douglas Knight Thu, 03 May 2012 03:01:57 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42343 What is the normal rate of crossover? It looks to me like you have a rate of about once per chromosome. Is that correct? Or is it an artifact of the limited data? But the mother appears to have twice that rate. Is that the normal variation between instances of meiosis? between people? What is the normal rate of crossover? It looks to me like you have a rate of about once per chromosome. Is that correct? Or is it an artifact of the limited data? But the mother appears to have twice that rate. Is that the normal variation between instances of meiosis? between people?

]]> By: Dm http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42342 Dm Mon, 30 Apr 2012 13:46:38 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42342 23's algorithm takes Xs and even makes specific corrections for sexes of the compared humans (like her matching blocks length threshold would have to be longer for matches with other females). But accounting for possible number of recombinations in regular English terms of relationship is next to impossible. The algorithm would have to infer how many female and male links are in the graph. I think that the Xs are really cool for historic genealogy, because the question of the direction of inheritance doesn't exist for the male ancestors, and so even relatively less informative ethnic marks on the X should be easier to put in the proper historic and genealogical context. Alas, 23andMe doesn't use HGDP data in its Ancestry Labs, and popular chromosome-painting utilities such as DYIDodecad don't even look at the X at all. BTW with so many nodes on your pedigree, you should be able to phase genotypes and to map recombinations quite well? 23′s algorithm takes Xs and even makes specific corrections for sexes of the compared humans (like her matching blocks length threshold would have to be longer for matches with other females). But accounting for possible number of recombinations in regular English terms of relationship is next to impossible. The algorithm would have to infer how many female and male links are in the graph.

I think that the Xs are really cool for historic genealogy, because the question of the direction of inheritance doesn’t exist for the male ancestors, and so even relatively less informative ethnic marks on the X should be easier to put in the proper historic and genealogical context. Alas, 23andMe doesn’t use HGDP data in its Ancestry Labs, and popular chromosome-painting utilities such as DYIDodecad don’t even look at the X at all.

BTW with so many nodes on your pedigree, you should be able to phase genotypes and to map recombinations quite well?

]]> By: Eurologist http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42341 Eurologist Mon, 30 Apr 2012 12:52:08 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42341 <i>females have two copies. one from mom, one from dad. so these can recombine. the male’s can not.</i> Yes, of course. I guess some of my brain cells temporarily switched to extreme male Chauvinism. females have two copies. one from mom, one from dad. so these can recombine. the male’s can not.

Yes, of course. I guess some of my brain cells temporarily switched to extreme male Chauvinism.

]]> By: Razib Khan http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42340 Razib Khan Mon, 30 Apr 2012 07:36:23 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42340 <i>It’s probably just generic software for both genders.</i> yeah. i assume the labor hours weren't worth it. most people are OK with just autosome. <i>Also, where could these have recombined</i> females have two copies. one from mom, one from dad. so these can recombine. the male's can not. i think the algorithm wasn't performed on the x though. It’s probably just generic software for both genders.

yeah. i assume the labor hours weren’t worth it. most people are OK with just autosome.

Also, where could these have recombined

females have two copies. one from mom, one from dad. so these can recombine. the male’s can not.

i think the algorithm wasn’t performed on the x though.

]]> By: Eurologist http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42339 Eurologist Mon, 30 Apr 2012 07:10:28 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42339 <i>And no, I don’t know why it has an XY in the plots.</i> It's probably just generic software for both genders. It does say "Not enough information" ;) As to the X chromosome, I wonder if the process/ software can even distinguish between two of them, or just simply assigns two 100% matches to the two plots of single Xs, each. Also, where could these have recombined? Aren't they expected to stay intact? And no, I don’t know why it has an XY in the plots.

It’s probably just generic software for both genders. It does say “Not enough information” ;)

As to the X chromosome, I wonder if the process/ software can even distinguish between two of them, or just simply assigns two 100% matches to the two plots of single Xs, each.

Also, where could these have recombined? Aren’t they expected to stay intact?

]]> By: Razib Khan http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42338 Razib Khan Mon, 30 Apr 2012 03:42:22 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42338 #4, you are correct. she is very close to her aunts/uncles to expected value. but varies more with her grandparents (0.22 to 0.28). also, you might be curious to know that two of my siblings are 0.41. #4, you are correct. she is very close to her aunts/uncles to expected value. but varies more with her grandparents (0.22 to 0.28). also, you might be curious to know that two of my siblings are 0.41.

]]> By: Isabel http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42337 Isabel Mon, 30 Apr 2012 03:20:50 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42337 This is super cool. I'm surprised there is not more variance in the relatedness to aunts and uncles, if I am reading it right. It has always fascinated me that while we are 50% identical to our parents, this is only true on average with siblings, and in fact it would seem unusual to end up right on 50% and then with another average she still ends up right around 25% with each it looks like. Hmm. This is super cool.
I’m surprised there is not more variance in the relatedness to aunts and uncles, if I am reading it right. It has always fascinated me that while we are 50% identical to our parents, this is only true on average with siblings, and in fact it would seem unusual to end up right on 50% and then with another average she still ends up right around 25% with each it looks like. Hmm.

]]> By: Razib Khan http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42336 Razib Khan Mon, 30 Apr 2012 01:12:35 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42336 #2, hm. i wonder if that alone might be responsible for why she's more genetically derived from her maternal grandmother than grandfather.... #2, hm. i wonder if that alone might be responsible for why she’s more genetically derived from her maternal grandmother than grandfather….

]]> By: Dm http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42335 Dm Mon, 30 Apr 2012 00:49:59 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42335 Isn't it unusual that she has an X-chromosome which is 100% from the mgm and 0% from the mgp? This thing is over 200cM in size yet must have had zero recombinations in the meiosis which led to the lucky oocyte? Isn’t it unusual that she has an X-chromosome which is 100% from the mgm and 0% from the mgp? This thing is over 200cM in size yet must have had zero recombinations in the meiosis which led to the lucky oocyte?

]]> By: Elizabeth http://blogs.discovermagazine.com/gnxp/2012/04/her-identity-by-descent-made-flesh/#comment-42334 Elizabeth Sun, 29 Apr 2012 22:54:09 +0000 http://blogs.discovermagazine.com/gnxp/?p=16509#comment-42334 That is so cool. It makes me wish I were still teaching a genetics course so that I could talk about these images with my students. That is so cool. It makes me wish I were still teaching a genetics course so that I could talk about these images with my students.

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