The genetic origin of Daunians

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31-12-21, 17:51
Salento

ORD010 … about 1078 - 1156 AD, around the time of the County of Apulia and Calabria:

“later the Duchy of Apulia and Calabria, was a Norman state founded by William of Hauteville in 1042 in the territories of Gargano, Capitanata, Apulia, Vulture, and most of Campania. It became a duchy when Robert Guiscard was raised to the rank of duke by Pope Nicholas II in 1059 …”

… “Bohemond of Taranto, son of Robert Guiscard, born in Calabria, in 1098 AD became Bohemond I of Antioch, he was the most experienced military leader of the First Crusade” ….

… speculating :) maybe ORD010 or one of the Parents originated in Antioch, …

https://i.imgur.com/k00nh8o.jpg

https://en.m.wikipedia.org/wiki/Coun...a_and_Calabria

https://en.m.wikipedia.org/wiki/Bohemond_I_of_Antioch
31-12-21, 18:12
Jovialis

Quote:

Originally Posted by Salento

ORD010 … about 1078 - 1156 AD, around the time of the County of Apulia and Calabria:

“later the Duchy of Apulia and Calabria, was a Norman state founded by William of Hauteville in 1042 in the territories of Gargano, Capitanata, Apulia, Vulture, and most of Campania. It became a duchy when Robert Guiscard was raised to the rank of duke by Pope Nicholas II in 1059 …”

… “Bohemond of Taranto, son of Robert Guiscard, born in Calabria, later became Bohemond I of Antioch, was the most experienced military leader of the First Crusade” ….

… speculating :) maybe ORD010 or one of the Parents originated in Antioch, …

https://i.imgur.com/k00nh8o.jpg

https://en.m.wikipedia.org/wiki/Coun...a_and_Calabria

https://en.m.wikipedia.org/wiki/Bohemond_I_of_Antioch

It is possible, there's a number different scenarios that could explain who he was. He could have had ancestry further from the east, from the more cosmopolitan era prior to the middle ages.

He could have had some Saracen/Moorish input.

The South underwent a series of ethnic cleansing in middle ages, where you saw the destruction of places like Lucera, the final Moorish stronghold. There was also persecution of Jewish people by Catholics, in the middle ages as well. That's what drove former Roman Jews into northern Europe.

Maybe some stayed behind in secret and were mixed out of existence, by the larger native Southern population.

The possibilities are endless.

At any rate, I don't think this person should have been used as a being representative of medieval Puglia in terms of autosomal proportion. The Apulian samples from the Viking paper are different from him as well, and they are from roughly the same era.
01-01-22, 16:12
Jovialis

Quote:

Originally Posted by ihype02

Since Pax Augusta mentioned it is true that David only uses academic samples.

That doesn't matter, his calculators within and of itself were modified to produce results to control for a "calculator effect".

Here is an old post where Dienekes addresses this issue of "calculator effect", and in the comment section, has a debate with Davidski about it.

http://dodecad.blogspot.com/2012/08/...or-effect.html

I myself have tried to make calculators in the past, with other collaborators. All of our attempts were unsuccessful in trying to replicate the results of academic studies. While trying to do that, I realized making a calculator itself is vulnerable to a high possibility of error, even when using the same exact samples used for studies.

Using samples to model population X has a high possibility of error.

Calculator X within and of itself could have something erroneous with it.

This is why I take these calculators with a grain of salt.
01-01-22, 19:26
Angela

Quote:

Originally Posted by Jovialis

That doesn't matter, his calculators within and of itself were modified to produce results to control for a "calculator effect".

Here is an old post where Dienekes addresses this issue of "calculator effect", and in the comment section, has a debate with Davidski about it.

http://dodecad.blogspot.com/2012/08/...or-effect.html

I myself have tried to make calculators in the past, with other collaborators. All of our attempts were unsuccessful in trying to replicate the results of academic studies. While trying to do that, I realized making a calculator itself is vulnerable to a high possibility of error, even when using the same exact samples used for studies.

Using samples to model population X has a high possibility of error.

Calculator X within and of itself could have something erroneous with it.

This is why I take these calculators with a grain of salt.

I completely agree.

Fwiw, I don't know if he only uses academic samples today. Has he ever published his complete set? I absolutely know he didn't when he first created his calculators because he solicited samples from his followers. So did Dienekes, of course, but he showed you the clusters and posted his complete methodology for the sake of transparency. So far as I know Davidski has yet to do that.

I want to add that some of K12b samples are not perfect either. The Ligurian one is too Tuscan-like, probably an outlier and the Greek Macedonian one is from the assimilated Slavophone minority, they are genetically closer to Bulgarians than to Peloponnesians, which is not true for other Greek Macedonians. Davidski himself knows that some of his modern samples are not good either. But overall the calculator is not amazing but it's decent.

Distance to: Italian_Liguria

0.01994164 Italian_Lombardy

0.02259627 Italian_Piedmont

0.02374994 Italian_Bergamo

0.02490093 Italian_Trentino-Alto-Adige

0.02570667 Italian_Veneto

0.02748159 Swiss_Italian

0.02848505 Italian_Tuscany

0.03041169 Spanish_Menorca

0.03137781 French_Corsica

0.03167126 Italian_Northeast

0.03182874 Spanish_Eivissa

0.03237525 Greek_Thessaly

0.03267611 Spanish_Mallorca

0.03379182 Italian_Marche

0.03387672 Spanish_Baleares

0.03449545 French_Provence

0.03564830 Spanish_Terres_de_l'Ebre

0.03616846 Spanish_Murcia

0.03625818 Albanian

0.03679837 Spanish_Andalucia

0.03701475 Italian_Umbria

0.03718578 Spanish_Castilla_La_Mancha

0.03756287 Greek_Macedonia

0.03762135 Portuguese

0.03818783 Spanish_Extremadura

Distance to:	Italian_Liguria
0.01994164	Italian_Lombardy
0.02259627	Italian_Piedmont
0.02374994	Italian_Bergamo
0.02490093	Italian_Trentino-Alto-Adige
0.02570667	Italian_Veneto
0.02748159	Swiss_Italian
0.02848505	Italian_Tuscany
0.03041169	Spanish_Menorca
0.03137781	French_Corsica
0.03167126	Italian_Northeast
0.03182874	Spanish_Eivissa
0.03237525	Greek_Thessaly
0.03267611	Spanish_Mallorca
0.03379182	Italian_Marche
0.03387672	Spanish_Baleares
0.03449545	French_Provence
0.03564830	Spanish_Terres_de_l'Ebre
0.03616846	Spanish_Murcia
0.03625818	Albanian
0.03679837	Spanish_Andalucia
0.03701475	Italian_Umbria
0.03718578	Spanish_Castilla_La_Mancha
0.03756287	Greek_Macedonia
0.03762135	Portuguese
0.03818783	Spanish_Extremadura

Quote:

Originally Posted by ihype02

I want to add that some of K12b samples are not perfect either. The Ligurian one is too Tuscan-like, probably an outlier and the Greek Macedonian one is from the assimilated Slavophone minority, they are genetically closer to Bulgarians than to Peloponnesians, which is not true for other Greek Macedonians. Davidski himself knows that some of his modern samples are not good either. But overall the calculator is not amazing but it's decent.

Distance to: Italian_Liguria

0.01994164 Italian_Lombardy

0.02259627 Italian_Piedmont

0.02374994 Italian_Bergamo

0.02490093 Italian_Trentino-Alto-Adige

0.02570667 Italian_Veneto

0.02748159 Swiss_Italian

0.02848505 Italian_Tuscany

0.03041169 Spanish_Menorca

0.03137781 French_Corsica

0.03167126 Italian_Northeast

0.03182874 Spanish_Eivissa

0.03237525 Greek_Thessaly

0.03267611 Spanish_Mallorca

0.03379182 Italian_Marche

0.03387672 Spanish_Baleares

0.03449545 French_Provence

0.03564830 Spanish_Terres_de_l'Ebre

0.03616846 Spanish_Murcia

0.03625818 Albanian

0.03679837 Spanish_Andalucia

0.03701475 Italian_Umbria

0.03718578 Spanish_Castilla_La_Mancha

0.03756287 Greek_Macedonia

0.03762135 Portuguese

0.03818783 Spanish_Extremadura

These samples were not made by Dienekes. They are very recent additions from apricity members. We aren't sure where they come from.

02-01-22, 04:29
Angela

Quote:

Originally Posted by Jovialis

These samples were not made by Dienekes. They are very recent additions from apricity members. We aren't sure where they come from.

I agree with that. Amazing how people feel free to comment when they're not in possession of the facts

As for the Ligurian sample mentioned above, the only way anyone could know if it's an "outlier" and "not representative" is if it could be compared to a large sample of Ligurians, preferably elderly people, all of whose grandparents were from Liguria. That's because migration to Liguria began in the late 19th century. Also, it would be important to gather samples from both western and eastern Liguria, because despite being such a small region, the history and genetic influences were quite different depending on the area.

It would also be useful to compare that one lone sample added by apricity members to the so-called "Piemonte" samples, who are really mountain Ligures speaking a Ligurian dialect who were only very, very recently made a part of Piemonte.

That's unless, of course, someone has a crystal ball, and I hear they're in short supply. :)

Distance to:	Italian_Liguria
0.01994164	Italian_Lombardy
0.02259627	Italian_Piedmont
0.02374994	Italian_Bergamo
0.02490093	Italian_Trentino-Alto-Adige
0.02570667	Italian_Veneto
0.02748159	Swiss_Italian
0.02848505	Italian_Tuscany
0.03041169	Spanish_Menorca
0.03137781	French_Corsica
0.03167126	Italian_Northeast
0.03182874	Spanish_Eivissa
0.03237525	Greek_Thessaly
0.03267611	Spanish_Mallorca
0.03379182	Italian_Marche
0.03387672	Spanish_Baleares
0.03449545	French_Provence
0.03564830	Spanish_Terres_de_l'Ebre
0.03616846	Spanish_Murcia
0.03625818	Albanian
0.03679837	Spanish_Andalucia
0.03701475	Italian_Umbria
0.03718578	Spanish_Castilla_La_Mancha
0.03756287	Greek_Macedonia
0.03762135	Portuguese
0.03818783	Spanish_Extremadura

Quote:

Originally Posted by ihype02

I want to add that some of K12b samples are not perfect either. The Ligurian one is too Tuscan-like, probably an outlier and the Greek Macedonian one is from the assimilated Slavophone minority, they are genetically closer to Bulgarians than to Peloponnesians, which is not true for other Greek Macedonians. Davidski himself knows that some of his modern samples are not good either. But overall the calculator is not amazing but it's decent.

Distance to: Italian_Liguria

0.01994164 Italian_Lombardy

0.02259627 Italian_Piedmont

0.02374994 Italian_Bergamo

0.02490093 Italian_Trentino-Alto-Adige

0.02570667 Italian_Veneto

0.02748159 Swiss_Italian

0.02848505 Italian_Tuscany

0.03041169 Spanish_Menorca

0.03137781 French_Corsica

0.03167126 Italian_Northeast

0.03182874 Spanish_Eivissa

0.03237525 Greek_Thessaly

0.03267611 Spanish_Mallorca

0.03379182 Italian_Marche

0.03387672 Spanish_Baleares

0.03449545 French_Provence

0.03564830 Spanish_Terres_de_l'Ebre

0.03616846 Spanish_Murcia

0.03625818 Albanian

0.03679837 Spanish_Andalucia

0.03701475 Italian_Umbria

0.03718578 Spanish_Castilla_La_Mancha

0.03756287 Greek_Macedonia

0.03762135 Portuguese

0.03818783 Spanish_Extremadura

The one you posted is the G25 and the Ligurian average on G25 is based only on 1 individual (ALP099), as anyone can check in the datasheet. Apart from the fact that the K12b average is accurate or not, the Ligurian average in G25 is really unlikely to be accurate, it is not even an average but a single individual (unclear from what area of Liguria, AFAIK the only sampled area of Liguria in the previous studies is the Savona area, which linguistically contains Western Ligurian areas, Genoese areas, and transitional area between Ligurian and Piedmontese).

The only Ligurian individual on the G25 datasheet

Italian_Liguria:ALP099,0.113823,0.146236,0.027153,-0.011951,0.029236,-0.002231,0.00235,0.001154,0.009613,0.025331,-0.009743,0.002847,-0.013082,0.001101,-0.001086,-0.012463,-0.00665,-0.00038,0.003771,0.00075,-0.00025,0.000989,0.003944,0.000723,0.000599

The Ligurian average on G25

Italian_Liguria,0.113823,0.146236,0.027153,-0.011951,0.029236,-0.002231,0.00235,0.001154,0.009613,0.025331,-0.009743,0.002847,-0.013082,0.001101,-0.001086,-0.012463,-0.00665,-0.00038,0.003771,0.00075,-0.00025,0.000989,0.003944,0.000723,0.000599

As you can check for yourself, there is no difference.

So, the Ligurian Dodecad K12b average is not accurate? Maybe yes, but you certainly can't use the Ligurian G25 average to prove it as it is definitely not even an average. But Davidski is not to blame, it is some Italian geneticist who plays games.

02-01-22, 23:10
ihype02

Quote:

Originally Posted by Pax Augusta

The one you posted is the G25 and the Ligurian average on G25 is based only on 1 individual (ALP099), as anyone can check in the datasheet. Apart from the fact that the K12b average is accurate or not, the Ligurian average in G25 is really unlikely to be accurate, it is not even an average but a single individual (unclear from what area of Liguria, AFAIK the only sampled area of Liguria in the previous studies is the Savona area, which linguistically contains Western Ligurian areas, Genoese areas, and transitional area between Ligurian and Piedmontese).

The only Ligurian individual on the G25 datasheet

Italian_Liguria:ALP099,0.113823,0.146236,0.027153,-0.011951,0.029236,-0.002231,0.00235,0.001154,0.009613,0.025331,-0.009743,0.002847,-0.013082,0.001101,-0.001086,-0.012463,-0.00665,-0.00038,0.003771,0.00075,-0.00025,0.000989,0.003944,0.000723,0.000599

The Ligurian average on G25

Italian_Liguria,0.113823,0.146236,0.027153,-0.011951,0.029236,-0.002231,0.00235,0.001154,0.009613,0.025331,-0.009743,0.002847,-0.013082,0.001101,-0.001086,-0.012463,-0.00665,-0.00038,0.003771,0.00075,-0.00025,0.000989,0.003944,0.000723,0.000599

As you can check for yourself, there is no difference.

So, the Ligurian Dodecad K12b average is not accurate? Maybe yes, but you certainly can't use the Ligurian G25 average to prove it as it is definitely not even an average. But Davidski is not to blame, it is some Italian geneticist who plays games.

Ligurians in an Academic PCA come up as, strictly, Northern Italian not Central Italian. The paper was probably discussed here, even though I cannot find it.

Also the Ethnic Macedonian sample were very Greek-shifted compared to Bulgarians, some that I have seen. Davidski has updated the (ethnic) Macedonian samples and they are Romanian/Bulgarian-like now. In Academic PCA ethnic Macedonians are pretty much like Bulgarians but a little more South-western shifted.

There is one Macedonian t.roll saying that South Slavs are 80% Ballkanic, I would not be surprised if he twisted his own samples that he gave.
02-01-22, 23:39
Pax Augusta

Quote:

Originally Posted by ihype02

Ligurians in an Academic PCA come up as, strictly, Northern Italian not Central Italian. The paper was probably discussed here, even though I cannot find it.

Ligurians do not come out as Central Italian in K12b, regardless of whether it is really accurate as an average. The most comprehensive paper on Italy so far, from which that sample used on G25 came from, is Raveane 2019. The PCAs have been posted several times.

The Northern Italian is the biggest Italian cluster.

In the Raveane 2019 paper in green are Ligurians and Emilians (NItaly3) with a minority of Piedmontese and Venetians, in pink and red are Tuscans (NCItaly 1, 2, 3). Mainland Italy this time was divided in two parts, not into three clusters as in previous studies. Ligurians came out together with Emilians as the southernmost part of the Northern Italian cluster, while Tuscans ended up just behind Ligurians and Emilians in a cluster called Northern-Central Italian grouped with the Northern Italian clusters.

Quote:

A sharp north-south division in cluster distribution was detected, the separation between northern and southern areas being shifted north along the peninsula (Fig. 1B) (12). The reported structure dismissed the possibility that the Central Italian populations differentiated from the Northern and Southern Italian groups (Fig. 1A) (13). Individuals from Central Italy were, in fact, assigned mostly to the Southern Italian clusters, except for samples from Tuscany, which grouped instead with the Northern Italian clusters (Fig. 1, A and B) (12).

Do you need me to show you better?

https://www.science.org/cms/10.1126/...aw3492-f1.jpeg

Quote:

Originally Posted by ihype02

Also the Ethnic Macedonian sample were very Greek-shifted compared to Bulgarians, some that I have seen. Davidski has updated the (ethnic) Macedonian samples and they are Romanian/Bulgarian-like now. In Academic PCA ethnic Macedonians are pretty much like Bulgarians but a little more South-western shifted.

There is one Macedonian t.roll saying that South Slavs are 80% Ballkanic, I would not be surprised if he twisted his own samples that he gave.

Which calculator are we talking about now? The K12b or the G25? Likely the updated K12b averages may have been made by several different users. The G25 updated averages are based on available academic samples. But not all available academic samples are accurate and exhaustive.
03-01-22, 00:24
ihype02

Quote:

Originally Posted by Pax Augusta

Which calculator are we talking about now? The K12b or the G25? Likely the updated K12b averages may have been made by several different users. The G25 updated averages are based on available academic samples. But not all available academic samples are accurate and exhaustive.

The G25 ones, but they are different now though.
03-01-22, 00:38
Pax Augusta

Quote:

Originally Posted by ihype02

The G25 ones, but they are different now though.

Got it, so a different set of academic samples.
13-01-22, 23:54
SandbagsIA

Re: Jovialis Models

New here, but these models are interesting. From what I read of the Daunian paper it does seem that ancient Daunian samples carry more WHG-related and Anatolia_N (likely EEF-related ancestry) so some of these results indicate that imo.

But you say that the fits are bad, do you mean those with distance >2.0? Also, would these be scaled or unscaled coordinates?

I think it's worth adding Anatolia_BA to at least check if any of these samples have Anatolian-related ancestry distinct from Minoan or if bad fits are more of a consequence of low coverage.
15-01-22, 13:44
Jovialis

Quote:

Originally Posted by SandbagsIA

New here, but these models are interesting. From what I read of the Daunian paper it does seem that ancient Daunian samples carry more WHG-related and Anatolia_N (likely EEF-related ancestry) so some of these results indicate that imo. But you say that the fits are bad, do you mean those with distance >2.0? Also, would these be scaled or unscaled coordinates? I think it's worth adding Anatolia_BA to at least check if any of these samples have Anatolian-related ancestry distinct from Minoan or if bad fits are more of a consequence of low coverage.

Here you go:https://www.eupedia.com/forum/thread...l=1#post638321
15-01-22, 13:57
SandbagsIA

Quote:

Originally Posted by Jovialis

Here you go

Thank you, these results make sense to me, and I suspect this Anatolia_BA may reflect some antiquity (Hellenistic/Roman) events of Anatolia-South Europe interactions (possibly due to the Greek colonies)

Btw, which population are you using as Greek? Is it one of of the Global_25 presets like Greek_Macedonia or Greek_Peloponnese or a composite?
15-01-22, 14:28
Jovialis

Quote:

Originally Posted by SandbagsIA

Thank you, these results make sense to me, and I suspect this Anatolia_BA may reflect some antiquity (Hellenistic/Roman) events of Anatolia-South Europe interactions (possibly due to the Greek colonies)Btw, which population are you using as Greek? Is it one of of the Global_25 presets like Greek_Macedonia or Greek_Peloponnese or a composite?

The Greek sample comes from Dodecad. But I believe it is from Central Greece.
15-01-22, 16:35
SandbagsIA

Quote:

Originally Posted by Jovialis

The Greek sample comes from Dodecad. But I believe it is from Central Greece.

Then the results are even more reasonable imo, though if it is the samples I think of they are likely Central Greek islanders (If it's the Central_Greek labeled-ones from the Dodecad project) rather than Central Greeks from mainland Greece. They should be close to Peloponnesians but likely have some more Anatolia_BA-ancestry.
19-01-22, 19:59
Angela

The paper is officially out. Link provided by Lazaridis; many thanks as always.

https://academic.oup.com/mbe/advance...searchresult=1

I've already said it, but I do wish academics would stop talking about the genetic history of "The Italians". Just look at the space we occupy on the PCA. Everybody else in Europe starts looking like the Han by comparison.

As I probably also said, the Daunians look to me like western shifted Central Italians and Tuscans.
19-01-22, 20:49
Hawk

Quote:

Originally Posted by Angela

The paper is officially out. Link provided by Lazaridis; many thanks as always.

https://academic.oup.com/mbe/advance...searchresult=1

I've already said it, but I do wish academics would stop talking about the genetic history of "The Italians". Just look at the space we occupy on the PCA. Everybody else in Europe starts looking like the Han by comparison.

As I probably also said, the Daunians look to me like western shifted Central Italians and Tuscans.

Yes, but that J2b2-L283 was probably brought by the Illyrian part of Daunians. It's interesting that they give an indirect hint that the J2b2-L283 might have been potentially richer in CHG.

Quote:

Another signal coming from qpAdm analyses is the apparent excess of CHG ancestry in IAA; however, the predominant contribution of CHG to the Steppe-related ancestry that, by the Iron Age, had already spread to the Mediterranean area makes it hard to properly detect a CHG signature independent from the Steppe wave, possibly brought by pan-Mediterranean influxes. When directly investigated with an f4 framework, IAA shows generally more CHG than Mycenaean, less CHG than contemporary Croatian_EIA and, in some cases (ORD019, SGR002 and the Mediaeval SGR001 with Z-scores higher than 2) more CHG than older Croatian samples (_N=Neolithic and _MN=Middle Neolithic) (Supplementary fig. 8).
20-01-22, 01:52
Angela

I think the authors are pretty circumspect about all of this.

"It is not clear whether these connections indicate a movement of people or a sharing ofcultural ideas and a conclusive answer to the origin of the Daunians remains elusive. From aparsimony perspective, the genetic results point to an autochthonous origin (e.g. a geneticcontinuity of Daunians with the population that inhabited the area prior to the examined historicalperiod), here mainly marked by the presence of WHG signature, although we cannot excludeadditional influences from Croatia (ancient Illyria), as described by available historical sourcesand by the material remains (De Juliis 1988; Norman 2016)."

In another part of the paper they say that some contribution from the Balkans is plausible.

". Three of them, which clustered close to modern Italians in the PCA (ORD001, ORD014 and SGR003, Fig. 1C), show higher affinity with the Iron Age Croatian sample (ORD004 followed this pattern too, but with lower f3 values). However, the remaining majority are closest to the Roman Republicans, which can be interpreted as representative of local Iron Age peninsular Italy ancestry, as also indicated by our MDS results."

I think it's interesting, going over the text of this paper once again, to think of the work Jovialis has done with the Balkan samples, as well as the Roman Republican samples.
20-01-22, 02:01
torzio

Quote:

Originally Posted by Hawk

Yes, but that J2b2-L283 was probably brought by the Illyrian part of Daunians. It's interesting that they give an indirect hint that the J2b2-L283 might have been potentially richer in CHG.

we do not know who the Daunian merged/absorbed with as per italic people around Foggia ................but their next door neighbours to the west where always the samnites until the 3rd Roman-Samnite war.......then the Romans moved in after this war

IIRC Venosa was also Samnite in origin
20-01-22, 02:52
enter_tain

Quote:

Originally Posted by Angela

I think the authors are pretty circumspect about all of this.

"It is not clear whether these connections indicate a movement of people or a sharing ofcultural ideas and a conclusive answer to the origin of the Daunians remains elusive. From aparsimony perspective, the genetic results point to an autochthonous origin (e.g. a geneticcontinuity of Daunians with the population that inhabited the area prior to the examined historicalperiod), here mainly marked by the presence of WHG signature, although we cannot excludeadditional influences from Croatia (ancient Illyria), as described by available historical sourcesand by the material remains (De Juliis 1988; Norman 2016)."

In another part of the paper they say that some contribution from the Balkans is plausible.

". Three of them, which clustered close to modern Italians in the PCA (ORD001, ORD014 and SGR003, Fig. 1C), show higher affinity with the Iron Age Croatian sample (ORD004 followed this pattern too, but with lower f3 values). However, the remaining majority are closest to the Roman Republicans, which can be interpreted as representative of local Iron Age peninsular Italy ancestry, as also indicated by our MDS results."

I think it's interesting, going over the text of this paper once again, to think of the work Jovialis has done with the Balkan samples, as well as the Roman Republican samples.

The archeological/linguistic data is pretty clear on this. The Albanian language is undeniably linked with Messapian. There are countless comparisons between the two.

Messapians were always a mixture of Western Balkan migrants and native Italians. I just wish we did a deep subclade analysis on those J2B2-L283 samples, to see which part of the Western Balkans they came from.

"The Iapygians most likely left the eastern coasts of the Adriatic for Italy from the 11th century BC onwards,^[25] merging with pre-existing Italic and Mycenean cultures and providing a decisive cultural and linguistic imprint"

That was written in 2005^.
20-01-22, 18:00
Angela

Yes, well, "linguists" were wrong about the Etruscans. As for the Indo-European linguists, put five of them in a room and you'll get five different opinions. That's why I stay away from such discussions. It's like being on a merry-go-round.

The majority of these samples are closest to the Iron Age Central Italians, i.e. the Etruscans and the Latins. That's why the authors come down on the side of saying it was an authochthonous culture. Does that mean there wasn't some genetic impact from across the Adriatic? No, it doesn't.

It's not implausible, although the fact that a minority of the samples show a similarity to Iron Age Croatians is not dispositive in and of itself for me. Northern Italians are very close to ancient Illyrians. Does that mean that Illyrians came and settled in Italy, or does it mean that similar people settled both Northern Italy and "Illyria". I think the latter is much more "plausible"

As for the Messapian people, let's wait and see their genetic profile. They were different from the Daunians in that they accepted foreign influences much more readily. Perhaps that translated to admixture as well.

Distance to:	Italian_Liguria
0.01994164	Italian_Lombardy
0.02259627	Italian_Piedmont
0.02374994	Italian_Bergamo
0.02490093	Italian_Trentino-Alto-Adige
0.02570667	Italian_Veneto
0.02748159	Swiss_Italian
0.02848505	Italian_Tuscany
0.03041169	Spanish_Menorca
0.03137781	French_Corsica
0.03167126	Italian_Northeast
0.03182874	Spanish_Eivissa
0.03237525	Greek_Thessaly
0.03267611	Spanish_Mallorca
0.03379182	Italian_Marche
0.03387672	Spanish_Baleares
0.03449545	French_Provence
0.03564830	Spanish_Terres_de_l'Ebre
0.03616846	Spanish_Murcia
0.03625818	Albanian
0.03679837	Spanish_Andalucia
0.03701475	Italian_Umbria
0.03718578	Spanish_Castilla_La_Mancha
0.03756287	Greek_Macedonia
0.03762135	Portuguese
0.03818783	Spanish_Extremadura

Quote:

Originally Posted by Angela

Yes, well, "linguists" were wrong about the Etruscans. As for the Indo-European linguists, put five of them in a room and you'll get five different opinions. That's why I stay away from such discussions. It's like being on a merry-go-round.

The majority of these samples are closest to the Iron Age Central Italians, i.e. the Etruscans and the Latins. That's why the authors come down on the side of saying it was an authochthonous culture. Does that mean there wasn't some genetic impact from across the Adriatic? No, it doesn't.

It's not implausible, although the fact that a minority of the samples show a similarity to Iron Age Croatians is not dispositive in and of itself for me. Northern Italians are very close to ancient Illyrians. Does that mean that Illyrians came and settled in Italy, or does it mean that similar people settled both Northern Italy and "Illyria". I think the latter is much more "plausible"

As for the Messapian people, let's wait and see their genetic profile. They were different from the Daunians in that they accepted foreign influences much more readily. Perhaps that translated to admixture as well.

How were linguists wrong about Etruscans? Etruscans and Romans are genetically linked, but the Etruscan language is clearly non-Indo European. That's not an uncommon occurrence. The Frankish royalty spoke a Germanic language, while the common people spoke French. The Normans spoke French, while the lower class spoke English. With the Bulgars, they were Turkic, but the population spoke Slavic. Some times the royalty imposes their language on the population, sometimes they don't. And the Etruscans seems to have initially adopted the language of their rulers, but later switched to Latin like their kin.

Messapian and Albanian are undeniably linked. They show you an entire section of cognates from whatever inscriptions we have. Not to mention all the grammar similarities too.

Messapic lexical item English translation Proto-Messapic form Paleo-Balkan languages Other Indo-European cognates Sources

ana mother *annā (a nursery word) Proto-Albanian: *na(n)nā, *amma; Albanian: nënë/nana, ëmë/âmë ('mother') Hittite: annaš ('mother'); Latin: amma ('mother'); Greek: ámma ('mother, nurse'); ^[61]

anda and, as well Proto-Abanian: *edhō/êndō; Albanian: edhe/ênde ('and', 'yet', 'therefore') Latin: ante ("opposite, in front of"); Hittite: anda; Greek: endha/ΕΝΘΑ; ('and' , 'as well') ^[62]

apa from *apo Proto-Albanian: *apo; Albanian: (për-)apë ('from'); Albanian (Gheg): pi (PI < apa) ('from') or pa (PA < *apa) ('without') Greek: apó; Sanskrit: ápa ^[63]

atabulus sirocco Proto-Albanian: *abula; Albanian: avull ('steam, vapor') Proto-Germanic: *nebulaz ('fog') ^[64]

aran field *h₂r°h₃ā- Proto-Albanian: *arā: Albanian: arë, ara ('field') Hittite: arba- ('border, area'); Latvian: ara ('field') ^[65]

bàrka belly Proto-Albanian: *baruka; Albanian: bark ('belly') ^[66]

Barzidihi (personal name) Illyrian: Bardyl(l)is;Proto-Albanian: *bardza; Albanian: bardhë/bardhi, Bardha ('white', found also in anthroponyms, e.g., Bardhyl)^[a] ^[68]

bennan (a sort of vehicle) *benna Gaulish: benna (a kind of 'carriage') ^[69]

biles/bilihi son Proto-Albanian: *bira; Albanian: bir, pl. bilj - bij ('son') Latin: fīlius ('son') ^[70]

biliā/bilina daughter *bhu-lyā Proto-Albanian: *birilā; Albanian: bijë - bija ('daughter'); older dialect bilë - bila ('daughter') Latin: fīlia ('daughter') ^[70]

bréndon; bréntion stag; stag's head Proto-Albanian: *brina; Albanian: bri, brî ('horn'; 'antler') Lithuanian: briedis, ('elk'); Swedish: brinde ('elk')The Messapic word is at the origin of the toponym Brendésion (Βρενδέσιον), Brentḗsion (Βρεντήσιον), modern Brindisi ^[71]

Damatura Mother Earth (goddess) *dʰǵʰ(e)m- matura Proto-Albanian: *dzō; Albanian: dhe ('earth') Latvian: Zemes Māte ('Mother Earth')Whether the (pre-)Illyrian form is at the origin of the Greek goddess Demeter or the contrary is unclear.^[72] ^[73]

deiva; dīva god; goddess Sanskrit: devá ('heavenly, divine'); Lithuanian Diēvas; Old Norse: Týr ^[74]

den voice *ghen Proto-Albanian: *džana; Albanian: zë/zâ, zër/zân ('voice') ^[75]

hazavaθi to offer (sacral) ha- is a prefix, zav- is the same root as in Greek: χεών, Sanskrit ju-hô-ti and Avestan: zaotar- ('sacrificer') ^[76]

hipades he/she/it offers, dedicates, sets up *supo dhē-s-t Proto-Albanian: *skūpa: Albanian: hip ('go up') and dha/dhash ('he gave/I gave') ^[77]

hipakaθi offer, set up Albanian: hip ('go up') and ka/kam ('he has/I have') > hip-ka- ^[78]

klaohi/klohi hear, listen (invocative) *kleu-s- Albanian: kluoj/kluaj/kluhem ('call, hear') Greek: klythí ('hear'); Sanskrit: śrudhí ('hear'); Slavic: slušati ('hear'); Lithuanian: klausyti ('hear') ^[79]

kos someone *q^wo Proto-Albanian: *kuša; Albanian: kush ('who') Tocharian A: Kus ('who') ^[80]

ma not *meh₁ Albanian: ma, me, mos Greek: mē; Sanskrit: mā ^[81]

menza foal *mendyo Proto-Albanian: *mandja; Albanian: mëz - maz ('foal'); mend ('to suckle'); Romanian (< Dacian) mînz ('foal') Gaulish: mandus ('foal') ^[82]

ner man *ner- Proto-Albanian: *nera; Albanian: njeri ('man') Greek: ανηρ ('man'); Sanskrit: nar- ('man') ^[83]

penkaheh five Proto-Albanian: *pentše; Albanian: pesë ('five') Lithuanian: penki ('five') ^[84]

rhīnós fog, mist, cloud Proto-Albanian: *rina: Albanian: re, rê, rên ('cloud') ^[85]

tabarā; tabaras priestess; priest (lit. 'offerer') *to-bhorā; *to-bhoros Albanian: të bie/të bar, bjer/bar ('bring', 'carry') Greek: ϕορός ('bring'); Latin: ferō ('bring') ^[86]

teutāTaotor community, people(name of a god) *Toutor Illyrian: Teuta(na) ('mistress of the people', 'queen') Oscan: touto ('community'); Old Irish: túath ('tribe, people'); Lithuanian: tautà ('people'); Gothic þiuda 'folk' ^[87]

veinan his; one's Albanian: vetë ('himself, oneself') Sanskrit: svayàm ('himself') ^[88]

Venas desire (name of a goddess) *wenos Latin: Venus; Old Indic: vánas ('desire') ^[89]

Zis sky-god *dyēs Illyrian: dei- or -dí ('heaven, god', as a prefix or suffix);Albanian Zojz ('sky-god') Hittite: šīuš ('god'); Sanskrit: Dyáuṣ; Greek: Zeus; Latin: Jove ('sky-god') ^[90]

20-01-22, 19:36
Angela

Just stop. Messapians weren't Daunians, for one thing. We have no inscriptions for the Daunian language.

For another, I've occasionally read some posts in the Albanian language thread, where everybody has their favorite linguist. It doesn't inspire confidence.

As to the Etruscan language, there were "linguists" here and at anthrogenica and theapricity and on and on who argued vociferously that the Etruscan language couldn't be a European language; it had to come from somewhere in the east. None of them, including people who post here, wanted to know that inscriptions found further east were probably left by Etruscan traders. Btw, I have yet to see ANYONE man up and say "I WAS WRONG." Don't presume to tell me the history of this or what the arguments were; I've been at this for 12 years. Btw, you're still wrong about the Etruscans. The steppe admixed people who brought R1b lineages adopted the language of the native Italian Chalcolithic people already here, unlike the "Latins"; unless, that is, someone can explain how steppe admixed people spoke a non-Indo-European language. Think Basques.

Now go play this game on your Albanian threads. This is a paper about THE GENETIC ORIGIN of the Daunians, and we're talking about genetics. If you have something interesting to add in that regard which hasn't yet been addressed, by all means post it.
20-01-22, 20:12
Maxximo55#

it being understood that the Daunian were different from the Messapi, but since we are also talking about Messapi here, I consider the recent discovery (08.01.2022) which took place in the Lower Salento to be relevant.
New light on the Messapi, research in the necropolis of Alezio (Lower Salento). An excavation campaign unearths tombs and the ceremonial square of the site in Puglia. The grave of a child; olives as an offering to propitiate the afterlife. The Messapian necropolis of Monte d'Elia, in Alezio, thanks to an initial research campaign conducted by the Archeology Laboratory of the University of Salento, offers new evidence of an ancient civilization. The findings: a ceremonial square, numerous tombs, including that of a child, an ossuary, the remains of olives, are just some of the new discoveries. Having concluded the excavation operations in recent days, we now continue with the analysis of the finds. Over the course of a few weeks of research, new fundamental data emerged for the knowledge of Messapian civilization, first of all through the topographical reconstruction of the Monte d'Elia area and the recognition of the funerary rituals practiced there in ancient times. Of extreme importance is the fact that concerns the identification of a large ceremonial square around which, within enclosures built with large boulders, the groups of tombs belonging to nuclei of families or clans were concentrated. This was the arrival point of the processions that accompanied the deceased on the last journey from the house to the place of burial. More detailed elements come from the excavation of burials that were not intercepted during the investigations of the 1980s by the Archaeological Superintendence of Puglia. In fact, a pit was identified, with a floor in limestone blocks and a frame in carparo, inside which the remains of at least 12 individuals were accumulated. In short, an ossuary linked to the functioning of the necropolis and to the practice of reusing funerary structures for various depositions. Some objects belonging to the grave goods were found, such as a lamp, a plate, a trozzella, a typical Messapian vase, two loom weights and a javelin point.
20-01-22, 22:31
enter_tain

Quote:

Originally Posted by Angela

Just stop. Messapians weren't Daunians, for one thing. We have no inscriptions for the Daunian language.

For another, I've occasionally read some posts in the Albanian language thread, where everybody has their favorite linguist. It doesn't inspire confidence.

As to the Etruscan language, there were "linguists" here and at anthrogenica and theapricity and on and on who argued vociferously that the Etruscan language couldn't be a European language; it had to come from somewhere in the east. None of them, including people who post here, wanted to know that inscriptions found further east were probably left by Etruscan traders. Btw, I have yet to see ANYONE man up and say "I WAS WRONG." Don't presume to tell me the history of this or what the arguments were; I've been at this for 12 years. Btw, you're still wrong about the Etruscans. The steppe admixed people who brought R1b lineages adopted the language of the native Italian Chalcolithic people already here, unlike the "Latins"; unless, that is, someone can explain how steppe admixed people spoke a non-Indo-European language. Think Basques.

Now go play this game on your Albanian threads. This is a paper about THE GENETIC ORIGIN of the Daunians, and we're talking about genetics. If you have something interesting to add in that regard which hasn't yet been addressed, by all means post it.

Mind being a little more respectful? All I said is that Etruscan is not an Indo-European language. That's an established fact. I didn't say it's not a European language, because not all European languages are Indo-European in nature. Look at Basques.

As for the Daunians, they are all classified as Iapygians along with Messapians, and they spoke the Messapian language. We have inscriptions from their civilizations. I don't understand the controversy here. Pardon me for being a "biased Albanian" though.

The Iapygians were a "relatively homogeneous linguistic community" speaking a non-Italic, Indo-European language, commonly called 'Messapic'. The language, written in variants of the Greek alphabet, is attested from the mid-6th to the late-2nd century BC.^[6]
20-01-22, 22:51
torzio

Quote:

Originally Posted by enter_tain

Mind being a little more respectful? All I said is that Etruscan is not an Indo-European language. That's an established fact. I didn't say it's not a European language, because not all European languages are Indo-European in nature. Look at Basques.

As for the Daunians, they are all classified as Iapygians along with Messapians, and they spoke the Messapian language. We have inscriptions from their civilizations. I don't understand the controversy here. Pardon me for being a "biased Albanian" though.

The Iapygians were a "relatively homogeneous linguistic community" speaking a non-Italic, Indo-European language, commonly called 'Messapic'. The language, written in variants of the Greek alphabet, is attested from the mid-6th to the late-2nd century BC.^[6]

The term Iapygians
the area includes all of modern Apulia and part of northeastern Basilicata (mainly the Melfese). This area corresponds roughly to ancient Iapygia (or Apulia), which, according to Greek and Roman literary tradition as well as in the archaeological record, was occupied by three Iapygian peoples: the Messapians to the south (roughly the Salentine Peninsula), the Peucetians in central Apulia, and the Daunians to the north, including the Melfese, now in Basilicata

The iapodes/Japodes refers to the Croatian Illyrian tribes that the Daunians are linked to
20-01-22, 22:55
Angela

Quote:

Originally Posted by enter_tain

Mind being a little more respectful? All I said is that Etruscan is not an Indo-European language. That's an established fact. I didn't say it's not a European language, because not all European languages are Indo-European in nature. Look at Basques.

As for the Daunians, they are all classified as Iapygians along with Messapians, and they spoke the Messapian language. We have inscriptions from their civilizations. I don't understand the controversy here. Pardon me for being a "biased Albanian" though.

The Iapygians were a "relatively homogeneous linguistic community" speaking a non-Italic, Indo-European language, commonly called 'Messapic'. The language, written in variants of the Greek alphabet, is attested from the mid-6th to the late-2nd century BC.^[6]

Mind not posting under yet another sock?

You asked how linguists were wrong about the Etruscan language; I told you. You seemed confused about who adopted whose language, so I tried to clear up the confusion.

Maybe you think it's disrespectful to say that linguists always disagree with one another, and consensus is hard to come by, or that the thread on the Albanian language is full of people spitting out their favorite linguist's opinion and how the linguist of someone else is completely wrong? I don't see how you can deny that, and I don't think it's disrespectful.

Now I "will" be disrespectful, but not to you, unless you happen to be a inguist. I don't think linguistics is a "science" at all, so someone's linguistic theory is never going to be a determining factor for me. It's like psychology and sociology, which are called social sciences but are also not sciences, and whose conclusions, quoted by everyone and his mother, can rarely be replicated. I'm entitled to my opinion about all of this, whether or not it bothers linguists and social scientists.

My point is that there is nothing in this paper to suggest that the Daunians are transplanted people from the Balkans. How could they be, when the majority of them are closest to CENTRAL ITALIAN Iron Age people? Could there have been some influx from the Balkans? It's certainly possible, even plausible. Somehow that's not good enough for you?

Instead of taking offense at the littlest thing, maybe people should just get on with the actual work of analyzing genetic data as logically and reasonably and with as little, yes, bias, as possible.
21-01-22, 00:01
enter_tain

Quote:

Originally Posted by Angela

Mind not posting under yet another sock?

You asked how linguists were wrong about the Etruscan language; I told you. You seemed confused about who adopted whose language, so I tried to clear up the confusion.

Maybe you think it's disrespectful to say that linguists always disagree with one another, and consensus is hard to come by, or that the thread on the Albanian language is full of people spitting out their favorite linguist's opinion and how the linguist of someone else is completely wrong? I don't see how you can deny that, and I don't think it's disrespectful.

Now I "will" be disrespectful, but not to you, unless you happen to be a inguist. I don't think linguistics is a "science" at all, so someone's linguistic theory is never going to be a determining factor for me. It's like psychology and sociology, which are called social sciences but are also not sciences, and whose conclusions, quoted by everyone and his mother, can rarely be replicated. I'm entitled to my opinion about all of this, whether or not it bothers linguists and social scientists.

My point is that there is nothing in this paper to suggest that the Daunians are transplanted people from the Balkans. How could they be, when the majority of them are closest to CENTRAL ITALIAN Iron Age people? Could there have been some influx from the Balkans? It's certainly possible, even plausible. Somehow that's not good enough for you?

Instead of taking offense at the littlest thing, maybe people should just get on with the actual work of analyzing genetic data as logically and reasonably and with as little, yes, bias, as possible.

Sock? It's amusing that you'd think I'd waste my time with making sock accounts on a random forum. I haven't posted here since like 2013 or something.

There is a difference between analyzing unattested language/s like "Illyrian". That's the source of the argument in that other thread. That there's no first hand accounts to extensively analyze.

You're denying basic facts of attested languages. That's a whole other debate. Messapian and Albanian are both attested languages (as is Etruscan), and I don't know of any linguist that denies a link between the two. If that's the case, please show me. Messapian is studied by Albanian, because there are very little other cognates outside of it.
21-01-22, 02:18
torzio

might be of use

http://www.asciatopo.altervista.org/illyria.html

The Roman province of Illyricum was bounded by the Ras^a river (toward Venetia), the river Drin (toward Macedonia), and the Adriatic sea. Toward Pannonia and Moesia in the interior the boundaries are less clear but they should have followed the mountain ranges of Velebit, Bosnia, and Montenegro.

From the river Ras^a to the river Zrmanja and then to the Krka, the land was inhabited by Iapydes and Liburni, from the Krka to the river Neretva, it was called Dalmatia, and from the Neretva to the Drin, Illyria proper (Barbara or Romana).

Illyrian Proper is Pliny term for Southern Illyrian who where not celtinized.

Illyricum in Pliny times was from south Slovenia to South Montenegro.

Italian terms of Barbara or Romana needs to be looked at
21-01-22, 15:19
MOESAN

Quote:

Originally Posted by Angela

Mind not posting under yet another sock?

You asked how linguists were wrong about the Etruscan language; I told you. You seemed confused about who adopted whose language, so I tried to clear up the confusion.

Maybe you think it's disrespectful to say that linguists always disagree with one another, and consensus is hard to come by, or that the thread on the Albanian language is full of people spitting out their favorite linguist's opinion and how the linguist of someone else is completely wrong? I don't see how you can deny that, and I don't think it's disrespectful.

Now I "will" be disrespectful, but not to you, unless you happen to be a inguist. I don't think linguistics is a "science" at all, so someone's linguistic theory is never going to be a determining factor for me. It's like psychology and sociology, which are called social sciences but are also not sciences, and whose conclusions, quoted by everyone and his mother, can rarely be replicated. I'm entitled to my opinion about all of this, whether or not it bothers linguists and social scientists.

My point is that there is nothing in this paper to suggest that the Daunians are transplanted people from the Balkans. How could they be, when the majority of them are closest to CENTRAL ITALIAN Iron Age people? Could there have been some influx from the Balkans? It's certainly possible, even plausible. Somehow that's not good enough for you?

Instead of taking offense at the littlest thing, maybe people should just get on with the actual work of analyzing genetic data as logically and reasonably and with as little, yes, bias, as possible.

Here I disagree: linguistic, spite not a "hard" science, is science when practised by someones who stay on facts and distinguish between acquired certitudes and hypothesis: serious linguists in some way. What is true is that we see today a lot of new theories on languages popping up, which I modestly find science fiction. It isn't to say we can put all linguists in the same bag...
21-01-22, 15:41
MOESAN

Concerning the ties between some ancient Italy people and Northwestern Balkans we ought to be careful because it seems Italy has received a lot of people from this region at least between Chalcolithic and Iron, and not only across sea but also through the northeastern lands.
It's of little value as an hazardous hypothesis, but I wonder if the principal factor of differenciation between Celts and Italics (I see between bronze and early Iron) geographic distance left aside is not this geographic proximity of Italics with N-W Balkans and the exchanges made possible?
21-01-22, 19:16
Angela

Quote:

Originally Posted by MOESAN

Concerning the ties between some ancient Italy people and Northwestern Balkans we ought to be careful because it seems Italy has received a lot of people from this region at least between Chalcolithic and Iron, and not only across sea but also through the northeastern lands.
It's of little value as an hazardous hypothesis, but I wonder if the principal factor of differenciation between Celts and Italics (I see between bronze and early Iron) geographic distance left aside is not this geographic proximity of Italics with N-W Balkans and the exchanges made possible?

Most of the migration into Italy north of Rome, at least, came, imo, through the flat lands in the northeast which skirt the Alps. From France into Italy and vice versa in, say, Liguria, it's easier to travel by boat. Yes, there are mountain passes from the central Alps into Italy; I was born and lived along one of the major routes, the Via Francigena. It's much easier to skirt them.

That doesn't mean that I think the gene flow necessarily came from the Balkans around Croatia, for example. I think that it is just as plausible that the similarities between Balkan people and Italians are due in some part to the fact that the same groups migrated to both places.

That's as true for the steppe admixed groups in central Europe as it is for the eastern admixed groups which influenced Italy on a cline from south to north.

I see all of this in my own results using Jovialis' calculator. My results are a combination of Italian Chalcolithic, La Tene, Bulgarian Bronze Age, and Minoan.
22-01-22, 21:25
MOESAN

My aim was to say the possible (relatively important) ties could be multifolds. But Croatia (before today political name) could have been an important point of departure for Italy at different times even if of course things are a bit more complicated.
21-02-22, 06:10
Salento

I tested ORD001 … the paper says that they aligned the fastq files with bwa mem … disabled seeding, … though I get the same results with the default settings, and I get the same combined raw-data output as the .bam on ENA.

https://i.imgur.com/xstVvt2.jpg

I decided to run the fastq of ORD001 with bwa aln (short reads) with disabled seedlings, the standard for Ancient samples, … though is much slower than bwa mem.

--- as reference:

... linux based:

ORD001 mapping as per the paper (bwa mem modified settings for Ancient samples):

Code:

bwa mem -k 19 -r 2.5 ref.fa ORD001.fastq.gz | samtools view -bS - > ORD001_bwa_mem_K19-2_5.bam samtools sort ORD001_bwa_mem_K19-2_5.bam -o ORD001_bwa_mem_K19-2_5.sort.bam samtools index ORD001_bwa_mem_K19-2_5.sort.bam # coordinates ORD001_bwa_mem_K19-2-5_Dod_K12b,2.13,0,3.17,1.09,29.50,31.57,0,0.75,9.39,1.76,20.64,0

ORD001 mapping with default setting:

Code:

bwa mem ref.fa ORD001.fastq.gz | samtools view -bS - > ORD001_bwa_mem_default.bam samtools sort ORD001_bwa_mem_default.bam -o ORD001_bwa_mem_default.sort.bam samtools index ORD001_bwa_mem_default.sort.bam # coordinates ORD001_bwa_mem_default_Dod_K12b,2.13,0,3.17,1.09,29.50,31.57,0,0.75,9.39,1.76,20.64,0

ENA .bam coordinates:

Code:

ORD001_ENA_bam_Dod_K12b,2.13,0,3.17,1.09,29.50,31.57,0,0.75,9.39,1.76,20.64,0

ORD001 mapping with bwa aln with disabled seedlings, ... modified settings for Ancient samples:

Code:

bwa aln ref.fa ORD001.fastq.gz -n 0.01 -o 2 -l 1024 > ORD001.sai bwa samse ref.fa ORD001.sai ORD001.fastq.gz -f ORD001.sam samtools view -Sb ORD001.sam > ORD001.bam samtools sort ORD001.bam -o ORD001.sort.bam samtools index ORD001.sort.bam ####### to Add Read Group tags and index bam files: java -jar build/libs/picard.jar AddOrReplaceReadGroups INPUT=ORD001.sort.bam OUTPUT=ORD001.RG.bam RGID=rg_id RGLB=lib_id RGPL=platform RGPU=plat_unit RGSM=sam_id VALIDATION_STRINGENCY=LENIENT samtools index ORD001.RG.bam ####### to Mark and remove duplicates: java -jar build/libs/picard.jar MarkDuplicates I=ORD001.RG.bam O=ORD001.DR.bam M=output_metrics.txt REMOVE_DUPLICATES=True VALIDATION_STRINGENCY=LENIENT &> logFile.log samtools index ORD001.DR.bam ####### Local reads realignment java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ref.fa -I ORD001.DR.bam -o target.intervals java -jar GenomeAnalysisTK.jar -T IndelRealigner -R ref.fa -I ORD001.DR.bam -targetIntervals target.intervals -o ORD001.final.bam --filter_bases_not_stored samtools sort ORD001.final.bam -o ORD001.final.sort.bam samtools index ORD001.final.sort.bam ####### flagstat file (some info about the .bam) samtools flagstat ORD001.final.sort.bam > ORD001.final.sort.txt coordinates: ORD001_bwa-aln_Dod_K12b,2.45,0,2.89,1.61,30.29,31.24,0,0.86,8.77,1.24,20.63,0

... the created files:

https://i.imgur.com/6xgDlHp.png?1

more info:
https://paleogenomics-course.readthe...apping_v2.html
21-02-22, 06:55
torzio

Quote:

Originally Posted by Salento

I tested ORD001 … the paper says that they aligned the fastq files with bwa mem … disabled seeding, … though I get the same results with the default settings, and I get the same combined raw-data output as the .bam on ENA.

https://i.imgur.com/xstVvt2.jpg

I decided to run the fastq of ORD001 with bwa aln (short reads) with disabled seedlings, the standard for Ancient samples, … though is much slower than bwa mem.

--- as reference:

... linux based:

ORD001 mapping as per the paper (bwa mem modified settings for Ancient samples):

Code:

bwa mem -k 19 -r 2.5 ref.fa ORD001.fastq.gz | samtools view -bS - > ORD001_bwa_mem_K19-2_5.bam samtools sort ORD001_bwa_mem_K19-2_5.bam -o ORD001_bwa_mem_K19-2_5.sort.bam samtools index ORD001_bwa_mem_K19-2_5.sort.bam # coordinates ORD001_bwa_mem_K19-2-5_Dod_K12b,2.13,0,3.17,1.09,29.50,31.57,0,0.75,9.39,1.76,20.64,0

ORD001 mapping with default setting:

Code:

bwa mem ref.fa ORD001.fastq.gz | samtools view -bS - > ORD001_bwa_mem_default.bam samtools sort ORD001_bwa_mem_default.bam -o ORD001_bwa_mem_default.sort.bam samtools index ORD001_bwa_mem_default.sort.bam # coordinates ORD001_bwa_mem_default_Dod_K12b,2.13,0,3.17,1.09,29.50,31.57,0,0.75,9.39,1.76,20.64,0

ENA .bam coordinates:

Code:

ORD001_ENA_bam_Dod_K12b,2.13,0,3.17,1.09,29.50,31.57,0,0.75,9.39,1.76,20.64,0

ORD001 mapping with bwa aln with disabled seedlings, ... modified settings for Ancient samples:

Code:

bwa aln ref.fa ORD001.fastq.gz -n 0.01 -o 2 -l 1024 > ORD001.sai bwa samse ref.fa ORD001.sai ORD001.fastq.gz -f ORD001.sam samtools view -Sb ORD001.sam > ORD001.bam samtools sort ORD001.bam -o ORD001.sort.bam ####### to Add Read Group tags and index bam files: java -jar build/libs/picard.jar AddOrReplaceReadGroups INPUT=ORD001.sort.bam OUTPUT=ORD001.RG.bam RGID=rg_id RGLB=lib_id RGPL=platform RGPU=plat_unit RGSM=sam_id VALIDATION_STRINGENCY=LENIENT samtools index ORD001.RG.bam ####### to Mark and remove duplicates: java -jar build/libs/picard.jar MarkDuplicates I=ORD001.RG.bam O=ORD001.DR.bam M=output_metrics.txt REMOVE_DUPLICATES=True VALIDATION_STRINGENCY=LENIENT &> logFile.log samtools index ORD001.DR.bam ####### Local reads realignment java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R ref.fa -I ORD001.DR.bam -o target.intervals java -jar GenomeAnalysisTK.jar -T IndelRealigner -R ref.fa -I ORD001.DR.bam -targetIntervals target.intervals -o ORD001.final.bam --filter_bases_not_stored samtools index ORD001.final.sort.bam ####### flagstat file (some info about the .bam) samtools flagstat ORD001.final.sort.bam > ORD001.final.sort.txt coordinates: ORD001_bwa-aln_Dod_K12b,2.45,0,2.89,1.61,30.29,31.24,0,0.86,8.77,1.24,20.63,0

... the created files:

https://i.imgur.com/6xgDlHp.png?1

more info:
https://paleogenomics-course.readthe...apping_v2.html

thanks

I ran the ENA results

Target: ORD001_ENA_bam_Dod_K12b
Distance: 0.8054% / 0.80540055 | ADC: 0.25x RC
33.6 C7-Villa_Magna_MA
16.6 I3592
13.5 I1311
11.6 VEN022
8.8 NE_Iberia_c6CE_PL
8.4 ETR007
7.5 NE_Iberia_c8-12CE

I3592 ...............I3592 2457–2203 calBCE (3844±33 BP, BRAMS-1218) Alburg-Lerchenhaid, Spedition Häring, Stkr. Straubing, Bavaria Germany

I cannot find I1311
21-02-22, 07:24
Salento

Quote:

Originally Posted by torzio

thanks
I ran the ENA results
Target: ORD001_ENA_bam_Dod_K12b
Distance: 0.8054% / 0.80540055 | ADC: 0.25x RC
33.6 C7-Villa_Magna_MA
16.6 I3592
13.5 I1311
11.6 VEN022
8.8 NE_Iberia_c6CE_PL
8.4 ETR007
7.5 NE_Iberia_c8-12CE
I3592 ...............I3592 2457–2203 calBCE (3844±33 BP, BRAMS-1218) Alburg-Lerchenhaid, Spedition Häring, Stkr. Straubing, Bavaria Germany
I cannot find I1311

,, it's on the Dod, K12b SOURCE (Vahaduo) ... by Jovialis .. I think:

Code:

I1311:Olalde_2019,0,1.99,0,0,29.92,32.2,0,2.84,17.19,0.03,15.82,0
21-02-22, 07:42
torzio

Quote:

Originally Posted by Salento

,, it's on the Dod, K12b SOURCE (Vahaduo) ... by Jovialis .. I think:

Code:

I1311:Olalde_2019,0,1.99,0,0,29.92,32.2,0,2.84,17.19,0.03,15.82,0

seems odd ...............

Target: I1311:Olalde_2019
Distance: 0.0141% / 0.01414175 | ADC: 0.25x RC
99.7 I1311
0.1 Beaker_Central_Europe
0.1 I1982
0.1 NE_Iberia_Hel_(Empúries2)

closest to it is LBK_EN I5755 Central Europe .....Olande paper 2018
21-02-22, 08:02
Archetype0ne

Guys keep in mind that outside ORD009... the rest of the samples have ~5% coverage/quality...

Messapic lexical item	English translation	Proto-Messapic form	Paleo-Balkan languages	Other Indo-European cognates	Sources
ana	mother	*annā (a nursery word)	Proto-Albanian: *na(n)nā, amma;* Albanian: nënë/nana, ëmë/âmë ('mother')	Hittite: annaš ('mother'); Latin: amma ('mother'); Greek: ámma ('mother, nurse');	^[61]
anda	and, as well		Proto-Abanian: edhō/êndō; Albanian: edhe/ênde* ('and', 'yet', 'therefore')	Latin: ante ("opposite, in front of"); Hittite: anda; Greek: endha/ΕΝΘΑ; ('and' , 'as well')	^[62]
apa	from	*apo	Proto-Albanian: apo; Albanian: (për-)apë* ('from'); Albanian (Gheg): pi (PI < apa) ('from') or pa (PA < *apa) ('without')	Greek: apó; Sanskrit: ápa	^[63]
atabulus	sirocco		Proto-Albanian: abula; Albanian: avull* ('steam, vapor')	Proto-Germanic: *nebulaz ('fog')	^[64]
aran	field	*h₂r°h₃ā-	Proto-Albanian: arā: Albanian: arë, ara* ('field')	Hittite: arba- ('border, area'); Latvian: ara ('field')	^[65]
bàrka	belly		Proto-Albanian: baruka; Albanian: bark* ('belly')		^[66]
Barzidihi	(personal name)		Illyrian: Bardyl(l)is;Proto-Albanian: bardza; Albanian: bardhë/bardhi, Bardha* ('white', found also in anthroponyms, e.g., Bardhyl)^[a]		^[68]
bennan	(a sort of vehicle)	*benna		Gaulish: benna (a kind of 'carriage')	^[69]
biles/bilihi	son		Proto-Albanian: bira; Albanian: bir, pl. bilj - bij* ('son')	Latin: fīlius ('son')	^[70]
biliā/bilina	daughter	*bhu-lyā	Proto-Albanian: birilā; Albanian: bijë* - bija ('daughter'); older dialect bilë - bila ('daughter')	Latin: fīlia ('daughter')	^[70]
bréndon; bréntion	stag; stag's head		Proto-Albanian: brina; Albanian: bri, brî* ('horn'; 'antler')	Lithuanian: briedis, ('elk'); Swedish: brinde ('elk')The Messapic word is at the origin of the toponym Brendésion (Βρενδέσιον), Brentḗsion (Βρεντήσιον), modern Brindisi	^[71]
Damatura	Mother Earth (goddess)	*dʰǵʰ(e)m- matura	Proto-Albanian: dzō; Albanian: dhe* ('earth')	Latvian: Zemes Māte ('Mother Earth')Whether the (pre-)Illyrian form is at the origin of the Greek goddess Demeter or the contrary is unclear.^[72]	^[73]
deiva; dīva	god; goddess			Sanskrit: devá ('heavenly, divine'); Lithuanian Diēvas; Old Norse: Týr	^[74]
den	voice	*ghen	Proto-Albanian: džana; Albanian: zë/zâ, zër/zân* ('voice')		^[75]
hazavaθi	to offer (sacral)			ha- is a prefix, zav- is the same root as in Greek: χεών, Sanskrit ju-hô-ti and Avestan: zaotar- ('sacrificer')	^[76]
hipades	he/she/it offers, dedicates, sets up	*supo dhē-s-t	Proto-Albanian: skūpa: Albanian: hip* ('go up') and dha/dhash ('he gave/I gave')		^[77]
hipakaθi	offer, set up		Albanian: hip ('go up') and ka/kam ('he has/I have') > hip-ka-		^[78]
klaohi/klohi	hear, listen (invocative)	*kleu-s-	Albanian: kluoj/kluaj/kluhem ('call, hear')	Greek: klythí ('hear'); Sanskrit: śrudhí ('hear'); Slavic: slušati ('hear'); Lithuanian: klausyti ('hear')	^[79]
kos	someone	*q^wo	Proto-Albanian: kuša; Albanian: kush* ('who')	Tocharian A: Kus ('who')	^[80]
ma	not	*meh₁	Albanian: ma, me, mos	Greek: mē; Sanskrit: mā	^[81]
menza	foal	*mendyo	Proto-Albanian: mandja; Albanian: mëz* - maz ('foal'); mend ('to suckle'); Romanian (< Dacian) mînz ('foal')	Gaulish: mandus ('foal')	^[82]
ner	man	*ner-	Proto-Albanian: nera; Albanian: njeri* ('man')	Greek: ανηρ ('man'); Sanskrit: nar- ('man')	^[83]
penkaheh	five		Proto-Albanian: pentše; Albanian: pesë* ('five')	Lithuanian: penki ('five')	^[84]
rhīnós	fog, mist, cloud		Proto-Albanian: rina: Albanian: re, rê, rên* ('cloud')		^[85]
tabarā; tabaras	priestess; priest (lit. 'offerer')	to-bhorā; to-bhoros	Albanian: të bie/të bar, bjer/bar ('bring', 'carry')	Greek: ϕορός ('bring'); Latin: ferō ('bring')	^[86]
teutāTaotor	community, people(name of a god)	*Toutor	Illyrian: Teuta(na) ('mistress of the people', 'queen')	Oscan: touto ('community'); Old Irish: túath ('tribe, people'); Lithuanian: tautà ('people'); Gothic þiuda 'folk'	^[87]
veinan	his; one's		Albanian: vetë ('himself, oneself')	Sanskrit: svayàm ('himself')	^[88]
Venas	desire (name of a goddess)	*wenos		Latin: Venus; Old Indic: vánas ('desire')	^[89]
Zis	sky-god	*dyēs	Illyrian: dei- or -dí ('heaven, god', as a prefix or suffix);Albanian Zojz ('sky-god')	Hittite: šīuš ('god'); Sanskrit: Dyáuṣ; Greek: Zeus; Latin: Jove ('sky-god')	^[90]

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