Genomic analysis of two Pompeians that died during the eruption of Vesuvius in 79 AD

kingjohn

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Y-DNA haplogroup
e-fgc7391 500CE
mtDNA haplogroup
h3ap
The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian’ genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.

pDdT82A.png




source:

https://www.nature.com/articles/s41598-022-10899-1


p.s
fascinating the male carried y haplogroup A-M13

Sex determination and uniparental genetic markers

The genetic sex determination (estimated by RY parameter26, and by the X chromosome coverage) confirmed the morphological determination that individual A was a male (Table 1).
The mitochondrial DNA haplogroup was identified using HaploGrep227,28 (Table 1), and revealed that the individual belongs to the haplogroup clade HV0a, the main monophyletic branch of HV0 and subclade of haplogroup HV. This mitochondrial lineage is absent among published Roman Imperial individuals from Italy29. In Europe, the first evidence of the HV haplogroup is from a Magdalenian period individual from Spain30 while in Italy from a Mesolithic individual from Sicily (Favignana)31. The HV haplogroup is actually associated with the early human dispersal in Eurasia after the Last Glacial Maximum (LGM)32. It is unevenly spread across Europe with highest frequencies in the Near East (~11%)33, in south Europe (from ~4% to ~11%)34 and in the Balkan peninsula (~8%)35. HV0a coalesces around 12.5–11.0 kya ago34 and, among the extant populations, is common in Sardinia36.
Individual A, albeit at low coverage (Table 1), was found to belong to the Y-chromosome lineage A-M13 (A1b1b2b), a rare lineage absent among ancient individuals from the Italian Peninsula29, mainly found in Eastern Africa (~ 40%), but with known occurrences, at much lower frequencies, in the Near East (Turkey, Yemen, Egypt, Palestine, Jordan, Oman and Saudi Arabia) and the Mediterranean islands of Sardinia, Cyprus and Lesbos37,38,39,40. Downstream of A-M13 and restricting the analysis to transversions polymorphisms, the individual can be placed at A-V5880, a sub-haplogroup that contains all A-M13 positive Sardinians from past studies39,40, and that has been dated to coalesce around 7.62 (± 0.92) thousands of years ago, using Bayesian analysis40.


according to user teenpean47 from anthrogenica
he was here in the A-m13 tree:


Yleaf 3.0:

Code:
A-V6275


Snipsa:

Code:
Result (40.0% 344 -5 +479): A-V3663



thats the european branch that was found in sardinians:)

https://www.yfull.com/tree/A-V6275*/
 
Very Interesting indeed. It also has the mtdna of HV0a

indeed thats what so cool in ancient dna
we can find branches who are pretty rare nowdays(y)
any way his autosomal from the paper


iUyBYpa.png




his
eurogenes k15:

f1R,2.85,12.49,3.85,0,15.79,21.28,31.41,9.93,0.53,0,0,0,0,0.99,0.88

Distance to: f1R
8.94930724 Sephardic_Jewish
9.21028773 Italy_East_Sicily
9.25833138 Italy_Calabria


he is close to imperial roman averege in his k15 values ( user ajeje from anthrogenica run)(y)



SampleNorth_SeaAtlanticBalticEastern_EuroWest_MedWest_AsianEast_MedRed_SeaSouth_AsianSoutheast_AsianSiberianAmerindianOceanianNortheast_AfricanSub-Saharan
Rome_Imperial_proxy4,8013,483,110,9217,4019,2031,996,980,630,100,050,080,300,750,23
Pompeian f1R2,8512,493,85015,7921,2831,419,930,5300000,990,88

FrcgHA0.png
 
thanks KingJohn :)

Code:
f1R_Pompeii_Dodecad_K12b,9.89,0.00,7.71,2.10,21.94,4.65,0.00,0.00,16.49,0.00,36.41,0.81


Distance to:f1R_Pompeii
4.06247462C4-ANAS_Imperial_Rome:R73:Antonio_2019
6.07334340C5-Marcellino_&_Pietro_Imperial_Rome:R134:Antonio_2019
6.20552173C5-Necropolis_of_Monte_Agnese_Imperial_Rome:R1543:Antonio_2019
6.43018662C5-Mausole_di_Augusto_Late_Antiquity:R34:Antonio_2019
6.48233754C4-Isola_Sacra_Necropolis_Imperial_Rome:R41:Antonio_2019
6.82000000Collegno30:Amorim_2018
7.26622323C5-Marcellino_&_Pietro_Imperial_Rome:R130:Antonio_2019
7.41182164MAS002:Etruscan_Pre-Print_2021
7.50069997C5-Viale_Rossini_Necropolis_Imperial_Rome:R81:Antonio_2019
7.62155496Ashkelon_IA1:ASH067:Feldman_2019_(Jul.)
7.75602347C5-Via_Paisiello_Necropolis_Imperial_Rome:R115:Antonio_2019
8.39610624Latini_o:R850:Antonio_2019
8.47413712C5-Isola_Sacra_Necropolis_Imperial_Rome:R39:Antonio_2019
8.66876000C4-Viale_Rossini_Necropolis_Imperial_Rome:R75:Antonio_2019
8.79847714Collegno38:Amorim_2018
8.85150835C5-Marcellino_&_Pietro_Imperial_Rome:R133:Antonio_2019
9.26573257C5-Isola_Sacra_Necropolis_Imperial_Rome:R45:Antonio_2019
9.46565898C5-Mausole_di_Augusto_Late_Antiquity:R30:Antonio_2019
9.47827516C4-ANAS_Imperial_Rome:R70:Antonio_2019
10.15801654Collegno25:Amorim_2018
10.17498403C5-Monterotondo_Imperial_Rome:R1548:Antonio_2019
10.26901164C6-Centocelle_Necropolis_Imperial_Rome:R51:Antonio_2019
10.37483976C5-Casale_del_Dolce_Imperial_Rome:R123:Antonio_2019
10.42934801C5-Centocelle_Necropolis_Imperial_Rome:R50:Antonio_2019
10.46644161C5-ANAS_Imperial_Rome:R66:Antonio_2019
 
Very cool Kingjohn and Salento. When I got to know ancient Pompeii together with my wife, I realized a youthful dream. A magical place. Out of curiosity, I used the coordinates of the ancient Pompeian to compare it with the modern Italians whose coordinates were presented by Salento in the thread https://www.eupedia.com/forum/threa...Italy-using-ancient-and-modern-samples/page33

Distance to:f1R_Pompeii_Dodecad_K12b
9.16212857NaN275IS_Campania
9.32100316Pu8_Apulia
9.92619766ALP582_Calabria
9.95910137NaN65DFG_Campania
11.31461002NaN77FAM_Campania
11.63029664W-Sicily21
11.95650032ALP596_Calabria
12.09518499PG16_Basilicata
12.34910523Pu7_Apulia
12.64443356W-Sicily3
12.64869163TP07_Trapani_LazaridisNat2014
12.84183787W-Sicily5a
12.86452098NaN58AC_Campania
13.00637536NaN195ST_Campania
13.03057942NaN128LA_Campania
13.06731036Ag-Sicily8
13.12561999NaN207MM_Campania
13.15046387Ag-Sicily5
13.33566646W-Sicily1
13.37872939Pu3_Apulia
13.44177444W-Sicily9
13.54138472NaN46TC_Campania
13.69120886TP05_Trapani_LazaridisNat2014
13.77893320PG20_Basilicata
13.85775956PG25_Basilicata

Distance to:f1R_Pompeii_Dodecad_K12b
9.0742316537.20% Pu8_Apulia + 62.80% NaN275IS_Campania
9.3073986487.20% Pu8_Apulia + 12.80% ALP582_Calabria
9.8552686754.80% ALP582_Calabria + 45.20% NaN65DFG_Campania
11.1666478123.40% TP07_Trapani_LazaridisNat2014 + 76.60% NaN77FAM_Campania
11.2083983733.20% W-Sicily21 + 66.80% NaN77FAM_Campania
11.2645214614.60% NaN58AC_Campania + 85.40% NaN77FAM_Campania
11.290069408.80% TP05_Trapani_LazaridisNat2014 + 91.20% NaN77FAM_Campania
11.312862032.60% W-Sicily9 + 97.40% NaN77FAM_Campania
11.5805724873.40% W-Sicily21 + 26.60% ALP596_Calabria
11.6281632795.00% W-Sicily21 + 5.00% Pu7_Apulia
11.6302928599.80% W-Sicily21 + 0.20% Pu3_Apulia
11.8156077428.80% TP07_Trapani_LazaridisNat2014 + 71.20% ALP596_Calabria
11.9068188981.80% ALP596_Calabria + 18.20% NaN58AC_Campania
11.946989266.60% TP05_Trapani_LazaridisNat2014 + 93.40% ALP596_Calabria
11.9489253918.40% PG16_Basilicata + 81.60% ALP596_Calabria
11.9533899995.00% ALP596_Calabria + 5.00% NaN195ST_Campania
11.9559670342.80% TP07_Trapani_LazaridisNat2014 + 57.20% Pu7_Apulia
11.9977491827.60% TP07_Trapani_LazaridisNat2014 + 72.40% PG16_Basilicata
12.0792947787.80% PG16_Basilicata + 12.20% NaN58AC_Campania
12.094691561.80% W-Sicily9 + 98.20% PG16_Basilicata
12.1473915661.40% TP07_Trapani_LazaridisNat2014 + 38.60% Pu3_Apulia
12.2297113270.00% Pu7_Apulia + 30.00% NaN58AC_Campania
12.2635121620.80% W-Sicily9 + 79.20% Pu7_Apulia
12.2901016258.80% TP07_Trapani_LazaridisNat2014 + 41.20% NaN195ST_Campania
12.3043201014.80% TP05_Trapani_LazaridisNat2014 + 85.20% Pu7_Apulia
 
… nice Duarte, … too bad there’s only one Pompeii sample, … is not close to modern Italians, … maybe f1R is only half Italian, or … :)
 
Despite this high genetic variability in the Imperial period29 the Pompeian individual A shows a higher level of shared genetic drift with the central Italy Roman Imperial Age group. This result strongly suggests that the individual that we have analysed should come from the Italian peninsula. Whether this individual belongs to the local population of Pompeii or is part of the 5% of the internal migrants characterizing the imperial population of Italy85 is difficult to address, but very likely he is not part of the large external migrations related to the practice of enslavement.



p.s
in other words
the reserchers think he was native to italy not a slave
could be from pompeii or internal immigrant from south


 
Despite this high genetic variability in the Imperial period29 the Pompeian individual A shows a higher level of shared genetic drift with the central Italy Roman Imperial Age group. This result strongly suggests that the individual that we have analysed should come from the Italian peninsula. Whether this individual belongs to the local population of Pompeii or is part of the 5% of the internal migrants characterizing the imperial population of Italy85 is difficult to address, but very likely he is not part of the large external migrations related to the practice of enslavement.



p.s
in other words
the reserchers think he was native to italy not a slave
could be from pompeii or internal immigrant from south



I said half Italian, … According to their PCA, f1R is to the right of most imperial Romans:


RsMPd4L.jpg
 
I said half Italian, … According to their PCA, f1R is to the right of most imperial Romans:


RsMPd4L.jpg

ok,
in your opinion was he half levnatine ?



We extracted and sequenced DNA from a petrous bone from each Pompeian individual with identical procedures (see “Materials and methods”) and obtained 0.4 X (individual A) and 0.0013 X (individual B) average genome-wide depth of coverage (Table 1). Both individuals displayed typical signatures of aDNA25 (Supplementary Fig. S2). Low rates of contamination with modern human DNA (0.8% for the mtDNA and between 0.6 and 0.8% for the X chromosome, Table 1 and Supplementary Figs. S2, S3) for individual A confirmed the authenticity of the aDNA. The low coverage obtained for individual B prevented us from reaching any further assessments of quality parameters. Herein, we report the details of the analyses only for individual A.


1585.jpg
9W5BoOE.png



p.s
to bad that the female individual_B was in low coverage :unhappy:
would have been interesting to see her autosomal profile
 
I guess I could say that f1R is almost a C4, but C5 shifted :)
 
Despite this high genetic variability in the Imperial period29 the Pompeian individual A shows a higher level of shared genetic drift with the central Italy Roman Imperial Age group. This result strongly suggests that the individual that we have analysed should come from the Italian peninsula. Whether this individual belongs to the local population of Pompeii or is part of the 5% of the internal migrants characterizing the imperial population of Italy85 is difficult to address, but very likely he is not part of the large external migrations related to the practice of enslavement.



p.s
in other words
the reserchers think he was native to italy not a slave
could be from pompeii or internal immigrant from south



Pretty much in line with the stance I have been holding last few years. Can't say I am surprised, but might blindside some others.
 
"The position of the Pompeian individual A in the PCA falls also close to the distribution of modern Mediterranean and Near Eastern populations, such as Greeks, Maltese, Cypriots, and Turks. Such a result allowed us to hypothesize a genetic contribution from the Near East. This hypothesis can be also supported by a cline from Neolithic Iran (Iran_N) to Italy Imperial Roman Age (Italy_IRA, including the Pompeian individual) passing through Chalcolithic Iran (Iran_CA) and Iron Age Iran (Iran_IA)."
 
ok,
in your opinion was he half levnatine ?


It doesn't look so, the study characterises him as:
1)"positioned close to the well-documented Neolithic cline of Anatolians to European populations"
2)We further attempted to investigate if the fit could be improved by including Morocco_Iberomaurusian as a fifth source, but no three-, four- or five-way mixture with this last component produced significant results"

Basically he is described like an European with heavy caucasus-related ancestry, in my opinion the best bet is to think he was from (western, at least) Anatolia, whose genetic gene pool has been tentatively modelled as half Balkan_IA and half Anatolian_BA; also the autosomal modelling seems to me compatible with Anatolian origins.

Furthermore, historically one would expect that the bulk of the greek-speaking foreigners in the empire came from Anatolia, since it was by far the most populous greek-speaking region.

Anyway let's keep in mind that the coverage isn't great, though so far it does suggest he is compatible with previous samples from the imperial era.
 
Someone ran the coordinates over at the other forum.

Thanks!


Italy_Roman_Empire_Pompeii:f1r_K13_sim,0.0921,0.152,-0.0282,-0.0622,-0.0013,-0.0224,-0.0031,-0.0036,0.0074,0.0238,0.0022,0.0039,-0.01,0.0028,-0.0067,-0.006,-0.0085,-0.0056,-0.0029,0.0016,0.0044,0.0033,0.0049,-0.0095,0.0039


Distance to: f1r_K13_sim
0.02499165 Romaniote_Jew
0.02578224 Sephardic_Jew_Turkey
0.02606108 Sephardic_Jew_Bulgaria
0.02813043 Italy_Roman_Empire_Isola_Sacra_(East_Med_Profile)
0.02983147 Italian_Jew
0.03068052 Syrian_Jew
0.03075081 Turkish_Cyprus
0.03118686 Greek_Dodecanese_Kastellorizo
0.03120488 Greek_Cyprus
0.03221559 Italy_Roman_Empire_Mazzano_Romano_(East_Med_Profile)
0.03303802 Italy_Medieval_Lombard_Period_Collegno_(East_Med_Profile)
0.03379413 Italy_Late_Antiquity_Rome_(Anatolian_Profile)
0.03428852 Italy_Late_Antiquity_Rome_(East_Med_Profile)
0.03429758 Israel_IAI_Ashkelon_Philistine_(Mixed_East_Med/Near_East_Profile)
0.03467091 Ashkenazi_Jew_France
0.03516780 Greek_Dodecanese_Rhodes
0.03539949 Italy_Roman_Empire_Isola_Sacra_(Anatolian_Profile)
0.03548958 Italy_Roman_Empire_Rome_(East_Med_Profile)
0.03550317 Iberia_Catalonia_Empuries_Roman_Empire_(East_Med_Profile)_(low_res)
0.03614354 Greek_Dodecanese_Symi
0.03638095 Greek_Dodecanese_Karpathos
0.03650923 Algerian_Jew
0.03661224 Ashkenazi_Jew_Germany


To think people used to get banned from this forum for even mentioning Cyprus or Anatolia.
Shoutout to dosas.

Anybody have K13 coords for it yet? Since there's a K15 version, here's a K15-to-G25 sim for F1R:


Code:
Italy_Roman_Empire_Pompeii:f1r_K15_sim,0.0926,0.15,-0.0292,-0.0607,-0.0016,-0.0204,-0.0018,-0.0023,0.0066,0.0215,0.0037,0.0028,-0.0072,0.0039,-0.0041,-0.0071,-0.0088,-0.004,-0.0024,-0.0005,0.0029,0.0006,0.0055,-0.0099,0.0023


Distance to: Italy_Roman_Empire_Pompeii:f1r_K15_sim
0.02290785 Sephardic_Jew_Bulgaria
0.02309899 Sephardic_Jew_Turkey
0.02350077 Romaniote_Jew
0.02707769 Turkish_Cyprus
0.02783179 Italy_Roman_Empire_Isola_Sacra_(East_Med_Profile)
0.02825899 Syrian_Jew
0.02853540 Italian_Jew
0.02879994 Italy_Roman_Empire_Mazzano_Romano_(East_Med_Profile)
0.02930734 Greek_Dodecanese_Kastellorizo
0.02988457 Greek_Cyprus
0.03160058 Italy_Medieval_Lombard_Period_Collegno_(East_Med_Profile)
0.03232923 Ashkenazi_Jew_France
0.03310888 Greek_Dodecanese_Rhodes
0.03318322 Italy_Late_Antiquity_Rome_(East_Med_Profile)
0.03434856 Italy_Roman_Empire_Rome_(East_Med_Profile)
0.03435879 Ashkenazi_Jew_Germany
0.03459865 Italy_Late_Antiquity_Rome_(Anatolian_Profile)
0.03463475 Greek_Dodecanese_Symi
0.03469388 Greek_Dodecanese_Nisyros
0.03471493 Greek_Dodecanese_Karpathos
0.03483847 Turkish_Cyprus_(Levant-Shifted_Profile)
0.03502949 Iberia_Catalonia_Empuries_Roman_Empire_(East_Med_Profile)_(low_res)
0.03543995 Italy_Late_Antiquity_Marsiliana_d'Albegna_(East_Med_Profile)


Basic components:
0.4% Iberomaurusian
0.6% WHG
49.6% ANF
14.8% CHG
10.8% Iran Neo
15.4% Natufian
8.4% Yamnaya


Extremely East Med, more on the hither-Cypriot end of the continuum, probably very similar to Vranas Marathon.


I mean with all the rumors going around, and the marathon sample being part of the Danubian Limes paper as a placeholder for East Med admixture composition, one would think the writing was on the wall.
From what I gather more samples are probably going to be published from Pompei, so talking about outliers might be a faux pas.
 
Someone ran the coordinates over at the other forum.




To think people used to get banned from this forum for even mentioning Cyprus or Anatolia.
Shoutout to dosas.

It is simulated coordinates though

I mean with all the rumors going around, and the marathon sample being part of the Danubian Limes paper as a placeholder for East Med admixture composition, one would think the writing was on the wall

The same paper argued that so far the data suggested that the near eastern foreigners did not contribute to the subsequent gene pool of the Balkans, and this very recent paper does the same https://www.biorxiv.org/content/10.1101/2022.05.15.491973v1.article-metrics, though I see how one can argue for a partial Anatolian input in south east Europe and south Italy.

There's no such thing as an "east med" genetic component, it is either Levantine or Anatolian, since the latter virtually lacked (was extremely low compared to Anatolian_N) the natufian present in the former, and indeed the Daunubian limes paper showed that even using the least natufian-like and most anatolian-like Levantine (Alalakh samples) provided bad fits when modelling the near eastern (Anatolian) samples and the only near eastern outlier was easily told apart because he was genetically like a northern Levantine.

Thus, the only thing faintly written on the wall is a partial Anatolian contributio, maybe.
 
True. Do you think the actual ones will be much different though?
 
True. Do you think the actual ones will be much different though?


Though it can be that the Iberomaurasian could be too low to detect in formal stats if the sample was half Levantine, the fact that the tests showed this sample showed no significant affinities is a hint that he was not, furthermore he is described as "positioned close to the documented Neolithic cline of Anatolians to European populations", though with a considerable caucasus-related gene flow ("Iran_N" here).
In the Danubian limes paper Anatolians were modelled as half Balkan_IA and half Anatolian_BA, he looks like more consistent with such an analysis rather than with a Levantine-Italic combination
 
Though it can be that the Iberomaurasian could be too low to detect in formal stats if the sample was half Levantine, the fact that the tests showed this sample showed no significant affinities is a hint that he was not, furthermore he is described as "positioned close to the documented Neolithic cline of Anatolians to European populations", though with a considerable caucasus-related gene flow ("Iran_N" here).
In the Danubian limes paper Anatolians were modelled as half Balkan_IA and half Anatolian_BA, he looks like more consistent with such an analysis rather than with a Levantine-Italic combination

Fair enough. What are your thoughts on some of the Croatian samples from the recent paper showing the same Anatolian/Levantine, or whatever one wants to call the East-Med shift?

I mean, there is a less than 0 chance, and by rumors quite possible, that such a population was prevalent in the Balkans, just look at the Marathon sample. For all we know populations that were not usually associated with the east might turn up east shifted well into the BCs, and might have been in Italy earlier than Imperial period, as we already have had a couple of late republic samples showing such autosomal admixture. Maybe the Balkan_IA, Anatolian_Ba holds the key, but I still have to see what Balkan IA they are talking about, since there might have been a couple of profiles... As for Anatolian BA, which sample do they mean?

Edit: In fact I am really interested in this Anatolian_BA profile... is it some yet unpublished Western Anatolian sample? Troy or whatever was supposedly coming out some time ago? Also, I am not really talking about Iberomaurusian here, talking about Greek Islander like profile.
 

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