PDA

View Full Version : D-Stat Compilation



Kale
05-13-2015, 03:42 PM
Here is a list of all D-Stats I have seen posted, organized in Excel for easy viewing. 'Outgroups' are in column A, Z-Scores are bolded. Credit goes mostly to Chad and Davidski for running them.

I'll dig through some highlights, and maybe suggest a few I'd like to see run.

4566

Some Interesting Stats

Kostenki has nothing Basal to Ust-Ishim; none of the Basal Eurasian found in Stuttgart.
MbutiPygmy Ust'-Ishim Kostenki14 Loschbour 0.0004 0.055
MbutiPygmy Ust'-Ishim Kostenki14 Dai 0.0006 0.096
MbutiPygmy Ust'-Ishim Loschbour Dai 0.0006 0.105
MbutiPygmy Ust'-Ishim Kostenki14 Stuttgart -0.0252 -3.503

East Asians prefer WHG over Kostenki, signaling ENA<>WHG geneflow (as mentioned as a possibility in Haak. Et. Al.)
Chimp Japanese Loschbour Kostenki14 -0.0211 -3.488 16065 15401 329585
Chimp Dai Loschbour Kostenki14 -0.0187 -3.034 16025 15438 329585
Chimp Onge Loschbour Kostenki14 -0.019 -2.918 15967 15372 329585

Iceman has some very odd affinities (Yoruba, Neanderthal) that he doesn't share with his contemporaries
Chimp Yoruba BedouinB Iceman 0.013 3.535 14015 14384 351770
Chimp Yoruba BedouinB LBKT_EN -0.0171 -1.602 1300 1256 30718
Chimp Yoruba BedouinB Spain_EN -0.002 -0.848 14452 14394 348093
Chimp Yoruba BedouinB Starcevo_EN -0.0105 -1.707 4200 4112 101653
Chimp Yoruba BedouinB Stuttgart -0.0044 -1.519 14539 14411 348539
Chimp Altai Armenian Iceman 0.0266 4.13 8018 8457 351682
Chimp Altai Armenian LBKT_EN 0.001 0.052 737 739 30710
Chimp Altai Armenian Spain_EN 0.0019 0.448 8401 8432 348004
Chimp Altai Armenian Starcevo_EN -0.0043 -0.395 2452 2431 101630
Chimp Altai Armenian Stuttgart 0.0009 0.164 8416 8431 348451

Some Stats That Would Be Interesting To Run

Perhaps tease out the suspected West Eurasian ancestry in Africans?
Chimp Mbuti/Yoruba/Other Africans Kostenki Dai/Han/Japanese

See if there is any gene flow between ANE and particular East Asian groups.
Chimp MA1 ENA ENA

Test out the early coastal model a bit.
Chimp Ust-Ishim Onge ENA/WHG

Kale
06-24-2015, 02:15 PM
Just updating. Too many to fit in one attachment now so it's split into two files. Extract, combine the two excel files and you'll be good to go. 3700 stats, double what there was last time. Most recent additions are some from the Allentoft paper and the one about Oase 1.

50405041

Vadim Verenich
06-26-2015, 07:39 AM
Very interesting.
Is Oase 1 genome publicly available somewhere?

Kale
06-26-2015, 12:40 PM
Very interesting.
Is Oase 1 genome publicly available somewhere?

The Oase stats I have are the ones from the paper.

Kale
08-20-2015, 02:55 AM
I have a request for anyone that is able to run some stats. Of course, as I don't wish to resurrect a dead thread, I will not do so without contribution. Here is an updated excel sheet. 2 parts, 4200 stats, 500 more than last time.

56315632

And for some stat's I'd like to see run...I'm not sure the format easiest to run them in, I will change it to suit your convenience if necessary, but I've got it in an excel sheet now.

5633

Thanks in advance :)

Kale
08-20-2015, 08:17 PM
...In regards to 'Basal Eurasian'.

Looking through the list of IBD sharing for Loschbour and Kostenki14 it's hard to believe how similar they are. I don't think we'd expect to see this at all if Loschbour was anything less than overwhelmingly descended from a Kostenki-like population. This gives us a great opportunity to analyze potential WHG related ancestry levels, without it being inflated or deflated by how long ago that mixture occured. So if we treat Loschbour and Kostenki as 100% West Eurasian...we can see how other populations compare in their relatedness to West Eurasian.

Checking that on the d-stats, we get Karitiana as 30% West Eurasian. But seeing as Loschbour and Kostenki are both on the WHG branch of West Eurasian, and Karitiana is on the ANE branch, the real level of West Eurasian should be a little higher, but not a whole lot (maybe 35 to 40). That's consistent with other results we see.

Now extrapolating that on other populations...
Lithuanians = 86%
French = 84%
Sardinian = 82% (so that means early farmers should be right around here as well)
BedouinB = 72%
Yemenite Jew = 61%