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Thread: Similarity rate with different ancient genomes

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    Attachment 10863Cranial deformed Bavarian represent!

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    Quote Originally Posted by Ygorcs View Post
    Intuitively, some of these comparative results look so weird. I mean, less similarity with Minoans from the BA Aegean (18) than with Paleolithic Ust' Ishim, who barely contributed anything to the modern European population? Ust'Ishim looks much closer than Mal'ta (3), which is demonstrably connected to the ANE that does exist in most modern Europeans via the steppe ancestry. There are other strange results like that. Or are each of these groups (e.g. Paleolithic before glaciation, Northwestern Europe, etc.) to be judged on their own, that is, their results would not be comparable with those included in another group, only with those under the same label?
    Yeah that took me by surprise.

    To anyone: what does it even do? Does it compare calculator results with these samples and from there tries to predict your ancestry based on them like those gedmatch oracles?
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    Quote Originally Posted by Joey37 View Post
    Attachment 10863Cranial deformed Bavarian represent!
    Joey, it's not visible. Usually I make an imgur image of it and then post.

    Or if not, do you have a site?


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    Quote Originally Posted by Jovialis View Post
    I'm not Greek, my family is from the region of Bari. Though southern Italy was influenced by Greek settlement. At any rate, in the linked thread, I pointed out that the proposed ABA expansion into Southern Italy was very similar to that of the Mycenaean samples, as the K20 ADMIXTURE analysis chart shows. Not that the ABA in the early to middle bronze age were Mycenaean; I think the chart shows they were similar to each other genetically nonetheless.

    Note: I've merged some posts from another thread, about this calculator, into Carlos' thread.
    Yes, it makes sense! These Myceneans were close to South Italy. I am closer to Abruzzo genetically and I have only 65-66% genetic similarity with them. I have 72% with the medieval Greek str 300 sample. I would be interested to see your gedmatch results. Could you post eurogenes k15 and dodecad k12b?

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    Quote Originally Posted by davef View Post
    Yeah that took me by surprise.

    To anyone: what does it even do? Does it compare calculator results with these samples and from there tries to predict your ancestry based on them like those gedmatch oracles?
    I found out earlier that it uses your eurogenes "k36" results so it's a magic 8 ball. And I'm sure south Italians are in reality significantly more than 67 percent Mycenaean like so this calculator underestimates that affinity quite a bit

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    Quote Originally Posted by davef View Post
    I found out earlier that it uses your eurogenes "k36" results so it's a magic 8 ball. And I'm sure south Italians are in reality significantly more than 67 percent Mycenaean like so this calculator underestimates that affinity quite a bit
    These are general indicators and are fun to play around.
    Hopefully, as time goes on, and new data is collected, imputation will improve.

    check this one out:
    my genes leaving a mark :)

    Era of Empires (about 1700 to 2000 years ago)


    1700 years ago (Roman Era)


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    Quote Originally Posted by Salento View Post
    These are general indicators and are fun to play around.
    Hopefully, as time goes on, and new data is collected, imputation will improve.

    check this one out:
    my genes leaving a mark :)

    Era of Empires (about 1700 to 2000 years ago)


    1700 years ago (Roman Era)

    Hi Salento.
    From 1700 years ago I believe that both of us must have many skeletons of cousins in common. His cousins invaded the Iberian peninsula. What evil!!!! LOL. Some skeletons of our cousins have already been found, others are still waiting to be found. I hope none of them will be like Mumm-Ra of ThunderCats and will say: Ancient spirits of evil. Transform that decadent form into Mumm-Ra. Remember: The ancient spirits of evil often provide to Mumm-Ra with a source of knowledge of ancient or magical events. I hava afraid of the voodoo of these ancient mummies and skeletons. LOL.
    There is a superstition involving Ötzi. According to the belief, there is believed to be a curse around the quinque-milenar mummy who would be angry with people who disturbed her in her rest. So far 7 of the people who came in contact with the frozen corpse had strange accidents that resulted in death. Among them are scientists who studied the body and the discoverer of Ötzi, Helmut Simon, who died ironically in a strong snowstorm and died in the same position as Õtzi, while walking through Austria in a region 100 km from the original site. OMG!!!!

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    Do not be afraid of the Dead, be afraid of the Living.

    yep :) LOL

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    Mine:

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    Quote Originally Posted by xri34 View Post
    Yes, it makes sense! These Myceneans were close to South Italy. I am closer to Abruzzo genetically and I have only 65-66% genetic similarity with them. I have 72% with the medieval Greek str 300 sample. I would be interested to see your gedmatch results. Could you post eurogenes k15 and dodecad k12b?
    Eurogenes V2 K15 Oracle
    # Population (source) Distance
    1 Central_Greek 4.94


    Eurogenes V2 K15 Oracle-4
    Using 1 population approximation:
    1 Central_Greek @ 5.529039


    Dodecad K12b Oracle
    # Population (source) Distance
    1 C_Italian (Dodecad) 6.78


    Dodecad K12b Oracle-4
    Using 1 population approximation:
    1 C_Italian_Dodecad @ 7.297379

    If there was a population from my specific area in these calculators, it would be the closest match. Pugliese are between Central Italy, Central Greece, and other Southern Italians. They're all pretty close to each other nonetheless.

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    Quote Originally Posted by Jovialis View Post
    Eurogenes V2 K15 Oracle
    # Population (source) Distance
    1 Central_Greek 4.94


    Eurogenes V2 K15 Oracle-4
    Using 1 population approximation:
    1 Central_Greek @ 5.529039


    Dodecad K12b Oracle
    # Population (source) Distance
    1 C_Italian (Dodecad) 6.78


    Dodecad K12b Oracle-4
    Using 1 population approximation:
    1 C_Italian_Dodecad @ 7.297379

    If there was a population from my specific area in these calculators, it would be the closest match. Pugliese are between Central Italy, Central Greece, and other Southern Italians. They're all pretty close to each other nonetheless.
    We are close. I have similar distances from those populations and in general Greek and south-central/south Italian populations. Our difference must be that I have 10.5 and 12.5 distance from Bulgaria on these calculators while you must have over 15.

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    Quote Originally Posted by Jovialis View Post
    Eurogenes V2 K15 Oracle
    # Population (source) Distance
    1 Central_Greek 4.94
    Eurogenes V2 K15 Oracle-4
    Using 1 population approximation:
    1 Central_Greek @ 5.529039
    Dodecad K12b Oracle
    # Population (source) Distance
    1 C_Italian (Dodecad) 6.78
    Dodecad K12b Oracle-4
    Using 1 population approximation:
    1 C_Italian_Dodecad @ 7.297379
    If there was a population from my specific area in these calculators, it would be the closest match. Pugliese are between Central Italy, Central Greece, and other Southern Italians. They're all pretty close to each other nonetheless.
    Some of these calculators have no idea who we are.

    Eur. V2 K15, 3 RawData, 3 different Top populations.
    23, Anc, ...

    Last edited by Salento; 04-04-19 at 06:08. Reason: off topic

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    Quote Originally Posted by Duarte View Post
    Dear friend Carlos.
    It seems that the Roman soldier was really Iberian. See these two posts extracted from BLOG linked below:
    http://eurogenes.blogspot.com/2018/0...eriod.html?m=1
    POST 1:
    ---Germany_Roman:FN_2
    [1] "1. CLOSEST SINGLE ITEM DISTANCE”
    Spanish_Baleares / Spanish_Cataluna
    2.403037 / 2.657032
    Spanish_Murcia / Spanish_Cantabria
    2.766374 / 2.908718
    Spanish_Andalucia / Spanish_Castilla_La_Mancha
    2.940393 / 3.080841
    Hungary_BA / Spanish_Aragon
    3.084510 / 3.128334

    POST 2:
    The Roman soldier was probably from Aquitaine in South France/North Spain. He clusters with modern Basque & south French.
    Nice. :)

    But not sure he was from France or Spain. Maybe. However, his autosomal makeup resembles "modern" (!) North Spanish's and South French's. I'm not sure North Italians were the same those days, considering there were movements in Europe since 300 AD. We don't know either how people of Raeti stock looked like, for example, and apparently there were Raetian-speaking people in Northeastern Italy till ~3rd century AD. Raeti were related to Etruscans supposedly, and if that famous and controversial PCA is correct, Etruscans wouldn't be that different from modern Iberians.


    Indeed, the Roman Soldier belonged to Y haplogroup G-L42, typical of the Alps and surroundings. Switzerland, North Italy, SW Germany, Tyrol...
    FN2 shares a common patrilineal ancestor from 500 BC with a Swedish, a German and a South Italian.
    https://www.yfull.com/tree/G-Z40854/
    Last edited by Regio X; 04-04-19 at 21:07.

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    Quote Originally Posted by Regio X View Post
    Nice. :)

    But not sure he was from French or Spain. Maybe. However, his autosomal makeup resembles "modern" (!) North Spanish's and South French's. I'm not sure North Italians were the same those days, since there were movements in Europe since 300 AD. We don't know either how people of Raeti stock looked like, for example, and apparently there were Raetian-speaking people in Northeastern Italy till ~3rd century AD. Raeti were related to Etruscans supposedly, and if that famous and controversial PCA is correct, Etruscans wouldn't be that different from modern Iberians.


    Indeed, the Roman Soldier belonged to Y haplogroup G-L42, typical from the Alps and surroundings. Switzerland, North Italy, SW Germany, Tyrol... FN2 shares a common ancestor from 500 BC with a Swedish, a German and a South Italian.
    https://www.yfull.com/tree/G-Z40854/
    Yes, I was thinking that too. Perhaps he was from here:


    At any rate, my similarity to him is 67%. My only higher one is that "Bavarian" woman from 500 AD. at 70%. Apparently, she was Southern European, but not of the particularly "eastern" variety. I don't know. Maybe northern Balkans like?

    @Jovialis,

    I rechecked my husband's results, and he ties you for similarity to Myceneans: 76. It's for the second one, however. So ungrateful. His response was, "I hope it's not someone like that jerk Achilles or Agamemnon and his brother. Ulysees would be ok." :)

    I know what he means, but they had a very advanced civilization, and dominated their era. I too could do without all that militarism and glory seeking, however.

    He wants to be like Plato and Aristotle and Pericles, at any rate an Athenian, not a Spartan. Let's see if they're much different. :)

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    Quote Originally Posted by Angela View Post
    Yes, I was thinking that too. Perhaps he was from here:


    At any rate, my similarity to him is 67%. My only higher one is that "Bavarian" woman from 500 AD. at 70%. Apparently, she was Southern European, but not of the particularly "eastern" variety. I don't know. Maybe northern Balkans like?

    @Jovialis,

    I rechecked my husband's results, and he ties you for similarity to Myceneans: 76. It's for the second one, however. So ungrateful. His response was, "I hope it's not someone like that jerk Achilles or Agamemnon and his brother. Ulysees would be ok." :) I sort of agree.

    He wants to be like Plato and Aristotle and Pericles. Let's see if they're much different. :)
    Nice! It really is fascinating! They should re-make Troy starring us

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    Quote Originally Posted by Jovialis View Post
    Nice! It really is fascinating! They should re-make Troy starring us
    Can I ask which Raw-Data you ran? I don’t remember what I used, if I have it, I’ll run it again.

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    Quote Originally Posted by Salento View Post
    Can I ask which Raw-Data you ran? I don’t remember what I used, if I have it, I’ll run it again.
    It was the one that combines 23andme, AncestryDNA, Geno 2.0, and LivingDNA.

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    Fwiw, the only data I have for my husband is 23andme. He has both Campanian ( Benevento) and Calabrian (province of Regio) ancestry.

    I'm curious to see Sicilian results.

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    Quote Originally Posted by Jovialis View Post
    It was the one that combines 23andme, AncestryDNA, Geno 2.0, and LivingDNA.
    Thanks, I have to make a new one. :)

    also, in the South of Puglia the colonists were Spartans, but most of them got massacred by the Messapi, and to a degree in Calabria too.

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    Quote Originally Posted by Angela View Post
    Fwiw, the only data I have for my husband is 23andme. He has both Campanian ( Benevento) and Calabrian (province of Regio) ancestry.

    I'm curious to see Sicilian results.
    I want to emphasize this is for fun as far as I'm concerned, especially because the algorithm is based on Eurogenes calculators, which in my opinion are skewed toward Eastern and North Eastern Europeans.

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    Quote Originally Posted by Angela View Post
    Fwiw, the only data I have for my husband is 23andme. He has both Campanian ( Benevento) and Calabrian (province of Regio) ancestry.

    I'm curious to see Sicilian results.
    It is V3 of 23andme I recall? I remembered it tested for over a million SNPs with that version. The combined version from the other raw data files I used also brings it to over a million SNPs too.

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    Quote Originally Posted by Jovialis View Post
    It is V3 of 23andme I recall? I remembered it tested for over a million SNPs with that version. The combined version from the other raw data files I used also brings it to over a million SNPs too.
    That's right. I have both that and the newer one. Not a lot of difference, but some.

    I trust the 23andme results.

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    Quote Originally Posted by Angela View Post
    Yes, I was thinking that too. Perhaps he was from here:


    At any rate, my similarity to him is 67%. My only higher one is that "Bavarian" woman from 500 AD. at 70%. Apparently, she was Southern European, but not of the particularly "eastern" variety. I don't know. Maybe northern Balkans like?

    @Jovialis,

    I rechecked my husband's results, and he ties you for similarity to Myceneans: 76. It's for the second one, however. So ungrateful. His response was, "I hope it's not someone like that jerk Achilles or Agamemnon and his brother. Ulysees would be ok." :)

    I know what he means, but they had a very advanced civilization, and dominated their era. I too could do without all that militarism and glory seeking, however.

    He wants to be like Plato and Aristotle and Pericles, at any rate an Athenian, not a Spartan. Let's see if they're much different. :)
    Europe experienced a profound cultural transformation between Late Antiquity and the Middle Ages that laid the foundations of the modern political, social, and religious landscape. During this period, colloquially known as the “Migration Period,” the Roman Empire gradually dissolved, with 5th and 6th century historiographers and contemporary witnesses describing the formation and migration of numerous Germanic peoples, such as the Goths, Alamanni, Gepids, and Longobards. However, the genetic and social composition of groups involved and the exact nature of these “migrations” are unclear and have been a subject of substantial historical and archaeological debate (1).
    In the mid 6th century AD, the historiographer Jordanes and the poet and hagiographer Venantius Fortunatus provide the first mention of a group known as the Baiuvarii that resided in modern day Bavaria. It is likely that this group had already started to form in the 5th century AD, and that it emanated from a combination of the romanized local population of the border province of the former Roman Empire and immigrants from north of the Danube (2). While the Baiuvarii are less well known than some other contemporary groups, an interesting archaeological feature in Bavaria from this period is the presence of skeletons with artificially deformed or elongated skulls (Fig. 1A).

    Artificial cranial deformation (ACD), which is only possible during early childhood, is a deliberate and permanent shaping of the head performed with great effort. In some societies reshaping the human skull has been seen as an ideal of beauty, while it may also have acted as a marker of status, nobility, or affiliation to a certain class or group.


    Fig. 2.Procrustes-transformed PCA of ancient samples using pseudohaploid calls based on off-target reads using an imputed POPRES modern reference dataset. Blue, green, and red male or female symbols are ancient Bavarian individuals with normal, intermediate, and elongated skulls, respectively. Orange circles are Anglo-Saxon era individuals. Large circles are medians for regions, dots are individuals. CE, central Europe; EE, eastern Europe; NE, northern Europe; NEE, northeastern Europe; NEW, northwestern Europe; SE, southern Europe; SEE, southeast Europe; WE, western Europe. Percentage of variation explained by PCs 1 and 2 for modern populations only is 0.25% and 0.15%.


    Fig. 3.

    Supervised model-based clustering ADMIXTURE analysis for ancient samples based on phased haplotypes for individual 1,000 bp loci from the 5-Mb neutralome. Analysis is based on the best of 100 runs for K = 8, but NC_EUR is the ancestry summed across 1000 Genomes CEU, 1000 Genomes GBR, and GoNL populations (i.e., it represents a northern/central European ancestry). Blue, green, and red male or female symbols are ancient Bavarian individuals with normal, intermediate, and elongated skulls, respectively.

    A population assignment analysis (PAA) at the level of individual modern nation states suggested greatest genetic similarity of these normal-skulled individuals with modern Germans, consistent with their sampling location (Fig. 4 A and B and SI Appendix, Table S35). The only exceptions to this general pattern of northern/central European ancestry were the two women, STR_300 and STR_502, which were of a more southern ancestry associated with present day Greece and Turkey, respectively (SI Appendix, Fig. S29).



    Fig. 4.

    Geographic distribution of population assignment analysis (PAA) results on pseudohaploid calls from off-target reads summed across individuals for (A) all Bavarian males, (B) all Bavarian females with normal skulls, (C) all Bavarian females
    with elongated skulls, and (D) KER_1 and VIM_2.

    A much more diverse ancestry was observed among the females with elongated skulls, as demonstrated by a significantly greater group-based FIS (SI Appendix, Fig. S35). All these females had varying amounts of genetic ancestry found today predominantly in southern European countries [as seen by the varying amounts of ancestry inferred by model-based clustering that is representative of a sample from modern Tuscany, Italy (TSI), Fig. 3], and while the majority of samples were found to be closest to modern southeastern Europeans (Bulgaria and Romania, Fig. 4C), at least one individual, AED_1108, appeared to possess ∼20% East Asian ancestry (Fig. 3), which was also evident from the high number of haplotypes within the 5-Mb neutralome that were private to modern East Asian 1000 Genomes individuals (EAS), while also demonstrating an overall ancestry profile consistent with Central Asian populations (SI Appendix, Fig. S33). No modern European individual from the Simons Genome Diversity Panel (SGDP) (11) showed any evidence of significant East Asian ancestry except one Hungarian individual with less than 5%. A higher amount of East Asian ancestry was inferred for AED_1108 than all modern Caucasus and Middle Eastern individuals, and 28 of 33 South Asian individuals.

    See full article in the link below:
    https://www.pnas.org/content/115/13/3494

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    Quote Originally Posted by Duarte View Post
    Europe experienced a profound cultural transformation between Late Antiquity and the Middle Ages that laid the foundations of the modern political, social, and religious landscape. During this period, colloquially known as the “Migration Period,” the Roman Empire gradually dissolved, with 5th and 6th century historiographers and contemporary witnesses describing the formation and migration of numerous Germanic peoples, such as the Goths, Alamanni, Gepids, and Longobards. However, the genetic and social composition of groups involved and the exact nature of these “migrations” are unclear and have been a subject of substantial historical and archaeological debate (1).
    In the mid 6th century AD, the historiographer Jordanes and the poet and hagiographer Venantius Fortunatus provide the first mention of a group known as the Baiuvarii that resided in modern day Bavaria. It is likely that this group had already started to form in the 5th century AD, and that it emanated from a combination of the romanized local population of the border province of the former Roman Empire and immigrants from north of the Danube (2). While the Baiuvarii are less well known than some other contemporary groups, an interesting archaeological feature in Bavaria from this period is the presence of skeletons with artificially deformed or elongated skulls (Fig. 1A).

    Artificial cranial deformation (ACD), which is only possible during early childhood, is a deliberate and permanent shaping of the head performed with great effort. In some societies reshaping the human skull has been seen as an ideal of beauty, while it may also have acted as a marker of status, nobility, or affiliation to a certain class or group.


    Fig. 2.Procrustes-transformed PCA of ancient samples using pseudohaploid calls based on off-target reads using an imputed POPRES modern reference dataset. Blue, green, and red male or female symbols are ancient Bavarian individuals with normal, intermediate, and elongated skulls, respectively. Orange circles are Anglo-Saxon era individuals. Large circles are medians for regions, dots are individuals. CE, central Europe; EE, eastern Europe; NE, northern Europe; NEE, northeastern Europe; NEW, northwestern Europe; SE, southern Europe; SEE, southeast Europe; WE, western Europe. Percentage of variation explained by PCs 1 and 2 for modern populations only is 0.25% and 0.15%.


    Fig. 3.

    Supervised model-based clustering ADMIXTURE analysis for ancient samples based on phased haplotypes for individual 1,000 bp loci from the 5-Mb neutralome. Analysis is based on the best of 100 runs for K = 8, but NC_EUR is the ancestry summed across 1000 Genomes CEU, 1000 Genomes GBR, and GoNL populations (i.e., it represents a northern/central European ancestry). Blue, green, and red male or female symbols are ancient Bavarian individuals with normal, intermediate, and elongated skulls, respectively.

    A population assignment analysis (PAA) at the level of individual modern nation states suggested greatest genetic similarity of these normal-skulled individuals with modern Germans, consistent with their sampling location (Fig. 4 A and B and SI Appendix, Table S35). The only exceptions to this general pattern of northern/central European ancestry were the two women, STR_300 and STR_502, which were of a more southern ancestry associated with present day Greece and Turkey, respectively (SI Appendix, Fig. S29).



    Fig. 4.

    Geographic distribution of population assignment analysis (PAA) results on pseudohaploid calls from off-target reads summed across individuals for (A) all Bavarian males, (B) all Bavarian females with normal skulls, (C) all Bavarian females
    with elongated skulls, and (D) KER_1 and VIM_2.

    A much more diverse ancestry was observed among the females with elongated skulls, as demonstrated by a significantly greater group-based FIS (SI Appendix, Fig. S35). All these females had varying amounts of genetic ancestry found today predominantly in southern European countries [as seen by the varying amounts of ancestry inferred by model-based clustering that is representative of a sample from modern Tuscany, Italy (TSI), Fig. 3], and while the majority of samples were found to be closest to modern southeastern Europeans (Bulgaria and Romania, Fig. 4C), at least one individual, AED_1108, appeared to possess ∼20% East Asian ancestry (Fig. 3), which was also evident from the high number of haplotypes within the 5-Mb neutralome that were private to modern East Asian 1000 Genomes individuals (EAS), while also demonstrating an overall ancestry profile consistent with Central Asian populations (SI Appendix, Fig. S33). No modern European individual from the Simons Genome Diversity Panel (SGDP) (11) showed any evidence of significant East Asian ancestry except one Hungarian individual with less than 5%. A higher amount of East Asian ancestry was inferred for AED_1108 than all modern Caucasus and Middle Eastern individuals, and 28 of 33 South Asian individuals.

    See full article in the link below:
    https://www.pnas.org/content/115/13/3494
    Thanks so much, Duarte. :) I kept meaning to look it up but didn't get to it.

    My 70 sample is the NW sample. Seems about 2/3 IBS Iberian and 1/3 Tuscan in make up. Makes sense. In real life add about 20 points more of Tuscan and you get me. :)

    Actually, in calculators where there are no northern Italian or Tuscan samples I come out Bulgarian. :)

    Poor women. What torture.

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