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Thread: Genetica d'Italia

  1. #21
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    And problems as well as many Spanish averages.

    Spanish_Asturias, Spanish_Barcelones, Spanish_Castilla_Y_Leon Spanish_Andalucia with more than 50% of Yamnaya!

    These results are not at all plausible.




  2. #22
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    Color-blindness in Calabria (Southern Italy): A north-south decreasing trend

    https://www.ncbi.nlm.nih.gov/pubmed/11534000

    "The three Calabrian provinces, with the exception of the ethnic minorities, show a decreasing trend in the frequency of CB from north to south (Fig. 2): CS, 6.23%; CZ, 4.65%; RC, 3.43%, (x2 4 32.5; P < 0.0005; df 2). The frequencies also differ significantly between CS and CZ (x2 4 9.44; P < 0.005; df 1) and CS and RC (x2 4 28.913; P < 0.0005; df 1); there is a significant difference betweenCZandRCprovinces(x2 4 5.435;P< 0.001; df 1).

    [...] Cosenza province also shows some other peculiarities regarding genetic markers.Tagarelli et al. (1991a) showed an opposite trend for glucose-6-phosphate dehydrogenase (G6PD) deficiency in respect to that of CB. The mean frequency of this deficiency has a maximal value on the Ionian coast (1.92%) and a minimal value on Tyrrhenian coast (0.93%), passing through the internal area (1.67%). This trend may be explained by historical and environmental factors. All other areas with higher G6PD deficiency frequencies are those areas where, during the VIIIth to Vth centuries BC, the Greeks (people who brought the more common G6PD genotype Mediterranean G6PD into Calabria) made their more populous settlements. These areas are also the same where malaria was endemic in the past (Tagarelli et al., 1997), and where another inherited disorder, the thalassemias (Brancati and Tagarelli, 1982), are present. Filosa et al. (1993) showed a linkage disequilibrium between the G6PD deficiency locus with that for CB within a Tyrrhenian sample from Cosenza province. Another trend was demonstrated by Tagarelli et al. (1991b) for the phosphoglucomutase 1 locus (PGM1). There was an increase in the trend from the Ionian coast towards that Tyrrhenian coast for the PGM1*1S allele,and a decrease in the same direction for the PGM1*2S allele. There was no trend for the Gm polymorphism (De Benedictis et al., 1986) as for other Calabrian polymorphisms (Piazza et al., 1989).
    […]
    Furthermore, the precarious economic status and the geographical peculiarities of the territory did not allow communication between the three Calabrian provinces until the beginning of this century. Until this period, there was only one road, the state road “S.S.19” which follows the ancient “Via Popilia,” built for military reasons following the occupation by the Romans. Improvement of the roads during the period following World War II allowed better communication between Cosenza, Catanzaro, and Reggio Calabria. But, when the towns along the Tyrrhenian and Ionian coasts improved their communications with other towns, those in the internal region were again isolated. "






    X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans
    (Moroccans)

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2315647/

    In Figure 1a, the first two axes accounted for 39% of the total variability (first axis: 25%, second axis: 14%). Thus, the Mediterranean populations are quite homogeneous. Equivalently to the results of the AMOVA analysis, the Moroccan population was considerably displaced in the first axis, and the Majorcans were placed in the opposite direction. In the second axis, the differentiation was less, but it is interesting that the Cosenza and Ibiza populations were located opposite to their neighbouring populations (i.e. Catanzaro and Valencia, respectively).



    (Cosenza is CSZ, Reggio is RCA)


    As we have commented above, relative high genetic distances between neighbouring populations were found between Cosenza and (1) Catanzaro and (2) Reggio di Calabria and between Ibiza and (1) Majorca and (2) Valencia. The results support the hypothesis that the genetic differentiation of the Ibiza and Cosenza populations is a result of their particular demographic histories [15, 16, 23]. The Moroccan population showed a high level of differentiation in relation to the other populations, even to those that are geographically close to Morocco (Western side of the Mediterranean basin).

    [...]

    Tagarelli et al [16] described the Calabria province as a collection of many "human genetic isolates". In contrast to Catanzaro and Reggio di Calabria, Cosenza did not suffer destructive telluric events that would have modified its population structure. So, the population heterogeneity inside Cosenza is more patent than in any of the other two populations. This is reflected by the heterogenic distribution of various genetic markers at the coast compared to the internal areas [16]. The results obtained with the 25 X-chromosome markers were in agreement with the previous studies. Cosenza showed not just a relatively high genetic differentiation compared to the populations from Catanzaro and Reggio di Calabria but also a certain displacement in relation to other Mediterranean populations.

    [...]

    Moreover, when a parametric multilocus association analysis was performed, significant values of associations were only observed in the Ibiza and Cosenza populations."


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  3. #23
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    Try this, using scale coordinates:

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    WHG:Baltic_LVA_HG,0.1292603,0.1004104,0.1802636,0. 1972329,0.1064236,0.0560919,0.0083574,0.0207106,0. 0524476,-0.0261394,-0.0046788,-0.0181151,0.0281434,-0.0053759,0.0355759,0.0480141,0.003072,0.0040856,-0.0059236,0.042325,0.0613526,0.0130531,-0.0262979,-0.1110549,0.0095949
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    African:ZAF_2000BP,-0.641583,0.0558543,0.0258957,0.034884,0.001231,-0.0030677,0.2680687,-0.2072223,0.0104307,0.0153683,0.008715,-0.0659913,-0.0216053,0.0064223,0.023751,-0.0201537,0.034204,0.294593,-0.09574,0.0060447,-0.033857,-0.0039157,0.003163,-0.0029323,-0.000399
    African:TZA_Luxmanda_3100BP,-0.303908,0.087336,-0.022627,-0.066861,0.005539,-0.035419,0.00141,-0.018692,0.111465,-0.075992,-0.006333,-0.005395,0.001635,0.001789,0.022122,-0.012198,0.020731,0.013682,0.000754,-0.004877,0.003244,-0.001978,-0.006655,0.00494,0.001078
    African:CMR_Shum_Laka_8000BP,-0.602693,0.055346,0.0148965,0.0263245,-0.0064625,0.00502,0.1243205,-0.099919,0.0138055,-0.007016,-0.00065,-0.0242785,-0.0203665,-0.0052295,0.0021035,-0.00179,0.0127125,0.017356,-0.0011945,-0.0040645,-0.003494,-0.000371,0.0016025,-0.0009035,-0.0020955
    Africaninka,-0.577083,0.0507765,-0.0003773,-0.0075098,-0.0053855,-0.0016735,-0.0176848,0.0204222,0.081145,-0.0969495,-0.02107,0.022742,-0.0383172,-0.0011698,0.0101452,-0.021347,0.0186125,-0.0094382,0.0241968,-0.0241678,0.002402,0.003308,0.001479,0.0009038,0.0 096995

    East_Eurasian:NPL_Chokhopani_2700BP,0.012521,-0.410274,-0.011691,-0.031331,0.017542,0.011435,0.00658,0.011999,0.0100 22,0.021139,-0.081194,-0.006444,0.010109,-0.004679,-0.011401,0,0.011213,-0.001267,-0.009302,0.009379,0.004991,0.029306,0.004314,0.003 615,0.031734
    East_Eurasian:RUS_Shamanka_N,0.0309599,-0.4147422,0.0950344,-0.0157947,-0.0868469,-0.0482203,0.0053815,0.010061,0.0147054,0.0125196,-0.0160603,-0.0018134,0.0035828,-0.0078032,-0.0046552,-0.0032088,-0.0025164,0.0005827,0.0064608,0.0178333,-0.0170449,-0.0059478,-0.0165151,-0.0032051,0.0046943
    East_Eurasian:Nganassan,0.0476917,-0.4066181,0.1557885,0.0023902,-0.1594452,-0.0882129,0.0285066,0.0433367,0.0310876,0.0128477, 0.1028569,0.0094115,-0.0040734,-0.0261619,-0.0219731,-0.0123307,-0.0010952,0.0134165,0.0268365,-0.0008505,0.0431363,-0.0118954,0.0336096,0.0003977,0.0135556
    East_Eurasian:Even,0.0421147,-0.4319387,0.1399117,-0.015827,-0.138795,-0.0819007,0.0287493,0.036691,0.0328603,0.0261203,0 .0556993,0.007843,-0.0146187,0.0089913,-0.0159697,-0.011049,0.0022597,0.0133867,0.0288267,0.0127147,0 .050411,-0.045298,0.0072717,0.0127327,0.0190403
    East_Eurasian:Evenk,0.0409763,-0.421783,0.1272153,-0.0185187,-0.1392053,-0.0880367,0.0288277,0.041229,0.0226337,0.0232047,0 .0638727,0.0085423,-0.013677,0.016744,0.0012667,0.0009723,-0.00226,0.00663,0.0125697,-0.007087,0.030654,-0.010799,0.015488,0.0096397,0.0043507
    East_Eurasian:TON_2500BP,0.009675,-0.415859,-0.0499685,-0.0499035,0.1481815,0.061495,0.00047,-0.0080765,-0.0243385,-0.017039,0.0531825,0.0086925,-0.004683,-0.0128675,0.0129615,0.006099,-0.0083445,0.0033575,0.012947,-0.0086295,0.0023705,-0.024854,-0.0077645,-0.013255,-0.0644255
    East_Eurasian:VUT_2900BP_all,0.0087267,-0.4211063,-0.0467627,-0.0628773,0.145668,0.0595897,-0.0067367,-0.017307,-0.0191573,-0.0241163,0.0579187,0.0049457,-0.007532,0.006514,0.0184127,0.0109607,-0.00565,0.0032517,0.010601,-0.0117553,0.0045337,-0.0247717,-0.0013967,-0.0151023,-0.062629
    For Italians you can remove East Eurasian and African, they always are at "noise" levels(I mean African is definitely real and has a pattern but is still very small), those are the results I get:


  4. #24
    Veteran Member Vid Flumina's Avatar
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    Quote Originally Posted by SharpFork View Post
    For Italians you can remove East Eurasian and African, they always are at "noise" levels(I mean African is definitely real and has a pattern but is still very small), those are the results I get:
    Wouldn't Berber capture it anyway? African admixture in Europe is generally mediated by Afro-Asiatic speakers from North Africa/Arabia
    Last edited by Vid Flumina; 03-19-2020 at 09:08 PM.

  5. #25
    Veteran Member Vid Flumina's Avatar
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    Target: VFlumina_scaled
    Distance: 3.0018% / 0.03001793
    55.0 ENF
    38.4 Steppe
    5.6 WHG
    1.0 W_Asian

    Large chunk of Pinarbasi_HG is eating some WHG, otherwise nothing unusual

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    Quote Originally Posted by Vid Flumina View Post
    Wouldn't Berber capture it anyway? African admixture in Europe is generally mediated by Afro-Asiatic speakers from North Africa/Arabia
    When you use Berber samples from Sardinia and Iberia(immigrants that don't seem admixed at all), Guanches and earlier mostly Iberomaurusian people you end up with North Africans having around 10% Subsaharan DNA, even when modelling using modern Bedouin samples and Copper Age Levantines.

    They definitely have recent SSA admixture through the slave trade and surprisingly not that little, so some of it spilling into Sicily is not unexpected, but it's still under 1%.

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    Quote Originally Posted by Vid Flumina View Post
    Target: VFlumina_scaled
    Distance: 3.0018% / 0.03001793
    55.0 ENF
    38.4 Steppe
    5.6 WHG
    1.0 W_Asian

    Large chunk of Pinarbasi_HG is eating some WHG, otherwise nothing unusual
    I don't think it is, if I remove it the average of all results stays the same, if anything maybe all my ENF samples outside Anatolia are eating some WHG but it's really minor(but I guess 1-3% is a lot when talking about WHG admixture in Italians...), I made sure everything was >95% Anatolia Barcin N, I added those to improve fit by including drift, but maybe it wasn't so necessary, try using only the Anatolian Neolithic sample.

    BTW where are you from?
    Last edited by SharpFork; 03-19-2020 at 11:03 PM.

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    Southern Italian 23andme results, I can add other (there are many others results on Reddit)

    Calabrian and apulian results

    Apulians :
    Spoiler!


    Cosentians :
    Spoiler!


    Other Calabrian provinces :

    Spoiler!

    "Allobroges vaillants ! Dans vos vertes campagnes,
    Accordez-moi toujours asile et sûreté,
    Car j'aime à respirer l'air pur de vos montagnes,
    Je suis la Liberté ! la Liberté !"


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    Target: Italian_Abruzzo
    Distance: 0.9745% / 0.00974532
    46.0 Early_European_Farmer:HUN_Koros_N
    28.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    15.0 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    7.0 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    3.0 Satsurblia_Cluster:GEO_CHG
    0.4 Western_Hunter_Gatherer:ITA_Villabruna

    Target: Italian_Aosta_Valley
    Distance: 1.4786% / 0.01478631
    47.2 Early_European_Farmer:HUN_Koros_N
    43.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    5.0 Western_Hunter_Gatherer:ITA_Villabruna
    3.8 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    0.4 Iberomaurusian:MAR_Taforalt

    Target: Italian_Apulia

    Distance: 1.1555% / 0.01155501
    46.8 Early_European_Farmer:HUN_Koros_N
    25.2 Steppe_Pastoralist:Yamnaya_RUS_Samara
    15.6 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    7.0 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    5.4 Satsurblia_Cluster:GEO_CHG

    Target: Italian_Basilicata
    Distance: 0.9674% / 0.00967410
    46.6 Early_European_Farmer:HUN_Koros_N
    25.0 Steppe_Pastoralist:Yamnaya_RUS_Samara
    15.0 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    7.4 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    5.2 Satsurblia_Cluster:GEO_CHG
    0.8 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an

    Target: Italian_Bergamo
    Distance: 1.6038% / 0.01603807
    58.2 Early_European_Farmer:HUN_Koros_N
    36.2 Steppe_Pastoralist:Yamnaya_RUS_Samara
    3.8 Western_Hunter_Gatherer:ITA_Villabruna
    1.0 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an
    0.4 Iberomaurusian:MAR_Taforalt
    0.2 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    0.2 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N

    Target: Italian_Calabria
    Distance: 1.1755% / 0.01175527
    47.2 Early_European_Farmer:HUN_Koros_N
    22.4 Steppe_Pastoralist:Yamnaya_RUS_Samara
    15.2 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    7.4 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    6.4 Satsurblia_Cluster:GEO_CHG
    1.4 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an

    Target: Italian_Campania

    Distance: 0.9248% / 0.00924762
    44.4 Early_European_Farmer:HUN_Koros_N
    24.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    18.4 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    8.4 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    4.2 Satsurblia_Cluster:GEO_CHG

    Target: Italian_Lazio
    Distance: 1.0896% / 0.01089634
    47.0 Early_European_Farmer:HUN_Koros_N
    29.0 Steppe_Pastoralist:Yamnaya_RUS_Samara
    14.2 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    7.8 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    2.0 Western_Hunter_Gatherer:ITA_Villabruna

    Target: Italian_Liguria
    Distance: 2.2072% / 0.02207237
    52.6 Early_European_Farmer:HUN_Koros_N
    33.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    3.8 Western_Hunter_Gatherer:ITA_Villabruna
    3.8 Satsurblia_Cluster:GEO_CHG
    3.6 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    1.4 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an
    1.2 Iberomaurusian:MAR_Taforalt

    Target: Italian_Lombardy
    Distance: 2.0221% / 0.02022122
    57.2 Early_European_Farmer:HUN_Koros_N
    36.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    3.2 Western_Hunter_Gatherer:ITA_Villabruna
    2.0 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    1.0 Iberomaurusian:MAR_Taforalt

    Target: Italian_Marche
    Distance: 1.3005% / 0.01300489
    46.6 Early_European_Farmer:HUN_Koros_N
    31.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    13.6 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    3.6 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    3.2 Satsurblia_Cluster:GEO_CHG
    1.4 Western_Hunter_Gatherer:ITA_Villabruna

    Target: Italian_Molise
    Distance: 1.1317% / 0.01131699
    49.6 Early_European_Farmer:HUN_Koros_N
    28.4 Steppe_Pastoralist:Yamnaya_RUS_Samara
    10.6 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    6.8 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    3.6 Satsurblia_Cluster:GEO_CHG
    1.0 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an

    Target: Italian_Northeast
    Distance: 1.3551% / 0.01355140
    52.0 Early_European_Farmer:HUN_Koros_N
    41.0 Steppe_Pastoralist:Yamnaya_RUS_Samara
    3.8 Western_Hunter_Gatherer:ITA_Villabruna
    2.2 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    1.0 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an

    Target: Italian_Piedmont

    Distance: 1.3031% / 0.01303096
    52.2 Early_European_Farmer:HUN_Koros_N
    36.8 Steppe_Pastoralist:Yamnaya_RUS_Samara
    6.4 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    2.8 Western_Hunter_Gatherer:ITA_Villabruna
    1.4 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    0.2 Iberomaurusian:MAR_Taforalt
    0.2 Satsurblia_Cluster:GEO_CHG

    Target: Italian_Trentino-Alto-Adige
    Distance: 1.3968% / 0.01396845
    54.8 Early_European_Farmer:HUN_Koros_N
    37.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    5.2 Western_Hunter_Gatherer:ITA_Villabruna
    1.2 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    1.2 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an

    Target: Italian_Tuscany
    Distance: 1.0787% / 0.01078707
    51.2 Early_European_Farmer:HUN_Koros_N
    34.2 Steppe_Pastoralist:Yamnaya_RUS_Samara
    8.0 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    2.4 Western_Hunter_Gatherer:ITA_Villabruna
    2.4 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    1.6 Satsurblia_Cluster:GEO_CHG
    0.2 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an

    Target: Italian_Umbria
    Distance: 0.9175% / 0.00917538
    50.6 Early_European_Farmer:HUN_Koros_N
    31.2 Steppe_Pastoralist:Yamnaya_RUS_Samara
    9.0 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    4.4 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    2.6 Satsurblia_Cluster:GEO_CHG
    1.4 Western_Hunter_Gatherer:ITA_Villabruna
    0.8 Iberomaurusian:MAR_Taforalt

    Target: Italian_Veneto
    Distance: 1.2075% / 0.01207462
    53.2 Early_European_Farmer:HUN_Koros_N
    38.2 Steppe_Pastoralist:Yamnaya_RUS_Samara
    4.8 Western_Hunter_Gatherer:ITA_Villabruna
    3.8 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC

    Target: Sardinian
    Distance: 2.1235% / 0.02123492
    80.6 Early_European_Farmer:HUN_Koros_N
    10.4 Western_Hunter_Gatherer:ITA_Villabruna
    3.4 Iberomaurusian:MAR_Taforalt
    3.4 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    1.2 Steppe_Pastoralist:Yamnaya_RUS_Samara
    1.0 Ancient_Siberia:RUS_Tyumen_HG

    Target: Sicilian_East
    Distance: 1.5820% / 0.01582009
    45.2 Early_European_Farmer:HUN_Koros_N
    23.6 Steppe_Pastoralist:Yamnaya_RUS_Samara
    17.0 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    6.2 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    5.8 Satsurblia_Cluster:GEO_CHG
    1.8 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an
    0.4 Western_Hunter_Gatherer:ITA_Villabruna

    Target: Sicilian_West
    Distance: 1.5223% / 0.01522296
    42.8 Early_European_Farmer:HUN_Koros_N
    23.0 Steppe_Pastoralist:Yamnaya_RUS_Samara
    17.2 Pre-Pottery_Neolithic_B_Levant:Levant_PPNC
    8.2 Iran_Pastoral_Neolithic:IRN_Ganj_Dareh_N
    3.2 Western_Hunter_Gatherer:ITA_Villabruna
    3.2 Satsurblia_Cluster:GEO_CHG
    1.8 Africa_Pastoral_Neolithic:KEN_Pastoral_N_Elmenteit an
    0.6 Iberomaurusian:MAR_Taforalt

  10. #30
    Veteran Member Vid Flumina's Avatar
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    Quote Originally Posted by SharpFork View Post
    I don't think it is, if I remove it the average of all results stays the same, if anything maybe all my ENF samples outside Anatolia are eating some WHG but it's really minor(but I guess 1-3% is a lot when talking about WHG admixture in Italians...), I made sure everything was >95% Anatolia Barcin N, I added those to improve fit by including drift, but maybe it wasn't so necessary, try using only the Anatolian Neolithic sample.

    BTW where are you from?

    I must be the only one scoring it in significant amounts then, if I remove it WHG goes back up:

    Target: VFlumina_scaled
    Distance: 3.1328% / 0.03132803
    53.6 ENF
    38.2 Steppe
    8.0 WHG
    0.2 East_Eurasian


    I'm mostly from SW Piedmont and Eastern Veneto

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