Mega QAPDM Models thread

[Mr. M]

I had to substitute Russia_Karelia_HG to Russia_Samara_HG. For some reason I couldn't find it in IllustrativeDNA.

Karelia is Russia_YuzhniyOleniyOstrov_Mesolithic, the one I used in my model since Samara and Sidelkino already have CHG/Iran_N admix

[Gannicus]

Karelia is Russia_YuzhniyOleniyOstrov_Mesolithic, the one I used in my model since Samara and Sidelkino already have CHG/Iran_N admix

Added that into the reference list and removed Samara. The adjustment tightened up the standard errors and chi-squared a bit on the first 2-way:



pat wt dof chisq p f4rank Sweden_IA_2.SG_VK522.SG Egypt_ThirdIntermediatePeriod.AG_JK2134.AG feasible best dofdiff chisqdiff p_nested
00 0 13 16.755364121649443 0.21073012036400646 1 0.8319910986340255 0.1680089013659744 TRUE NA NA NA NA
01 1 14 30.340556470389895 0.006848638940157966 0 1 NA TRUE TRUE 0 -49.18801990975905 1
10 1 14 79.52857638014895 3.46030652820137e-11 0 NA 1 TRUE TRUE NA NA NA

[Gannicus]

Double post.

[drb234]

[Gannicus]

This is one of my best runs yet with the same rights as the previous. I used Ireland EBA Rathlin 2, a sample that I match on MyTrueAncestry:


Those that like to be too particular like to criticize results that produce Z-Scores less than 3. Here in this result the Z-score for Egypt TIP would be 3.25. I've already mentioned though that Z-Scores less than 3 make it into peer-reviewed published genetics papers.



pat wt dof chisq p f4rank Ireland_EBA.SG_rath2.SG Egypt_ThirdIntermediatePeriod.AG_JK2134.AG feasible best dofdiff chisqdiff p_nested
00 0 13 18.751626933192213 0.1310081143344856 1 0.7944860039558197 0.20551399604418025 TRUE NA NA NA NA
01 1 14 34.52252862395704 0.001728893048752092 0 1 NA TRUE TRUE 0 -43.68810958949282 1
10 1 14 78.21063821344985 6.067038308893523e-11 0 NA 1 TRUE TRUE NA NA NA

[Gannicus]

Trying to isolate Natufian:



Chi-squared = 17.91
Degrees of freedom = 9

p-value = 0.0363



pat wt dof chisq p f4rank Russia_Samara_EBA_Yamnaya.AG_I0231.AG Turkey_Central_Pinarbasi_Epipaleolithic.AG_ZBC_IPB 001.B-C0101_Luk2-Pinarbasi.AG Israel_Natufian.AG Luxembourg_Mesolithic.DG_Loschbour.DG feasible best dofdiff chisqdiff p_nested
0000 0 9 17.907109322604683 0.03626665845967619 3 0.4791685725273366 0.3266312318943904 0.08478275718187421 0.10941743839639882 TRUE NA NA NA NA
0001 1 10 59.05707348625523 5.463172094567697e-9 2 0.5803429292627148 0.3827221868253448 0.03693488391194047 NA TRUE TRUE 0 30.604401993030546 0
0010 1 10 28.45267149322468 0.0015271326634493005 2 0.5147056167631247 0.38014783771804256 NA 0.10514654551883273 TRUE TRUE 0 -91.15029459533007 1
0100 1 10 119.60296608855475 6.091319306297955e-21 2 0.5504406348257856 NA 0.32676212869675986 0.12279723647745458 TRUE TRUE 0 -188.55068871897544 1
1000 1 10 308.1536548075302 2.9333895170265636e-60 2 NA 0.7963751322345017 -0.019424186124213403 0.22304905388971172 FALSE TRUE NA NA NA
0011 2 11 67.10922592767723 4.313562300130967e-10 1 0.5965554447330063 0.4034445552669938 NA NA TRUE NA NA NA NA
0101 2 11 197.44040773961413 2.5256739456125005e-36 1 0.6777461704018504 NA 0.32225382959814963 NA TRUE NA NA NA NA
0110 2 11 253.34435098119383 5.568806304414893e-48 1 0.9237112307300359 NA NA 0.07628876926996417 TRUE NA NA NA NA
1001 2 11 349.41902395534134 3.2170424679394866e-68 1 NA 3.3860029662268123 -2.3860029662268123 NA FALSE NA NA NA NA
1010 2 11 330.8205549892451 2.753010405050842e-64 1 NA 0.7897004380171972 NA 0.21029956198280272 TRUE NA NA NA NA
1100 2 11 394.30124856187723 9.914763102157746e-78 1 NA NA 0.7387038103550781 0.26129618964492185 TRUE NA NA NA NA
0111 3 12 285.7497316796714 4.5834266966857024e-54 0 1 NA NA NA TRUE NA NA NA NA
1011 3 12 452.4788427898409 2.810539351885685e-89 0 NA 1 NA NA TRUE NA NA NA NA
1101 3 12 524.2693494803447 1.5070567436541544e-104 0 NA NA 1 NA TRUE NA NA NA NA
1110 3 12 1286.8672327226395 3.3655118335110553e-268 0 NA NA NA 1 TRUE NA NA NA NA


References:




It's getting somewhat close to passing.


Any suggestions on what to change?

[AndreiDNA]

Karelia is Russia_YuzhniyOleniyOstrov_Mesolithic, the one I used in my model since Samara and Sidelkino already have CHG/Iran_N admix

Karelia also has CHG admix. They even have 4 people with J1 from mesolithic karelia.

[Gannicus]

So far I've only been able to infer Natufian admix by using populations that have it "baked" in already:



pat wt dof chisq p f4rank Latvia_LN_CordedWare.AG Israel_PPNB.AG_I0867.AG Luxembourg_Mesolithic.DG_Loschbour.DG feasible best dofdiff chisqdiff p_nested
000 0 11 14.201740559702879 0.22203070363619803 2 0.5093364971235644 0.3120461889516757 0.17861731392476 TRUE NA NA NA NA
001 1 12 55.526177292551345 1.4562896862833555e-7 1 0.684297592393732 0.315702407606268 NA TRUE TRUE 0 -11.215171823926532 1
010 1 12 66.74134911647788 1.2970190791969662e-9 1 0.8278127622817596 NA 0.1721872377182404 TRUE TRUE 0 -195.33431875347333 1
100 1 12 262.0756678699512 4.1262485394475325e-49 1 NA 0.7093245146422447 0.29067548535775534 TRUE TRUE NA NA NA
011 2 13 88.95895111964444 2.2095624661751116e-13 0 1 NA NA TRUE NA NA NA NA
101 2 13 441.57560449532315 3.602664999464381e-86 0 NA 1 NA TRUE NA NA NA NA
110 2 13 1092.793181336491 2.0157458922755243e-225 0 NA NA 1 TRUE NA NA NA NA

Rights:

[Gannicus]

Here's what I get:



pat wt dof chisq p f4rank Scotland_IA.AG_I16504.AG Denmark_IA.SG France_Metz_GalloRoman.SG feasible best dofdiff chisqdiff p_nested
000 0 11 7.219826361226613 0.781012303144483 2 -2.3261454614434283 2.785332857996349 0.5408126034470794 FALSE NA NA NA NA
001 1 12 7.88697960512831 0.7938990014869362 1 -3.5984938615857565 4.598493861585757 NA FALSE TRUE 0 -12.150180270926757 1
010 1 12 20.037159876055068 0.06638628004148951 1 1.9493325459839783 NA -0.9493325459839783 FALSE TRUE 0 -2.3379103343145786 1
100 1 12 22.375070210369646 0.033524961639489155 1 NA 0.6639322060997479 0.33606779390025215 TRUE TRUE NA NA NA
011 2 13 23.834834534897645 0.03268374617987084 0 1 NA NA TRUE NA NA NA NA
101 2 13 29.125875695879426 0.006282002727272953 0 NA 1 NA TRUE NA NA NA NA
110 2 13 39.393485483175716 1.729800161953792e-4 0 NA NA 1 TRUE NA NA NA NA


Rights:

[drb234]

Here's what I get:



pat wt dof chisq p f4rank Scotland_IA.AG_I16504.AG Denmark_IA.SG France_Metz_GalloRoman.SG feasible best dofdiff chisqdiff p_nested
000 0 11 7.219826361226613 0.781012303144483 2 -2.3261454614434283 2.785332857996349 0.5408126034470794 FALSE NA NA NA NA
001 1 12 7.88697960512831 0.7938990014869362 1 -3.5984938615857565 4.598493861585757 NA FALSE TRUE 0 -12.150180270926757 1
010 1 12 20.037159876055068 0.06638628004148951 1 1.9493325459839783 NA -0.9493325459839783 FALSE TRUE 0 -2.3379103343145786 1
100 1 12 22.375070210369646 0.033524961639489155 1 NA 0.6639322060997479 0.33606779390025215 TRUE TRUE NA NA NA
011 2 13 23.834834534897645 0.03268374617987084 0 1 NA NA TRUE NA NA NA NA
101 2 13 29.125875695879426 0.006282002727272953 0 NA 1 NA TRUE NA NA NA NA
110 2 13 39.393485483175716 1.729800161953792e-4 0 NA NA 1 TRUE NA NA NA NA


Rights:

I used different rights that included bronze age samples from Britain, Scandinavia and Central Europe