The Arrival of Steppe & Iranian Related Ancestry in Islands of West Mediterranean

Ygorcs said:
Thought this might be of interest to some of you guys. From the look of it, I find it unlikely that Büyükkaya_EC, Kumtepe and Tepecik-Ciftlik really lacked any extra Levant_N/Natufian affinity higher than what you'd find in Barcin, Boncuklu or the earlier Pinarbasi_AHG and only had CHG/Iran added in an exclusively Anatolia-Caucasus-Iran cline. Unlike other ANF, who are consistently closest to Sardinians, those are strongly pulled much closer toward several individuals from groups that, even though today heavily admixed, are either Levantine (Lebanese), of Levantine origin (Jews) or living very close to the Levant (Cyprus, Kos), instead of any populations that are mainly just Anatolia+CHG/Iran with very no detectable (not already present in Barcin-like people) Levant_N. That tendency of comparatively closer affinity to partially Levant-derived populations is particularly strong in the majority (all but 1) of the Tepecik-Ciftlik samples. So, I keep my doubts that they are best modelled as simply part of an Anatolia:CHG/Iran cline without any even minor participation of the Levant in that history (though I'm sure they could be modelled without it, given how minor this admixture is and how relatively closely related it is to other ANF samples, so the fits won't get that worse just because you made your model without it).

Also, comparing Levant_PPNB samples to Anatolia_N ones, Tepecik-Ciftlik and Kumtepe appear consistently much closer to them than Barcin_N and Boncuklu_N as well as Buyukkaya_EC, with most individuals not much more distant than the confirmed Levant_N-shifted (according to the authors of the paper) Tell Kurdu. The higher distance of Buyukkaya_EC is probably explained by the significant extra (beyond what was already in Tepecik-like people) CHG/Iran_N, which was a far more divergent and thus more distant admixture, because on the whole it was clearly more Tepecik-like than Barcin-like.

CLOSEST GENETIC DISTANCES TO:

Distance to:TUR_Buyukkaya_EC:CBT018
0.05619294Cypriot:Cyprus22AJ19
0.05848623Greek_Kos:GreeceKos8
0.05896804Cypriot:Cyprus24AJ19
0.06036881Greek_Kos:GreeceKos1
0.06168936Italian_Jew:ItalyJew3
0.06244073Cypriot:CYP19
0.06252732Cypriot:CYP5
0.06313818Greek_Crete:Crete7
0.06327482Cypriot:CYP2
0.06413110Italian_Jew:ItalyJew5
0.06430862Lebanese_Christian:Lebanese4AQ115
0.06436686Greek_Kos:GreeceKos5
0.06456939Romaniote_Jew:Romaniote3
0.06503770Romaniote_Jew:Romaniote2
0.06521063Greek_Central_Anatolia:G2501
0.06524364Italian_Campania:NaN195ST
0.06542570Greek_Central_Anatolia:G2503
0.06572279Greek_Kos:GreeceKos7
0.06588541Romaniote_Jew:Romaniote5
0.06596438Italian_Calabria:ALP582
0.06605272Lebanese_Christian:Lebanese10AR37
0.06606180Greek_Kos:GreeceKos9
0.06612712Romaniote_Jew:Romaniote4
0.06636724Greek_Kos:GreeceKos4
0.06708272Italian_Campania:NaN275IS
0.06720562Sephardic_Jew:sephardic14bul
0.06724789Greek_Kos:GreeceKos10
0.06786895Romaniote_Jew:Romaniote1
0.06789378Greek_Kos:GreeceKos2
0.06795773Italian_Campania:NaN77FAM
0.06810467Italian_Jew:ItalyJew2
0.06870596Sephardic_Jew:SephardicJew24276
0.06903087Italian_Campania:CMP_b001_2
0.06927208Sephardic_Jew:SephardicJew4953
0.06928037Italian_Campania:CMP_b007_2

Distance to:TUR_Tepecik_Ciftlik_N:Tep006
0.07783184Italian_Jew:ItalyJew3
0.08119204Romaniote_Jew:Romaniote4
0.08383588Cypriot:Cyprus24AJ19
0.08582248Tunisian_Jew:TunisianJew1763
0.08620921Italian_Jew:ItalyJew5
0.08649028Sephardic_Jew:sephardic14bul
0.08656127Tunisian_Jew:TunisianJew1531
0.08712490Romaniote_Jew:Romaniote3
0.08853001Italian_Jew:ItalyJew4
0.08875517Moroccan_Jew:MoroccanJew5126
0.08900950Tunisian_Jew:TunisianJew1421
0.08911637Italian_Jew:ItalyJew9
0.08916056Italian_Jew:ItalyJew2
0.08935670Greek_Kos:GreeceKos1
0.08936558Italian_Campania:CMP_b007_2
0.08951174Sephardic_Jew:GRC12118122
0.08961138Sephardic_Jew:SephardicJew24276
0.08969244Sephardic_Jew:SephardicJew4953
0.08990144Cypriot:Cyprus22AJ19
0.09009642Sephardic_Jew:GRC12118128
0.09022338Sardinian:HGDP00672
0.09026641Romaniote_Jew:Romaniote2
0.09092755Romaniote_Jew:Romaniote5
0.09177845Italian_Jew:ItalyJew8
0.09206306Tunisian_Jew:TunisianJew1170

Distance to:TUR_Tepecik_Ciftlik_N:Tep004
0.08161905Italian_Jew:ItalyJew3
0.08203562Romaniote_Jew:Romaniote4
0.08647044Italian_Jew:ItalyJew5
0.08689151Romaniote_Jew:Romaniote3
0.08918307Italian_Campania:CMP_b007_2
0.08985923Italian_Jew:ItalyJew2
0.09022619Sephardic_Jew:SephardicJew24276
0.09058792Tunisian_Jew:TunisianJew1763
0.09062833Tunisian_Jew:TunisianJew1531
0.09073282Italian_Jew:ItalyJew4
0.09078542Sephardic_Jew:sephardic14bul
0.09123784Sephardic_Jew:SephardicJew4953
0.09128026Cypriot:Cyprus24AJ19
0.09174334Sardinian:HGDP00672
0.09175816Italian_Jew:ItalyJew9
0.09180596Greek_Kos:GreeceKos1
0.09195126Cypriot:Cyprus22AJ19
0.09237083Tunisian_Jew:TunisianJew1421
0.09306355Italian_Apulia:pu3
0.09312719Moroccan_Jew:MoroccanJew5126
0.09317281Sephardic_Jew:GRC12118097
0.09330190Italian_Campania:NaN65DFG
0.09372744Romaniote_Jew:Romaniote2
0.09398185Romaniote_Jew:Romaniote5
0.09407079Italian_Calabria:ALP582

Distance to:TUR_Tepecik_Ciftlik_N:Tep003
0.06612069Italian_Jew:ItalyJew3
0.06752017Cypriot:Cyprus24AJ19
0.06864480Romaniote_Jew:Romaniote4
0.07016443Cypriot:Cyprus22AJ19
0.07054681Sephardic_Jew:SephardicJew24276
0.07145201Greek_Crete:Crete7
0.07206077Italian_Campania:CMP_b007_2
0.07261529Greek_Kos:GreeceKos5
0.07270155Romaniote_Jew:Romaniote3
0.07302899Greek_Kos:GreeceKos1
0.07310681Italian_Campania:NaN195ST
0.07324888Italian_Jew:ItalyJew5
0.07340100Italian_Jew:ItalyJew2
0.07348141Italian_Jew:ItalyJew10
0.07378319Italian_Apulia:pu3
0.07380864Romaniote_Jew:Romaniote2
0.07406104Romaniote_Jew:Romaniote5
0.07479388Sephardic_Jew:SephardicJew4953
0.07512701Italian_Calabria:ALP582
0.07524743Cypriot:CYP2
0.07565588Greek_Kos:GreeceKos2
0.07580079Greek_Kos:GreeceKos8
0.07600420Lebanese_Christian:Lebanese4AQ115
0.07602093Italian_Abruzzo:ALP205
0.07602826Ashkenazi_Germany:Ashk_DE_DE_4

Distance to:TUR_Tepecik_Ciftlik_N:Tep002
0.07949427Sardinian:HGDP00665
0.08027154Sardinian:HGDP00672
0.08327072Sardinian:HGDP01063
0.08692853Sardinian:HGDP01067
0.08862466Sardinian:HGDP01075
0.08985020Italian_Campania:CMP_b007_2
0.09127246Sardinian:HGDP01078
0.09159680Sardinian:S_Sardinian-2
0.09189573Sardinian:HGDP00671
0.09197428Italian_Campania:NaN195ST
0.09209790Sephardic_Jew:SephardicJew24276
0.09300752Sardinian:HGDP01073
0.09425037Italian_Jew:ItalyJew10
0.09527881Italian_Jew:ItalyJew2
0.09528242French_Corsica:Corsica03708
0.09608390Sardinian:HGDP01066
0.09701064Italian_Apulia:pu3
0.09724506Cypriot:Cyprus22AJ19
0.09728082Italian_Jew:ItalyJew3
0.09770383Italian_Calabria:ALP582
0.09773373Romaniote_Jew:Romaniote4
0.09813541Ashkenazi_Germany:Ashk_DE_DE_1
0.09858622Italian_Basilicata:pG25
0.09866615Italian_Jew:ItalyJew7
0.09885649Greek_Crete:Crete7

Distance to:TUR_Kumtepe_N:kum6
0.07448993Italian_Jew:ItalyJew3
0.07483299Italian_Campania:CMP_b007_2
0.07576479Romaniote_Jew:Romaniote4
0.07619072Italian_Apulia:pu3
0.07665219Italian_Campania:CMP_b005_2
0.07669434Sicilian_East:EastSicilian2H
0.07684932Sephardic_Jew:SephardicJew24276
0.07736460Italian_Jew:ItalyJew2
0.07800805Italian_Calabria:ALP582
0.07872851Italian_Basilicata:pG20
0.07912070Greek_Crete:Crete7
0.07935267Greek_Kos:GreeceKos1
0.07947786Sardinian:HGDP00672
0.07956981Italian_Campania:NaN195ST
0.07985500Italian_Campania:NaN46TC
0.07998311Italian_Jew:ItalyJew5
0.08011884Romaniote_Jew:Romaniote3
0.08058599Sephardic_Jew:sephardic14bul
0.08059896Italian_Jew:ItalyJew9
0.08072907Greek_Kos:GreeceKos5
0.08083146Maltese:Malta15AM91
0.08129719Sephardic_Jew:SephardicJew4953
0.08171840Italian_Apulia:pu7
0.08187716Italian_Calabria:ALP596
0.08194836Italian_Campania:NaN275IS

Distance to:TUR_Barcin_N:I1583
0.07842168Sardinian:HGDP00672
0.08064705Sardinian:HGDP01075
0.08275450Sardinian:HGDP00665
0.08387873Sardinian:HGDP01063
0.08451324Sardinian:HGDP01067
0.08631972Sardinian:HGDP01073
0.08993507Sardinian:HGDP01066
0.09310765Sardinian:HGDP00671
0.09375059Sardinian:HGDP01078
0.09512188Sardinian:S_Sardinian-2
0.09669250Sardinian:HGDP00674
0.11127426Italian_Campania:CMP_b007_2
0.11290561French_Corsica:CorsicaS10208
0.11386614French_Corsica:Corsica03708
0.11653179French_Corsica:corsica1308
0.11713637Italian_Campania:NaN195ST
0.11817232Italian_Apulia:pu3
0.11820644Sephardic_Jew:SephardicJew24276
0.11832132Italian_Jew:ItalyJew3
0.11856837Italian_Jew:ItalyJew2
0.11896434Romaniote_Jew:Romaniote4
0.11980303French_Corsica:Corsica19508
0.12000111French_Corsica:Corsica29708
0.12001038French_Corsica:CorsicaS29908
0.12029216Italian_Basilicata:pG20

Distance to:TUR_Barcin_N:I1581
0.08267126Sardinian:HGDP00665
0.08561970Sardinian:HGDP01063
0.08620401Sardinian:HGDP01075
0.08665795Sardinian:HGDP00672
0.08942567Sardinian:HGDP01067
0.09193371Sardinian:HGDP00671
0.09339714Sardinian:HGDP01066
0.09432365Sardinian:HGDP01073
0.09704821Sardinian:S_Sardinian-2
0.09770569Sardinian:HGDP01078
0.10703229Sardinian:HGDP00674
0.11552969Italian_Campania:CMP_b007_2
0.11824071French_Corsica:CorsicaS10208
0.11880621French_Corsica:Corsica03708
0.11967892French_Corsica:corsica1308
0.12005339Italian_Campania:NaN195ST
0.12157303French_Corsica:Corsica19508
0.12296745Sephardic_Jew:SephardicJew24276
0.12334248Italian_Jew:ItalyJew2
0.12344677Italian_Jew:ItalyJew10
0.12461101Italian_Apulia:pu3
0.12463992Italian_Jew:ItalyJew3
0.12501007Italian_Calabria:ALP582
0.12572558French_Corsica:CorsicaS29908
0.12615685Italian_Basilicata:pG20

Distance to:TUR_Barcin_N:I1580
0.08173157Sardinian:HGDP01063
0.08244882Sardinian:HGDP00665
0.08261927Sardinian:HGDP00672
0.08264346Sardinian:HGDP01075
0.08661107Sardinian:HGDP01067
0.08998998Sardinian:HGDP00671
0.09033272Sardinian:HGDP01073
0.09172584Sardinian:HGDP01066
0.09334882Sardinian:S_Sardinian-2
0.09347792Sardinian:HGDP01078
0.10404224Sardinian:HGDP00674
0.10964629Italian_Campania:CMP_b007_2
0.11159682French_Corsica:CorsicaS10208
0.11185453French_Corsica:Corsica03708
0.11301952French_Corsica:corsica1308
0.11428321Italian_Campania:NaN195ST
0.11676057Italian_Apulia:pu3
0.11678322Sephardic_Jew:SephardicJew24276
0.11776283French_Corsica:Corsica19508
0.11788291Italian_Jew:ItalyJew2
0.11858828French_Corsica:CorsicaS29908
0.11923746Italian_Basilicata:pG20
0.11978913Italian_Jew:ItalyJew10
0.11997743Italian_Jew:ItalyJew3
0.12023190Italian_Basilicata:pG25

Distance to:TUR_Barcin_N:I1103
0.07057967Sardinian:HGDP00672
0.07451939Sardinian:HGDP00665
0.07522570Sardinian:HGDP01075
0.07729441Sardinian:HGDP01063
0.07785505Sardinian:HGDP01067
0.08140553Sardinian:HGDP01073
0.08334604Sardinian:HGDP01066
0.08729519Sardinian:HGDP01078
0.08767246Sardinian:HGDP00671
0.08886065Sardinian:S_Sardinian-2
0.09164748Sardinian:HGDP00674
0.09791283Italian_Campania:CMP_b007_2
0.10156992French_Corsica:CorsicaS10208
0.10194984French_Corsica:Corsica03708
0.10250347Italian_Jew:ItalyJew2
0.10258455Italian_Jew:ItalyJew3
0.10286484Italian_Campania:NaN195ST
0.10327320Romaniote_Jew:Romaniote4
0.10445641Italian_Apulia:pu3
0.10469991Sephardic_Jew:SephardicJew24276
0.10482746Italian_Calabria:ALP582
0.10516255French_Corsica:corsica1308
0.10550685Sephardic_Jew:sephardic14bul
0.10555527Italian_Jew:ItalyJew10
0.10606162Italian_Jew:ItalyJew9

GENETIC DISTANCE: LEVANT VS. ANATOLIA

Distance to:Levant_PPNB:BAJ001
0.11467520TUR_Tell_Kurdu_EC:KRD006
0.11596302TUR_Tell_Kurdu_EC:KRD003
0.12337218TUR_Tell_Kurdu_EC:KRD001
0.13064692TUR_Tepecik_Ciftlik_N:Tep004
0.13099519TUR_Tepecik_Ciftlik_N:Tep006
0.13152104TUR_Tell_Kurdu_MC:KRD002
0.13864373TUR_Tepecik_Ciftlik_N:Tep003
0.14137715TUR_Tell_Kurdu_EC:KRD004
0.14802320TUR_Barcin_N:I1103
0.14802507TUR_Tepecik_Ciftlik_N:Tep002
0.15121699TUR_Kumtepe_N:kum6
0.15229100TUR_Barcin_N:I0745
0.15285341TUR_Barcin_N:I1098
0.15429851TUR_Buyukkaya_EC:CBT018
0.15471732TUR_Barcin_N:I1101
0.15620402TUR_Barcin_N:I1099
0.15631343TUR_Barcin_N:I1583
0.15878425TUR_Barcin_N:I0708
0.16030326TUR_Barcin_N:I0736
0.16035256TUR_Barcin_N:I1581
0.16047584TUR_Barcin_N:I0707
0.16098703TUR_Barcin_N:I1580
0.16224672TUR_Barcin_N:I1097
0.16260144TUR_Barcin_N:I1102
0.16294108TUR_Barcin_N:I0709

Distance to:Levant_PPNB:I0867
0.08503868TUR_Tell_Kurdu_EC:KRD006
0.08812055TUR_Tell_Kurdu_EC:KRD003
0.09477869TUR_Tell_Kurdu_EC:KRD001
0.09566242TUR_Tell_Kurdu_EC:KRD004
0.10648213TUR_Tell_Kurdu_MC:KRD002
0.10664054TUR_Tepecik_Ciftlik_N:Tep004
0.10770789TUR_Tepecik_Ciftlik_N:Tep006
0.10845840TUR_Tepecik_Ciftlik_N:Tep002
0.11227904TUR_Barcin_N:I1103
0.11475981TUR_Barcin_N:I1098
0.11563090TUR_Barcin_N:I1581
0.11716518TUR_Barcin_N:I1583
0.11721502TUR_Tepecik_Ciftlik_N:Tep003
0.11806050TUR_Barcin_N:I1580
0.12021710TUR_Barcin_N:I0736
0.12031092TUR_Barcin_N:I1099
0.12085351TUR_Barcin_N:I0707
0.12092333TUR_Barcin_N:I1101
0.12282823TUR_Barcin_N:I1097
0.12317659TUR_Barcin_N:I0708
0.12340227TUR_Barcin_N:I0745
0.12375812TUR_Barcin_N:I1102
0.12414747TUR_Barcin_N:I0723
0.12604482TUR_Barcin_N:I1100
0.12762267TUR_Barcin_N:I0744

Distance to:Levant_PPNB:I1704
0.08424608TUR_Tell_Kurdu_EC:KRD006
0.08952674TUR_Tell_Kurdu_EC:KRD003
0.09265701TUR_Tell_Kurdu_EC:KRD001
0.09887992TUR_Tepecik_Ciftlik_N:Tep004
0.10350613TUR_Tell_Kurdu_MC:KRD002
0.10496203TUR_Tell_Kurdu_EC:KRD004
0.10784249TUR_Tepecik_Ciftlik_N:Tep006
0.11313852TUR_Tepecik_Ciftlik_N:Tep003
0.11436927TUR_Tepecik_Ciftlik_N:Tep002
0.11616284TUR_Barcin_N:I1103
0.11660952TUR_Barcin_N:I1098
0.12153944TUR_Barcin_N:I1583
0.12188064TUR_Barcin_N:I0745
0.12265562TUR_Barcin_N:I1099
0.12321288TUR_Barcin_N:I1580
0.12327239TUR_Barcin_N:I1581
0.12352086TUR_Barcin_N:I1101
0.12369151TUR_Kumtepe_N:kum6
0.12631843TUR_Barcin_N:I0707
0.12651497TUR_Barcin_N:I0736
0.12706754TUR_Barcin_N:I0708
0.12782611TUR_Barcin_N:I1097
0.12848199TUR_Barcin_N:I1102
0.12975291TUR_Barcin_N:I1100
0.12993585TUR_Barcin_N:I0723

Distance to:Levant_PPNB:I1707
0.08824151TUR_Tell_Kurdu_EC:KRD006
0.09088006TUR_Tell_Kurdu_EC:KRD003
0.09330426TUR_Tell_Kurdu_EC:KRD001
0.10120114TUR_Tell_Kurdu_MC:KRD002
0.10764001TUR_Tepecik_Ciftlik_N:Tep004
0.11323937TUR_Tepecik_Ciftlik_N:Tep006
0.11432164TUR_Tell_Kurdu_EC:KRD004
0.11517000TUR_Tepecik_Ciftlik_N:Tep003
0.12008128TUR_Barcin_N:I1103
0.12026043TUR_Tepecik_Ciftlik_N:Tep002
0.12593508TUR_Barcin_N:I1098
0.12743434TUR_Barcin_N:I0745
0.12892241TUR_Kumtepe_N:kum6
0.12971536TUR_Barcin_N:I1101
0.12976708TUR_Barcin_N:I0708
0.12992724TUR_Barcin_N:I1583
0.13021591TUR_Buyukkaya_EC:CBT018
0.13128965TUR_Barcin_N:I1581
0.13257008TUR_Barcin_N:I0707
0.13260941TUR_Barcin_N:I1099
0.13438090TUR_Barcin_N:I1580
0.13445362TUR_Barcin_N:I1102
0.13471279TUR_Barcin_N:I1097
0.13544604TUR_Barcin_N:I0736
0.13844636TUR_Barcin_N:I1100

Distance to:Levant_PPNB:I1710
0.08183354TUR_Tell_Kurdu_EC:KRD006
0.08870011TUR_Tell_Kurdu_EC:KRD003
0.09032972TUR_Tell_Kurdu_EC:KRD001
0.09397471TUR_Tell_Kurdu_EC:KRD004
0.09507766TUR_Tepecik_Ciftlik_N:Tep002
0.09774276TUR_Tell_Kurdu_MC:KRD002
0.10031070TUR_Barcin_N:I1098
0.10058383TUR_Tepecik_Ciftlik_N:Tep006
0.10347375TUR_Tepecik_Ciftlik_N:Tep003
0.10400370TUR_Tepecik_Ciftlik_N:Tep004
0.10483433TUR_Barcin_N:I1581
0.10521050TUR_Barcin_N:I1103
0.10583914TUR_Barcin_N:I1580
0.10769646TUR_Barcin_N:I0736
0.10896576TUR_Barcin_N:I1583
0.11069886TUR_Barcin_N:I1099
0.11135791TUR_Barcin_N:I0708
0.11186268TUR_Barcin_N:I0707
0.11204973TUR_Barcin_N:I1101
0.11209743TUR_Barcin_N:I1097
0.11427244TUR_Barcin_N:I0724
0.11526345TUR_Barcin_N:I0723
0.11565291TUR_Barcin_N:I1102
0.11592432TUR_Barcin_N:I0745
0.11752732TUR_Barcin_N:I0744
Click to expand...

Well, I'm glad that you convinced yourself that Kilinc et al was correct.
 
kingjohn said:
nice (y)
nice to see the short distance of some of those ancients to italian jews :cool-v:
https://de.wikipedia.org/wiki/Tepecik-Çiftlik
Click to expand...

I have absolutely no proof for this; just a hunch, but I've always suspected that the Italian Jews, present in Italy for 2000 years or more, might be the closest to the Jews of the initial diaspora out of Israel.

We'll see if we ever get a first century Judean sample.

Rabbi of Rome's 2000 year old Jewish Community:
1516CNS-ToaffWEB2.jpg


Lay Leader of the Community:
Riccardo-Pacifici.jpg
 
Regio X said:
However, I noticed PPNB in Lazio for example seems too high, then I've tried to reproduce this last model using nMonte3 (penalty = 0.001) in R SW, rather than nMonte, just out of curiosity. (AFAIK pen = 0.001 instead pen = 0 in G25 is used by many.) Notice how PPNB drops, interestingly:

- Lazio
TUR_Tepecik_Ciftlik_N,40.6
TUR_Barcin_N,29
Yamnaya_RUS_Samara,15.8
IRN_Ganj_Dareh_N,4.6
WHG,4.4
RUS_Khvalynsk_En,3.6
GEO_CHG,1.4
Levant_PPNB,0.6

Total of 69.6 Anatolian Neo, 19.4 Steppe, 6.0 CHG/Iran, 4.4 WHG and 0.6 Levant PPNB only.

- Now the same approach (pen = 0.001) for Sicilian East

TUR_Tepecik_Ciftlik_N,54.4
Yamnaya_RUS_Samara,14.4
TUR_Barcin_N,14.2
IRN_Ganj_Dareh_N,5.2
RUS_Khvalynsk_En,4.4
Levant_PPNB,2.6
WHG,2.2
MAR_EN,1.4
GEO_CHG,1.2

Total of 68.6 Anatolian Neo, 18.8 Steppe, 6.4 CHG/Iran, 2.2 WHG, 2.6 Levant PPNB and 1.4 MAR EN. Also a big difference.
Click to expand...
Regio X said:
Bergamo, for comparison
TUR_Barcin_N,41.4
TUR_Tepecik_Ciftlik_N,25.2
Yamnaya_RUS_Samara,20.2
WHG,7.8
RUS_Khvalynsk_En,4.4
GEO_CHG,0.8
IRN_Ganj_Dareh_N,0.2

Total of 66.6 Anatolian Neo, 24.6 Steppe, 7.8 WHG and 1.0 CHG/Iran.
Click to expand...
Regio X said:
However, Angela (and also Ygorcs), importantly, I noticed that sources that get no score may still slightly interfere with results, which seems strange. Even worst, each run generates different results in R when using pen = 0.001. I still have to check if the order in the file also matters.
Well, not sure how to interpret it. The differences are not very big (we can have a notion of the contributions anyway), but they're there. This problem doesn't seem to happen with pen = 0. Perhaps a better approach would be working with averages from few runs when using pen = 0.001.
Click to expand...
I've tried it again with pen = 0.001 (for penalizing too distant admix), averaging few runs (which return slightly different results), to see how they compare with my previous single runs.(Used 5 sources for WHG and no Karelia.)

Lazio
TUR_Tepecik_Ciftlik_N,42.4
TUR_Barcin_N,27.5
Yamnaya_RUS_Samara,15.0
RUS_Khvalynsk_En,4.6
WHG,4.3
IRN_Ganj_Dareh_N,4.3
GEO_CHG,1.0
Levant_PPNB,0.6
MAR_EN,0.2

Total of 69.9% of Anatolia N, 19.7% Steppe, 5.3% CHG/Iran, 4.3% WHG, 0.6 Levant PPNB and 0.2% Morocco Early Neolithic.

East Sicily average
TUR_Tepecik_Ciftlik_N,53.5
TUR_Barcin_N,15.1
Yamnaya_RUS_Samara,13.2
IRN_Ganj_Dareh_N,5.8
RUS_Khvalynsk_En,3.8
WHG,2.9
Levant_PPNB,2.6
GEO_CHG,1.9
MAR_EN,1.0
CMR_Shum_Laka_8000BP,0.3

Total of 68.6% of Anatolia N, 17.0% Steppe, 7.6% CHG/Iran, 2.9% WHG, 2.6 Levant PPNB, 1.0% Morocco Early Neolithic and 0.3% SSA.

Bergamo average
TUR_Barcin_N,42.4
TUR_Tepecik_Ciftlik_N,23.8
Yamnaya_RUS_Samara,18.2
WHG,8.3
RUS_Khvalynsk_En,5.3
GEO_CHG,1.2
IRN_Ganj_Dareh_N,0.9

Total of 66.2% of Anatolia N, 23.4% Steppe, 8.3% WHG and 2.0% CHG/Iran.

Checking Veneto average in this model, out of curiosity (since it's my ancestry area)
TUR_Barcin_N,39.6
TUR_Tepecik_Ciftlik_N,24.0
Yamnaya_RUS_Samara,21.6
WHG,8.0
RUS_Khvalynsk_En,5.6
GEO_CHG,0.8
IRN_Ganj_Dareh_N,0.3

Total of 63.6% of Anatolia N, 27.2% Steppe, 8.0% WHG and 1.1% CHG/Iran.

I don't have my G25 coordinates, but judging by what I know on my own results in other calculators, I'd risk to say I would score not that far from Veneto average in Steppe, but (perhaps significantly) less WHG and (significantly) higher CHG/Iran.

Not sure it's highly accurate though. I mean, I'd expect more CHG in Veneto than in Bergamo, but I may be mistaken. I could try it also using Khvalynsk only and Yamnaya only, to see how they compare.

Anyway, the extra-Levant in Sicilians doesn't seem high, especially when Tepecik is also used as reference.
 
Regio_X: First off, your Anatolian Neolithic estimates are all within the ranges of Raveane et al 2019, which were lower bound 56% (SItaly1 sample) to 72% NItaly4 sample. So I think based on that published paper, you have done a darn good job. The Steppe numbers look consistent with what they reported, higher in the North in the South. Your finding the higher Iran_NEO in the South vs. the North, which was also documented in Raveane et al. 2019 and the other admixures, a little higher CHG in South vs. North, which they also found and you are picking up the Levant/North African signals in East Sicily. I would think the estimates for West Sicily not significantly different than East, a few % changes here and there, perhaps, but in substance not different.

Thanks again for your efforts.
 
Regio X said:
I've tried it again with pen = 0.001 (for penalizing too distant admix), averaging few runs (which return slightly different results), to see how they compare with my previous single runs.(Used 5 sources for WHG and no Karelia.)

Lazio
TUR_Tepecik_Ciftlik_N,42.4
TUR_Barcin_N,27.5
Yamnaya_RUS_Samara,15.0
RUS_Khvalynsk_En,4.6
WHG,4.3
IRN_Ganj_Dareh_N,4.3
GEO_CHG,1.0
Levant_PPNB,0.6
MAR_EN,0.2

Total of 69.9% of Anatolia N, 19.7% Steppe, 5.3% CHG/Iran, 4.3% WHG, 0.6 Levant PPNB and 0.2% Morocco Early Neolithic.

East Sicily average
TUR_Tepecik_Ciftlik_N,53.5
TUR_Barcin_N,15.1
Yamnaya_RUS_Samara,13.2
IRN_Ganj_Dareh_N,5.8
RUS_Khvalynsk_En,3.8
WHG,2.9
Levant_PPNB,2.6
GEO_CHG,1.9
MAR_EN,1.0
CMR_Shum_Laka_8000BP,0.3

Total of 68.6% of Anatolia N, 17.0% Steppe, 7.6% CHG/Iran, 2.9% WHG, 2.6 Levant PPNB, 1.0% Morocco Early Neolithic and 0.3% SSA.

Bergamo average
TUR_Barcin_N,42.4
TUR_Tepecik_Ciftlik_N,23.8
Yamnaya_RUS_Samara,18.2
WHG,8.3
RUS_Khvalynsk_En,5.3
GEO_CHG,1.2
IRN_Ganj_Dareh_N,0.9

Total of 66.2% of Anatolia N, 23.4% Steppe, 8.3% WHG and 2.0% CHG/Iran.

Checking Veneto average in this model, out of curiosity (since it's my ancestry area)
TUR_Barcin_N,39.6
TUR_Tepecik_Ciftlik_N,24.0
Yamnaya_RUS_Samara,21.6
WHG,8.0
RUS_Khvalynsk_En,5.6
GEO_CHG,0.8
IRN_Ganj_Dareh_N,0.3

Total of 63.6% of Anatolia N, 27.2% Steppe, 8.0% WHG and 1.1% CHG/Iran.

I don't have my G25 coordinates, but judging by what I know on my own results in other calculators, I'd risk to say I would score not that far from Veneto average in Steppe, but (perhaps significantly) less WHG and (significantly) higher CHG/Iran.

Not sure it's highly accurate though. I mean, I'd expect more CHG in Veneto than in Bergamo, but I may be mistaken. I could try it also using Khvalynsk only and Yamnaya only, to see how they compare.

Anyway, the extra-Levant in Sicilians doesn't seem high, especially when Tepecik is also used as reference.
Click to expand...

Nice work. Sorry I can't upvote.

Do you know if Davidski ever added the academic Emilia sample or if one is available?

Also, is that one Liguria sample available?

I know Tuscan ones are, so I suppose you'd have to do an average. I wish I had a pure Lunigiana one to use, but my relatives still won't test. Sometimes they act like those isolated HGs who think a picture will capture their soul. :)
 
Btw, about the studies which show the relationship between Italians and Bronze Age Hungary:

Here is one of my matches from mta:

17. Bronze Age Szolad Hungary
1000 BC - Genetic Distance: 9.718 - SZ1


Probably more Northern Italians or North Eastern Italians, get even better matches.
 
Palermo Trapani said:
Regio_X: First off, your Anatolian Neolithic estimates are all within the ranges of Raveane et al 2019, which were lower bound 56% (SItaly1 sample) to 72% NItaly4 sample. So I think based on that published paper, you have done a darn good job. The Steppe numbers look consistent with what they reported, higher in the North in the South. Your finding the higher Iran_NEO in the South vs. the North, which was also documented in Raveane et al. 2019 and the other admixures, a little higher CHG in South vs. North, which they also found and you are picking up the Levant/North African signals in East Sicily. I would think the estimates for West Sicily not significantly different than East, a few % changes here and there, perhaps, but in substance not different.

Thanks again for your efforts.
Click to expand...
Angela said:
Nice work. Sorry I can't upvote.

Do you know if Davidski ever added the academic Emilia sample or if one is available?

Also, is that one Liguria sample available?

I know Tuscan ones are, so I suppose you'd have to do an average. I wish I had a pure Lunigiana one to use, but my relatives still won't test. Sometimes they act like those isolated HGs who think a picture will capture their soul. :)
Click to expand...
Thanks. 100% amateur "experiments", obviously. :) The results are still highly dependent on the sources chosen.
I still have to check if it really makes sense using penalty in this specific case, but judging by Steppe ancestry for example, substantially lower and closer to what we'd expect, I thought it could be more realistic. WHG is possibly too high though. Don't know.

In Vahaduo (no penalty) I ran it using both sources for Anatolia and Steppe (you can check previous post), but curiously the model preferred Yamnaya entirely, while it distinguished Anatolians. If I add Yamnaya and/or Khvalynsk plus Karelia and penalty, it returns an supposed excess of Karelia, which makes me wonder if none of them is, say, the "right source". Anyway, it's an example how these models (and their interpretations) may be complicated, even for researchers.

@Palermo
I may be mistaken, but IIRC researchers were getting more Anatolian for the North than for the South, no? I really don't remember. If so, I wonder if it'd have something to do with Barcin N reference alone. If we consider these ABA-like contributions for South Europe, it should be tried different sources for Anatolian, given what we learned about Tepecik, for example.

@Angela
I cannot find any Emilian in G25, unfortunately. And last time I checked there was only one sample for Liguria, indeed.
I can try Tuscany average. In Vahaduo we already know how they score in this model (I posted earlier).
By the way, I couldn't find the Iceman in G25. Where is he?
As for your relatives, ah ah, yep, naturally we all here have an interest way above average in this field. Most people are not interested, I'd risk to say. Some of the folks that "donated" samples for me didn't even ask about their results. :unsure:
 
Angela said:
Btw, about the studies which show the relationship between Italians and Bronze Age Hungary:

Here is one of my matches from mta:

17. Bronze Age Szolad Hungary
1000 BC - Genetic Distance: 9.718 - SZ1


Probably more Northern Italians or North Eastern Italians, get even better matches.
Click to expand...

Here is R1's Bronze Age Italy map:

Mz8z8Wp.png
 
Regio X said:
Thanks. 100% amateur "experiments", obviously. :) The results are still highly dependent on the sources chosen.
I still have to check if it really makes sense using penalty in this specific case, but judging by Steppe ancestry for example, substantially lower and closer to what we'd expect, I thought it could be more realistic. WHG is possibly too high though. Don't know.

In Vahaduo (no penalty) I ran it using both sources for Anatolia and Steppe (you can check previous post), but curiously the model preferred Yamnaya entirely, while it distinguished Anatolians. If I add Yamnaya and/or Khvalynsk plus Karelia and penalty, it returns an supposed excess of Karelia, which makes me wonder if none of them is, say, the "right source". Anyway, it's an example how these models (and their interpretations) may be complicated, even for researchers.

@Palermo
I may be mistaken, but IIRC researchers were getting more Anatolian for the North than for the South, no? I really don't remember. If so, I wonder if it'd have something to do with Barcin N reference alone. If we consider these ABA-like contributions for South Europe, it should be tried different sources for Anatolian, given what we learned about Tepecik, for example.

@Angela
I cannot find any Emilian in G25, unfortunately. And last time I checked there was only one sample for Liguria, indeed.
I can try Tuscany average. In Vahaduo we already know how they score in this model (I posted earlier).
By the way, I couldn't find the Iceman in G25. Where is he?
As for your relatives, ah ah, yep, naturally we all here have an interest way above average in this field. Most people are not interested, I'd risk to say. Some of the folks that "donated" samples for me didn't even ask about their results. :unsure:
Click to expand...

I very much agree with the first.

As to the second, every sample in that paper was included in G25 except for the Emilian one. I have no idea why not.

Fwiw, I think you have precisely the right attitude toward all these experiments.
 
Jovialis said:
Here is R1's Bronze Age Italy map:

Mz8z8Wp.png
Click to expand...

Well, there you go. :)

Fwiw I'm at a 6 from R1. I think Stuvane is about a 4 and some other Northern Italians even closer. Probably my Tuscan part pulls me away a bit.

I've always thought the Italics might have come by way, ultimately, of Bronze Age Hungary.
 
Regio_X, yes, that is what Raveane et al 2019 documented. Here is the quote from the paper

"In the ultimate analysis, all the Italian clusters were characterized by relatively high amounts of Anatolian Neolithic (AN) contributions, ranging from 56% (SItaly1) to 72% (NItaly4), distributed along a north-south cline (Spearman  = 0.52, P < 0.05; Fig. 2, A to C, fig. S5A, and data file S3), with Sardinians showing values above 80%, as previously suggested (1, 21). A closer affinity of Northern Italian than Southern Italian clusters to AN was also supported by D-statistics (fig. S6A). The remaining ancestry was mainly assigned to WHG (western hunter-gatherer), CHG, and EHG. In particular, the first two components were more present in populations from the South of Italy (P < 0.05, Student’s t test), while the latter was higher in Northern Italian clusters (P < 0.05, Student’st test). These observations suggest the existence of different secondary source contributions to the two edges of the peninsula, with the north affected more by EHG-related populations and the south by
CHG-related groups. IN ancestry was detected in Europe only in Southern Italy (Fig. 2 and fig. S5A).
North-south differences across Italy"

So all your estimates are within the ranges that Raveane et al 2019 documented. So I think your modeling for Anatolian_Neolithic is well done.
 
I wonder which steppe samples work best for Hungarian Bronze Age and whether that might give us any clues about which steppe samples to use for Italians.
 
@Palermo
That's what I was saying. Researchers seem to have found higher Anatolian in North Italy, while these models I posted seem to indicate higher Anatolian in South Italy. Reason why I wondered if this is explained by the fact they used Barcin N only.

@Angela
Thanks. I was trying to check differences with penalty and with no penalty using even older sources such Anatolian Hunter-Gatherer, Kotias, EHG, WHG (5 individuals), Iran Meso, Natufian, Taforalt and Shum Laka (ancient SSA).

Here we have Bergamo, for example, scaled with pen = 0.001 (a single run seemed enough for this purpose)
TUR_Pinarbasi_HG,67.6
GEO_CHG,11.6
RUS_Karelia_HG,10.4
WHG,5.4
IRN_HotuIIIb_Meso,5

Oddly, no Natufian.

Now, scaled and pen = 0 (same as Vahaduo)
TUR_Pinarbasi_HG,64.6
RUS_Karelia_HG,17.8
GEO_CHG,16
WHG,1.4
Levant_Natufian,0.2

Too litle Natufian as well.

In this last one with no penalty, Iran disappears, and I would not expect such low WHG, since I used AHG rather than ENF, then I believe the first results (with penalty) are somewhat closer to what we'd expect, at least in this model specifically. Not perfect though. I think Bergamo should score some Natufian (?). :unsure:

ED: whatever the actual Steppe source was, it must have included EHG, some CHG and little ANF.
 
Angela said:
Well, I'm glad that you convinced yourself that Kilinc et al was correct.
Click to expand...

I never thought he wasn't. Levant_N always could have arrived as just a diluted admixtured in a more Levant-shifted population in my opinion, so the results of Kilinc et al. was never a problem to me. The millennia-long change from more Barcin-like to more Tepecik-like (which probably reflects the later Southern/Southwestern Anatolia_N makeup, not the Northern/Northwestern), which may be causing much of the higher Levantine and Caucasian affinities, still must have happened to explain what all these models are showing, and it must then be linked to demographic changes and new admixture events (for now the best explanations would be a heavy, gradual and very prolonged influence from Neolithic, Chalcolithic, Bronze Age and Iron Age Greece, some parts of the Balkans, Aegean islands and Anatolia, i.e. a millennia-long flow from the East Mediterranean to the Central Mediterranean, though I still don't doubt some part of it came from the Levant and North Africa).

As I already said repeatedly in dozens of posts, the Levant_N signal is an admixture, not a population, just like the CHG/Iran_N was not a population that arrived in Italy and other parts of Europe, but an admixture present in the gene pool of some population that was probably not CHG-like and Iran_N-like at all, but simply admixed. All those models, even the professional ones published in genetic papers, precisely because they actually indicate genetic relatedness, absolutely must not be interpreted literally as if the source samples represent the real and immediate ancestral groups.
 
Regio X said:
@Palermo
That's what I was saying. Researchers seem to have found higher Anatolian in North Italy, while these models I posted seem to indicate higher Anatolian in South Italy. Reason why I wondered if this is explained by the fact they used Barcin N only.
Click to expand...

It was certainly because of that. If we include all Anatolian samples, even Levant and Caucasus-shifted ones that probably reflect later Neolithic times and other regions of Anatolia outside western/northwestern Anatolia, there is no way you could say North Italy has higher Anatolian. Everything in these models, including the professional ones published in papers, relies completely on the assumptions made by those who defined the labels and chose the samples. That's why it always has to be understood as clues to the truth, not the literal truth to be taken as gospel (I think the ~46% Morocco_LN thing in Sicily in Fernandes et al. and the ~20% Lombard/Viking/Anglo-Saxon thing in medieval Italians in Antonio et al. should be proof enough for us that this issue also happens even to the best geneticists). Thus, if they assume "true/100%" Anatolia_N = Barcin, North Italy probably has the 2nd or 3rd closest ANF in all of Europe (after Sardinia of course).
 
Regio X said:
Here we have Bergamo, for example, scaled with pen = 0.001 (a single run seemed enough for this purpose)
TUR_Pinarbasi_HG,67.6
GEO_CHG,11.6
RUS_Karelia_HG,10.4
WHG,5.4
IRN_HotuIIIb_Meso,5

Oddly, no Natufian.

Now, scaled without pen = 0 (same as Vahaduo)
TUR_Pinarbasi_HG,64.6
RUS_Karelia_HG,17.8
GEO_CHG,16
WHG,1.4
Levant_Natufian,0.2
Click to expand...
Sicilian East, for comparison.

penalty (one run is enough for the purpose)
TUR_Pinarbasi_HG,57.2
GEO_CHG,17.4
Levant_Natufian,12.2
IRN_HotuIIIb_Meso,7.6
RUS_Karelia_HG,4.2
WHG,1.4

no penalty
TUR_Pinarbasi_HG,53
GEO_CHG,18.4
Levant_Natufian,12.2
IRN_HotuIIIb_Meso,9
RUS_Karelia_HG,7.4

No WHG in the last one. Unlikely. The little WHG in the first one could evidence some Anatolian source poorer in WHG. Tepecik? :) With such lower AHG, it's expected a lower Barcin as well.
The higher Karelia in Bergamo suggest a higher contribution of Steppe, which also means that part of this CHG in East Sicily is "extra-CHG" from another sources (such for example Tepecik, again).

@Ygorcs
Agreed. Indeed.
 
Since individual samples vary quite a bit, and averages are often a bit misleading if there is genetic structure within the population, I thought the best thing to understand the main trends in the genetic makeup of different areas and try to correlate them to historic and pre-historic demographic events was to model individuals and list them on a graph where you can really visualize the trends. I intend to do it for all European, Near Eastern and North African populations, but so far the graphs are complete for Italy, Greece, Balkans and Central-Eastern Europe.

These graphs also make it very visible what RegioX is also pointing out: North Italy is much more Barcin-like (with significant Tepecik/Kumtepe-like though), while the rest of Italy and especially Sicily is much more Tepecik/Kumtepe-like. The downside of using Tepecik/Kumtepe, though, is that the CHG/Iran_N flow pointed by genetic studies virtually disappears almost everywhere in Italy in the majority of individuals, but of course that flow was always more likely to have arrived there in heavily admixed form via mostly non-Caucasian and non-Iranian peoples of the East Mediterranean shores.

Also, some actual Levant-related admixture must be '"hidden" within the Tepecik/Kumtepe-like admixture, because Italian Jews appear here with just too low Levant_PPNB for my taste, and it's also very doubtful that Morocco_EN (Taforalt-like) arrived in individuals of some parts of South Italy and some Greek individuals in totally unadmixed form, not packed with a lot of Anatolia_L as well as Levant_N ancestry, too.
 
Ygorcs said:
Since individual samples vary quite a bit, and averages are often a bit misleading if there is genetic structure within the population, I thought the best thing to understand the main trends in the genetic makeup of different areas and try to correlate them to historic and pre-historic demographic events was to model individuals and list them on a graph where you can really visualize the trends. I intend to do it for all European, Near Eastern and North African populations, but so far the graphs are complete for Italy, Greece, Balkans and Central-Eastern Europe.

These graphs also make it very visible what RegioX is also pointing out: North Italy is much more Barcin-like (with significant Tepecik/Kumtepe-like though), while the rest of Italy and especially Sicily is much more Tepecik/Kumtepe-like. The downside of using Tepecik/Kumtepe, though, is that the CHG/Iran_N flow pointed by genetic studies virtually disappears almost everywhere in Italy in the majority of individuals, but of course that flow was always more likely to have arrived there in heavily admixed form via mostly non-Caucasian and non-Iranian peoples of the East Mediterranean shores.

Also, some actual Levant-related admixture must be '"hidden" within the Tepecik/Kumtepe-like admixture, because Italian Jews appear here with just too low Levant_PPNB for my taste, and it's also very doubtful that Morocco_EN (Taforalt-like) arrived in individuals of some parts of South Italy and some Greek individuals in totally unadmixed form, not packed with a lot of Anatolia_L as well as Levant_N ancestry, too.
Click to expand...
You have a point. I did use individuals as sources, but averages as target. Perhaps I could have used individuals as targets at least in Vahaduo. But I confess I didn't figure out how to run several targets at the same time in R. It's a problem that forces me to use averages.

As for Morocco, indeed. If we add this MAR EN/Shum Laka score in East Sicily to part of PPNB and some kind of Anatolian, we'd end up with a slightly higher North African contribution in East Sicily.
 
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