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View Full Version : DNA from medieval plague victims suggests long-term effect of Yersinia pestis



kingjohn
21-05-21, 17:37
Abstract

Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggests that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.


https://en.wikipedia.org/wiki/Ellwangen


https://imgur.com/eP8jTu2

source:
https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab147/6277411

ENA bam files:
https://www.ebi.ac.uk/ena/browser/view/PRJEB44124

someone ( anthrogenica) checked for there y calls
he used this tool :

https://github.com/alinja/snipsa


here :

ELW003:ELW003: Total SNPs: 5538
ELW003:Result (85.2% 75 -0 +13): R-S263
ELW003:Extra: FGC24758 M1299 Y130813 F176/M2314(H) Y24639 FGC39020 MF1122 Y23015/FGC49836 ACT4753 FGC63587 BZ1837 Z14156 BY43648/Y143745

ELW008:ELW008: Total SNPs: 11404
ELW008:Result (87.7% 153 -1 +18): R-M269
ELW008:Extra: Y45410 Y3184/FGC10846/B523 YP4584 Z41980/Y25912 FGC3467 Z25581 Y177584 BY6279 FGC32481 BY5214 BY203482 Y135097/BY50012 PH3948/V7242 FGC5237 ZS3228 Y131338 Y195182/FT257645 CTS12922

ELW012:ELW012: Total SNPs: 9974
ELW012:Result (89.1% 114 -0 +14): R-Y4355
ELW012:Extra: K664/Z7098 Y218901 FT344630 Y16362 Y29248 FGC53096 Y13977 FGC39459 CTS4174/Z932 Z35371 Y24728 Y75989 BY137992 FGC19454

ELW013:ELW013: Total SNPs: 6021
ELW013:Result (87.5% 70 -0 +10): J-M205
ELW013:Extra: BY25303 Y210364/FT353750 Y21542 FGC12477/YFS097057 A19488 Y23575 Y99420 Y20409 Y11889 FT54721

ELW017:ELW017: Total SNPs: 1639
ELW017:Result (81.0% 17 -0 +4): R-M269
ELW017:Extra: Z34625 Z18733 Z24804 F3150

ELW018:ELW018: Total SNPs: 8312
ELW018:Result (91.1% 113 -0 +11): E-Z1057
ELW018:Extra: F14154 A8555 Y88897 Y35189 BY98137 Y167928/MF69939 CTS5707 Y41594 ZS6407 Y183016 Y161058/V7408

ELW020:ELW020: Total SNPs: 9197
ELW020:Result (85.9% 116 -0 +19): R-Y28607
ELW020:Extra: ZS11714 Y21077 Y210364/FT353750 F1194 Y308/Z3278 FGC49258 Y37927/BY27595 FT1864 F312 L532 A2407 Z5543 CTS7412/PF4742 BY117387 FGC27132 F4286 ZS4326 PF6331 Y11600/Z30434

ELW023:ELW023: Total SNPs: 3655
ELW023:Result (93.5% 43 -0 +3): I
ELW023:Extra: Y193594 Y55500 YP4420

ELW024:ELW024: Total SNPs: 8191
ELW024:Result (83.3% 90 -0 +18): I-Y3259
ELW024:Extra: FT194743(H) FT223600 BY15859 Y1304 CTS1031 Y2770/FGC4873 SK701 YP1079 BY91188 Y32698 P244/PF5896/P244.1/P244.2 Y95380 Y11545/BY9/FGC14303 FT160542 FT5647 FGC49732 F25041 Y112334

ELW025:ELW025: Total SNPs: 5746
ELW025:Result (82.1% 55 -0 +12): J-Y15058
ELW025:Extra: FGC66076 Y136670 A2665/YP2748/V4962 Y199009/FT307714 Y26948 CTS4259/PF6186/M683 Y32384/Z32114 YP4027 Y34001 FT155425 FT14181/Y167684 F3655

ELW026:ELW026: Total SNPs: 8229
ELW026:Result (87.4% 111 -0 +16): R-Y140972
ELW026:Extra: F912 ZS4713 BZ182/ZS3313 Y23731 Z41987/Y25919 Y67770 FGC57630 Y137220 Y147111 BY201722 Y74335 FT30971 FGC27338 Y35950 Y59285 Y10762/FGC30041/Z24283

ELW027:ELW027: Total SNPs: 4982
ELW027:Result (83.3% 68 -1 +10): I-Y6098
ELW027:Extra: FGC7837/SK1172/Y12288 Z14803 MF1858 S9939 Y36187 Y410/E207 Y141863 Z6278 Y140512 Y191016

ELW028:ELW028: Total SNPs: 10146
ELW028:Result (89.1% 123 -0 +15): R-CTS1450
ELW028:Extra: ZS3928 FGC37316(H) BY199186 Y63066 F3896 ZS11772 CTS3332 A15393 Z3008/S962 ZS10665 CTS8956 Y75913 Y18036 PH5314 Y27135

ELW029:ELW029: Total SNPs: 7110
ELW029:Result (84.0% 89 -0 +17): E-FGC18981
ELW029:Extra: Y168632 Y29230 CTS1031 BY199186 BY3337 Y16303 Y20450 PF6120 Y30751 M8753 FGC22476 CTS3779 FGC59033 Y51350 Y175792/FT79440 Z26447 MF169067/Y197181

ELW030:ELW030: Total SNPs: 2295
ELW030:Result (75.0% 27 -0 +9): I-S2524
ELW030:Extra: Z12609 BY27323 Y30959 FGC75097/Y94684 Y19059/FGC41729 FGC49489 Z14146 Y32117 FT210981

ELW031:ELW031: Total SNPs: 2931
ELW031:Result (76.4% 45 -1 +10): R-Y34151
ELW031:Extra: BY3311 Z21197/V4826 Y16823 PF2440 BY47759 Y19428/BY14018 Y199142 CTS7984/PF4029 Z7460 PF2392/M5289

ELW032:ELW032: Total SNPs: 2963
ELW032:Result (75.8% 28 -1 +5): J-L283
ELW032:Extra: Y32553 BY54574 FGC71466(H) CTS3632 BY15965/Y32224

ELW033:ELW033: Total SNPs: 7200
ELW033:Result (86.0% 80 -0 +13): R-Z2103
ELW033:Extra: BY33765/Y39663 ZS11772 Y141139 Y3940/F4946 Y27615/Z42011 Y40976 Z1866/CTS5559/PF4730 Y21265 CTS6304 Z30308 Y101686/BY30637 Z22098 Z45709

ELW035:ELW035: Total SNPs: 5688
ELW035:Result (83.0% 76 -1 +12): R-YP4664
ELW035:Extra: M2380 V2034 FT174498 Y172388 F258 MF110071/FT116761 FGC87630 Y40809 Z30734/Y13114 Y19009/Z38852 Z18792 BY189555

ELW036:ELW036: Total SNPs: 7999
ELW036:Result (86.5% 112 -1 +14): E-M81
ELW036:Extra: Z36905 Y32001 Z24941 Y14904/FGC12125 M6094 Z32507 BY18522 Y50666 Z6379/V2959 FT96685 PH3173 S22069 ALK815 Y6287/FGC23830

ELW037:ELW037: Total SNPs: 8292
ELW037:Result (80.3% 104 -2 +18): C-F1756
ELW037:Extra: Z5984 BY23447 CTS1008/PF1516/M5391 F15662 Y13138 FGC32838 Y306/Z3265 Y199009/FT307714 FT248952 Y12794/F14141/MPB355/MPB409 CTS3337/PF1653 BY14327 FT180232 FT5337 CTS4746 Z33330 Z18235/Y13398 FT63401

ELW038:ELW038: Total SNPs: 2515
ELW038:Result (77.1% 30 -1 +5): J-L283
ELW038:Extra: FGC41448 Y1039 Y163141/BY201669 YP4027 CTS12478/PF6529

ELW040:ELW040: Total SNPs: 4358
ELW040:Result (86.2% 50 -0 +8): R-M269
ELW040:Extra: Y28221 Z22015 FT185350 Z20493 Y167716 Y22831 Z5972 M179/PAGE31/PAGES00031

p.s
interesting for me to see beyond e-v13 which is expected
also e-L19 > E-PF2438 individual and e-m81 individual :cool-v:
those 2 could arrived to germany in roman times :smile:

Yanis
19-07-21, 19:31
ELW029 is on FGC18981 subclade

kingjohn
19-07-21, 19:38
ELW029 is positive for one of my private snps, our branch is an offshoot of BY9849, this is a very big find for me.

yanis that is very cool :cool-v:
can you upload ELW029 to yfull ?

p.s
it might arrived to southern germany with roman army
or with auxilary troops attached to therm who were left behind

Yanis
19-07-21, 20:11
I sent them an email, they replied that they could not immediately add it to their tree because this sample is of poor quality and coverage. They plan to modify their algorithm to be able to add any sample anyway.
Regarding its origin, the Roman scenario is the one that is the consensus, given that the entire FGC18973 clade is inside the limes. See the distribution of FGC18981.

kingjohn
19-07-21, 21:30
I sent them an email, they replied that they could not immediately add it to their tree because this sample is of poor quality and coverage. They plan to modify their algorithm to be able to add any sample anyway.
Regarding its origin, the Roman scenario is the one that is the consensus, given that the entire FGC18973 clade is inside the limes. See the distribution of FGC18981.


yanis ,
small question not related to ELW029 dude :smile:

there is already 1 confirmed azeri from iran in ftdna
but i look at this site /page 4
https://www.pf2431.com/personalities
is this armenian leader is also e-L19
is it confirmed by relative of him ?

i am asking
because if he is maybe you to put him in the famous e1b1b1 thread :thinking:

Yanis
20-07-21, 00:04
Please John, the Armenian sample is my closest match, it is also BY9849. The person who manages this account has put all information about him in private, I don't think they want to have their identity made public. On the other hand there is another line which is also BY9849 and that of the Queen of England Catherine Pegg. Or, from the same Saint John Fisher branch.

kingjohn
20-07-21, 14:21
Please John, the Armenian sample is, after ELW029 my closest match, it is also BY9849. The person who manages this account has put all information about him in private, I don't think they want to have their identity made public. On the other hand there is another line which is also BY9849 and that of the Queen of England Catherine Pegg. Or, from the same Saint John Fisher branch.



i respect that ...
but it is a little bummer :sad-2:
because he is a very famous person
he was one of the top 5 back in the ussr after all :cool-v:

Yanis
20-07-21, 14:50
I find it a shame too, we can only respect his will, maybe he will change his mind later

kingjohn
20-07-21, 16:26
I find it a shame too, we can only respect his will, maybe he will change his mind later

your branch ( and also ELW029):cool-v:

https://www.yfull.com/live/tree/E-FGC18960*/

Yanis
20-07-21, 23:47
the results of ELW029 have been verified and corrected, in the end we only know that it is E-FGC18970 which is equivalent to E-FGC18981 ancestor of BY9849 / FGC18960. The latter is my subclade.

kingjohn
21-07-21, 00:45
the results of ELW029 have been verified and corrected, in the end we only know that it is E-FGC18970 which is equivalent to E-FGC18981 ancestor of BY9849 / FGC18960. The latter is my subclade.


So he can fall on the south german line in yfull
Or the swiss/ spanish line in yfull
under e-fgc18981
https://www.yfull.com/live/tree/E-FGC18981/
Thanks for update :good_job:
He is still very close to you :cool-v:

P.s
I am guessing he is not in best quality
Thats why we can't know the downstream branch under e-fgc18981 he belong to