The population genomic legacy of the second plague pandemic

[kingdavid]

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.


source:

https://www.sciencedirect.com/science/article/pii/S0960982222014671#mmc1

y haplogroups :

pre-plague
1175-1275 sk372 R1b1a1a2
1175-1225 sk328 R1b1a1a2a1a1c2b1b4e1a2c1


post -plague
1585-1897 wf629 "N1a1a1a1a1a1a5
1585-1897 wf193 R1b1a1a
1585-1897 wf131 I1a
1585-1897 wf301 I1a
1585-1897 wf531 R1b1a1a2a1a
1585-1897 wf305 R1a1a1b1a3a3b1
1585-1897 wf148 "R1a1a1b1a3a2e1
1585-1897 wf192 I1a1b1g


modern residents of trondheim
tr1 R1b1a1a2a2
tr11 R1b1a1a2a1a1c2b2a1b1a1a2b2
tr12 J2a1b
tr13 R1b1a1a2a1a1c2b1b4e1a2c1
tr14 R1a1a1b1a3a2e4b
tr15 I1a2a1a1d1a
tr17 I1a1b1a4a2f1a1a1
tr18 I1a1b1a4a2
tr20 R1a1a1b1a3a2a1
tr21 R1b1a1a2a1a1b1a
tr3 "I1a1b1a4a2f1a1a7
tr5 "R1a1a1b1a3a1
tr7 E1b1b1b2a1a4d2c ( interesting this is aschkenazi y subclade in 1880 there was jewish community in trondheim anyway autosomally this individual cluster with modern scandinavians)
tr8 "R1b1a1a2a1a1b1b
tr9 R1b1a1a2a1a1g

 

[Angela]

Makes sense to me. Has made sense to me for over twelve years, when I had a debate over it with Ken on dna-forums. He was very dismissive of the idea that it would have had any effect at all.

Well, at least in Norway it did, although it seems to me that in this particular case a lot of the effect was caused by a halt to migration, which reduced the "Celtic" ancestry component arriving from England.

As they admit, it's a difficult question to answer completely given the current state of the technology.

It seems to me now and it seemed to me then, that a massive population crash, in some areas, not so massive in others, might skew the composition of surviving generations by decreasing variation. As one example, one of my mother's ancestral towns lost 70% of its citizens. Others further up the mountains, not just in my father's part of the Apennine range, but in the Ligurian and Apuan Alps of my mother, had lower numbers, in the 30-40% range.

There may have also been effects caused by different susceptibility to the plague. Certainly, at lease mtDna and X might have changed given the importance of these to disease and overall health. Given the fact that other papers have found a greater susceptibility to plague in Southern European vs Northern European populations, I wonder if the difference will be found in the different percentages of mtDna and the composition of the X.

Do they do the same analysis in the paper for the mtDna at least?

 

[kingdavid]

Makes sense to me. Has made sense to me for over twelve years, when I had a debate over it with Ken on dna-forums. He was very dismissive of the idea that it would have had any effect at all.

Well, at least in Norway it did, although it seems to me that in this particular case a lot of the effect was caused by a halt to migration, which reduced the "Celtic" ancestry component arriving from England.

As they admit, it's a difficult question to answer completely given the current state of the technology.

It seems to me now and it seemed to me then, that a massive population crash, in some areas, not so massive in others, might skew the composition of surviving generations by decreasing variation. As one example, one of my mother's ancestral towns lost 70% of its citizens. Others further up the mountains, not just in my father's part of the Apennine range, but in the Ligurian and Apuan Alps of my mother, had lower numbers, in the 30-40% range.

There may have also been effects caused by different susceptibility to the plague. Certainly, at lease mtDna and X might have changed given the importance of these to disease and overall health. Given the fact that other papers have found a greater susceptibility to plague in Southern European vs Northern European populations, I wonder if the difference will be found in the different percentages of mtDna and the composition of the X.

Do they do the same analysis in the paper for the mtDna at least?

here are the mtdna types that been found from this paper:


pre -plague

sk152-H4a

sk223-J1b1a1a

sk271-H1bb

sk312- U5a2d1

sk328-H1a3a

sk332-R1a1a

sk333-J1b1a1a

sk339-H1o

sk340-T2e1

sk356-H10a1

sk372-U6a3






post- plague

wf131-T2b9

wf148-H1c3b

wf192-Z1a1a

wf193-H

wf301-U5a1a1h

wf305-U5a1b3a

wf383-U5a2a1(T152C)

wf471-U5b2a1a2

wf531-H1n3

wf627-G2a(T152C)

wf629-U5a2c3a

wf678-J1b1a1a

wf737-H28a





modern residents of trondheim

tr1-U5b1b1a3

tr3-K1a(T195C)

tr4-H5a1k

tr5-H1b1

tr7-H1(T152C)

tr8-V

tr9-V

tr10-H5

tr11-K1d

tr12-J1c7

tr13-H1e2a

tr14-V

tr15-H5a1g1a

tr16-K1b2a2a

tr17-T2b2b

tr18-J1c3(A189G)

tr19-U5b1c1a

tr20-T2b1

tr21-H5a1

tr22-H

tr25-J1c2a

tr26-J1c3

tr27-J1c2o

tr31-J1c2a

tr32-V14

tr33-H1a1b

tr34-U4a2

tr35-V

tr36-H1bn

 

[Angela]

here are the mtdna types that been found from this paper:


pre -plague

sk152-H4a

sk223-J1b1a1a

sk271-H1bb

sk312- U5a2d1

sk328-H1a3a

sk332-R1a1a

sk333-J1b1a1a

sk339-H1o

sk340-T2e1

sk356-H10a1

sk372-U6a3






post- plague

wf131-T2b9

wf148-H1c3b

wf192-Z1a1a

wf193-H

wf301-U5a1a1h

wf305-U5a1b3a

wf383-U5a2a1(T152C)

wf471-U5b2a1a2

wf531-H1n3

wf627-G2a(T152C)

wf629-U5a2c3a

wf678-J1b1a1a

wf737-H28a





modern residents of trondheim

tr1-U5b1b1a3

tr3-K1a(T195C)

tr4-H5a1k

tr5-H1b1

tr7-H1(T152C)

tr8-V

tr9-V

tr10-H5

tr11-K1d

tr12-J1c7

tr13-H1e2a

tr14-V

tr15-H5a1g1a

tr16-K1b2a2a

tr17-T2b2b

tr18-J1c3(A189G)

tr19-U5b1c1a

tr20-T2b1

tr21-H5a1

tr22-H

tr25-J1c2a

tr26-J1c3

tr27-J1c2o

tr31-J1c2a

tr32-V14

tr33-H1a1b

tr34-U4a2

tr35-V

tr36-H1bn

Lots more U5 after the plague. Perhaps it's something in that more WHG like mtDna like U5 and perhaps even U4 that confers more resistance to the plague.

Then later when the selection pressure eased off, and there was some migration from more southern areas or more eastern areas it's not as obvious.

They really should know about these papers concerning the influence of more northern ancestry on plague susceptibility if I know about it, and at least mention the possible mtDna or X factor.