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evon
08-19-2013, 03:41 PM
A new feature has just appeared on Gedmatch, our match with them are as follows:

Me:

DE:

Total SNPs in common: 696768
Match on at least one allele: 553140 (79.4%)
Match on both alleles: 338584 (48.6%)

NE:

Total SNPs in common: 697009
Match on at least one allele: 551231 (79.1%)
Match on both alleles: 335367 (48.1%)

Dont quite know how the read this, i mean what does it truly mean without a comparison?

DMXX
08-19-2013, 03:59 PM
Dont quite know how the read this, i mean what does it truly mean without a comparison?

Absolutely nothing - Which I'll take as a cue to share my results. :)



Denisovian (F999903) share for DMXX:
Total SNPs in common: 322401
Match on at least one allele: 256002 (79.4%)
Match on both alleles: 146240 (45.4%)

Neanderthal (F999902) share for DMXX:
Total SNPs in common: 322489
Match on at least one allele: 254656 (79%)
Match on both alleles: 144397 (44.8%)

Sangarius
08-19-2013, 05:44 PM
Denisovian (F999903) share for Sangarius:
Total SNPs in common: 685037
Match on at least one allele: 545111 (79.6%)
Match on both alleles: 331496 (48.4%)

Neanderthal (F999902) share for Sangarius:
Total SNPs in common: 685272
Match on at least one allele: 542615 (79.2%)
Match on both alleles: 327748 (47.8%)

So what does this mean? Shouldn't we share like 99% of our genomes with them, considering we share 96% with chimpanzees and 50% with bananas? :P

DMXX
08-19-2013, 05:55 PM
Denisovian (F999903) share for Sangarius:
Total SNPs in common: 685037
Match on at least one allele: 545111 (79.6%)
Match on both alleles: 331496 (48.4%)

Neanderthal (F999902) share for Sangarius:
Total SNPs in common: 685272
Match on at least one allele: 542615 (79.2%)
Match on both alleles: 327748 (47.8%)

So what does this mean? Shouldn't we share like 99% of our genomes with them, considering we share 96% with chimpanzees and 50% with bananas? :P

I'm guessing these values could be taken relative to 23andMe's Compare Genes feature? I don't see any explanation of this feature on Gedmatch.

Humanist
08-19-2013, 07:31 PM
Thanks for the link.


Denisovian
Total SNPs in common: 686029
Match on at least one allele: 547637 (79.8%)
Match on both alleles: 334431 (48.7%)

Neanderthal
Total SNPs in common: 686266
Match on at least one allele: 544846 (79.4%)
Match on both alleles: 330295 (48.1%)

Sangarius
08-20-2013, 04:58 PM
I just noticed a change. Yesterday the sample kits for comparison were from FtDNA. See the kit numbers, they begin with an F (Denisovian (F999903), Neanderthal (F999902)).
Today they changed to 23andme versions for both samples, since they provide more SNPs. You can see the Total SNPs in common got up quite a bit.


Denisovian (M071100) share for Sangarius:
Total SNPs in common: 923704
Match on at least one allele: 734240 (79.5%)
Match on both alleles: 444285 (48.1%)

Neanderthal (M113500) share for Sangarius:
Total SNPs in common: 924069
Match on at least one allele: 730940 (79.1%)
Match on both alleles: 439325 (47.5%)

N21163
08-20-2013, 10:27 PM
There is a Computer Scientist from South Australia, Felix Jeyareuben Chandrakumar, who has obtained the Denisovan and Neanderthal from the Max Planck Institute for Evolutionary Anthropology. At this stage the gedmatch feature compares rare SNPs from our genomes with that of the Denisovan and Neanderthal specimens. This is not the same as the 23andMe percentage estimation, provided in 23andme test results, but this may be developed in future. Felix has tested with FTDNA, developed some DNA analysis programs and makes regular submissions on the FTDNA forums. Felix's analysis tools can be found here (http://www.y-str.org/tools/)

N21163
08-28-2013, 11:15 AM
A "Neanderthal Calculator" has been developed (by felix) that compares 42 of the "out of Africa" Neanderthal SNPs with our raw data.

To test it's accuracy I suggest that people compare their current Neanderthal percentages (from Geno 2.0 or 23andme) with the results from this new calculator:

http://www.y-str.org/tools/neanderthal-calculator/

Mine came up with 1.19% (bit disappointed) :)

Sangarius
08-28-2013, 02:30 PM
With Felix calculator I got 3.57%. In comparison 23andme's tool calculated 2.7%.

palamede
08-28-2013, 04:09 PM
What I understand :

1) The 2 counters "Match on at least one allele" and "Match on both alleles " are only results of a probabilistic mathematical function depending on the first counter 'Total SNPs in common" according to a probabilstic distribution of the common SNPS in the loci .

2) The values of the counter 'Total SNPs in common" are depending on the quality of the laboratory coverages (low or medium or high)

3) In Homo Sapiens, there are a total of SNPs which are distributed in 2 parts

____- The first one is common to all the populations in a species (AMH only often but in this case AMH + Denosovan + Neandertal ) and in each population , they vary according to the individus. in Homo Sapiens the greater part of the SNPs are common to all human populations The values of the counter 'Total SNPs in common" give this first part.

____- The second one varies according to the population. It is this part used to determine the origins of an individu.l

The ratio between the two parts (second/first+second) give the Fst which measures the proximity between the 2 populations and allow to evaluate the date of common ancestors. http://en.wikipedia.org/wiki/Fixation_index

It is given in this paper :
http://www.nature.com/nature/journal/v468/n7327/full/nature09710.html?pagewanted=all

Genetic history of an archaic hominin group from Denisova Cave in Siberia

David Reich, Richard E. Green, Martin Kircher, Johannes Krause, Nick Patterson, Eric Y. Durand, Bence Viola, Adrian W. Briggs, Udo Stenzel, Philip L. F. Johnson, Tomislav Maricic, Jeffrey M. Good, Tomas Marques-Bonet, Can Alkan, Qiaomei Fu, Swapan Mallick, Heng Li, Matthias Meyer, Evan E. Eichler, Mark Stoneking, Michael Richards, Sahra Talamo, Michael V. Shunkov, Anatoli P. Derevianko, Jean-Jacques Hublin et al.
AffiliationsContributionsCorresponding authors
Nature 468, 1053–1060 (23 December 2010) doi:10.1038/nature09710
Received 15 August 2010 Accepted 30 November 2010 Published online 22 December 2010


Table S6.1: Genetic divergence for all pairs of samples uncorrected for sequencing error

________Han____Papuan__ San__ Yoruba__ Neandertal__ Denisova Chimp
French__ 22633__ 22948__ 22373__ 22805____ 25372____22138__ 101714
Han_____________ 23795__ 23596__ 24026____ 26542____ 23332__ 102939
Papuan_ _________________ 23801__ 24271____ 26562____ 23160__ 102894
San______________________________ 22042____23832_____20445__ 100000
Yoruba______________________________________25136_ ___ 21748__ 101328
Neandertal________________________________________ _____17963__ 100077
Denisova__________________________________________ ____________ 96501
Note: All numbers are normalized such that San-Chimpanzee divergence is 100,000

Table S6.2: Estimated genetic divergence dates for each pair of hominin samples
As a fraction of the human-chimpanzee divergence* 1000’s of years assuming 6,500 for human-chimp
________Han___Papuan__San____Yoruba__Neandertal_De nisova_ ________Han_____Papuan____San____Yoruba____Neander tal___Denisova

French__ .0622__ .0660__ .0907___ .0812____ .1218____ .1255__ F_______ 404_____429_____ 590_____ 528______ 794_______ 818
Han___________ .0620__ .0907__ .0811_____ .1212____ .1251___ H_______________ 403______589_____ 527______ 790_______ 815
Papuan________________ .0933__ .0842_____ .1219____ .1238___ P_____________________ ____607_____ 547______ 794_______ 807
San___________________________ .0913_____ .1237_____.1257___ S__________________________________ 593______ 806_______ 819
Yoruba____________________________________ .1234____ .1254___ Y____________________________________________ 804_______ 817
Neandertal________________________________________ __ .0984__ N_________________________________________________ ______ 644

Note: This table presents absolute dates of genetic divergence between a pair of samples dated relative to the present. For presentday samples, this is the same as the genetic divergence of the two samples, whereas for ancient samples which were interred tens
of thousands of years ago, the numbers are somewhat larger than the actual separation time between samples.
* Standard errors from a Block Jackknife are in the range 0.0005-0.0007, corresponding to 3-5 thousand years.


4) The part of the Denisovan or Neandertal in our genome (3,57% or 2,7%) shows the part of your variable genome which doesn't descend from the original african AMH ancestors, but due to the mixings with the euroasiatic "archaic races" Neandertal and Denisovan.

I hope to be comprehensible and if I am wrong, correct me.

N21163
08-28-2013, 09:09 PM
Hi palamede,

I agree with what you are saying, this is what I have been led to believe.

J Man
08-28-2013, 10:29 PM
Am I doing something wrong I wonder? I get 8.33% lol.