phylogenetics of medieval manuscripts christopher howe dept of biochemistry and corpus christi...
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Phylogenetics of Medieval Manuscripts
Christopher Howe
Dept of Biochemistryand Corpus Christi College
University of Cambridge
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Russell Gray & Quentin Atkinson (2003) “Language-tree divergence times support the Anatolian theory of Indo-European origin” Nature 426: 435-439
Phylogenetic analysis can be applied to many things other than sequence data
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Hengwrt Canterbury Tales, National Library of Wales, (MS Penarth 392D)
Application of molecular genetic techniques to the study of manuscripts
• Use of computer programs from phylogenetics to study copying history. Which extant versions of the manuscript were copied from the same earlier version? (‘Stemmatology’ - Lachmann 1830s).
• Study of the manuscript itself
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Stemmatology might be used:
• to understand more about the history of the manuscripts themselves - those copied from the same version may have been copied in the same place.
• to understand more about the history of particular variants - how they came to be introduced and why?
• to get a better idea of the original text.
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Jean Mielot, scribe and translator to the Duke of Burgundy
(from “Scribes and Illuminators”, C de Hamel, British Museum Press)
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(from “Scribes and Illuminators”, C de Hamel, British Museum Press)
Proof-reading - corrections sometimes highlighted to confirm accuracy
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Humpty Dumpty sat on a wall
Humpty Dumpty sat on a table
Humpty Dumpty stood by the door
Mr Dumpty stood by the door
Humpty Dumpty lay by the door
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A 0 0 0 0 0 0 B 0 0 0 0 0 1 C 0 0 1 1 1 2 D 1 0 2 1 1 2
Manuscripts Transcription
Transcripts
Alignment algorithm
Aligned texts e.g.
A Humpty Dumpty sat on a wall B Humpty Dumpty sat on a table C Humpty Dumpty lay by the door D Mr Dumpty stood by the door
Encoding to produce NEXUS file
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A 0 0 0 0 0 0 B 0 0 0 0 0 1 C 0 0 1 1 1 2 D 1 0 2 1 1 2
A B C D A - B 1 - C 4 4 - D 5 5 2 -
Construction of distance matrix
Construction of tree
A B
C D
0.5
3
0.5
1.5 0.5
Humpty Dumpty sat on a wall
Humpty Dumpty lay by the door Mr Dumpty stood
by the door
Humpty Dumpty sat on a table
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Canterbury Tales
• Written by Geoffrey Chaucer
• About 80 different manuscript versions
• Prologue to The Wife of Bath’s Tale in 58 extant 15th century MS versions
Wife of Bath, from Chaucer’s Canterbury Tales(GG.4.27(1) University Library, Cambridge
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SplitsTree analysis of the Prologue to the
Wife of Bath’s Tale
Nl
Cx1
Ry1
Ds
Bo1
He
Ii
Ln
En3
Tc2
Ph2
Si
Ne
Mg
Pw
Gg
Ry2
Tc1
En1 MaRa3
Ha5
Sl1
Ht
Cn
Fi
Ld1
Lc
Bw
Dd
Cp
Ad1
To
Sl2La
Ld2
Ph3
Mm
Ad3
Dl
Ch
Bo2
HgGroup E
Group O
GroupC/D
Group A
GroupB
Group F
Group O
Group O
Barbrook et al. (1998) Nature 394 839
‘Hengwrt Chaucer’
National Library of Wales (MS Penarth 392D) Around 1400
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Comparison of conclusions based on evolutionary methods with those based on conventional approaches:
John Lydgate’s ‘Kings of England Sithen William the Conqueror’ (1426)
105 lines, 35 extant manuscripts & 3 early printed copies
Analysed by occurrence of variants and other information (e.g. TCC601-1 and TCC601-2 are two copies bound in the same MS by the same “Trinity Anthologies” scribe)
4 groups, A, B, C and ‘others’
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Ashmole 59 Buryed at Caane thus seythe the Croniculer
Digby 186 Beryed att Cane & thus says the cronyclere
BL Ad 31042 Beryed at caene so seyth the cronyclere
Lansd. 762 Buried at cane this saith the croneclere
de Worde And is buried at Cane as the Cronycle sayes
R. Wyer And buryed at cane as the Cronycle sayes
William Rufus
Kings of England II
(British Library, Harley
4205 f.1v copyright)
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• Parsimony tree (weighted)
• Reproduces groups (Bodley 48, 686 were questionable in manual stemma)
• All pairings reproduced
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Contamination - scribe used more than one exemplar
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• Contamination - scribe used more than one exemplar in making a copy
• Can be successive (changes at a point) or simultaneous/incidental
• Analogous to lateral (horizontal) gene transfer or genetic recombination
With successive contamination, trees constructed from different parts of the text, e.g. first quarter versus last quarter should be different
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1st quarter Last quarter
Prologue to the Wife of Bath’s Tale
Hg
El
El
Hg
Relationship of Hengwrt and Ellesmere manuscripts
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So Ellesmere and Hengwrt had different exemplars for the first quarter, but shared the same exemplar for the last (Ellesmere may have been copied from Hengwrt).
This is analogous to recombination and lateral gene transfer.
We have a method for mapping recombination in DNA sequences. (Maximum chi-squared method of John Maynard Smith - compares observed distribution of differences between sequences with expected if no recombination occurred.) Can we use this with texts?
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X X X X X X X X X X
X X X X X X X X X X
Numbers of differences on each side of arrow
2,8 observed
1,9 expected if evenly distributed
X X X X X X X X X X
X X X X X X X X X X
X X X X X X X X X X
X X X X X X X X X X
X X X X X X X X X X
X X X X X X X X X X
X X X X X X X X X X
X X X X X X X X X X
10,0 observed
9,1 expected if evenly distributed
10,0 observed
7,3 expected if evenly distributed
10,0 observed
5,5 expected if evenly distributed
6,4 observed
3,7 expected if evenly distributed
(O-E)2/E
Score
1.1
4.3
1.1
4.3
10.0
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Character number
Chi-square
Maximum chi-squared analysis for Wife of Bath’s Prologue indicates breakpoint at character 3384 (line 404) in Hengwrt/Ellesmere comparison. (Manly & Rickert - line 400)
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The Mahabharata
One of the major Sanskrit epics of India
Ascribed to the mythological sage Vyasa – ‘the compiler or arranger’
It describes the dynastic struggle between two sets of cousins fighting for the rights to the Bharata kingdom.
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Mahabharata – a long poem!
100,000 stanzas
18 Books or Cantos
1200 chapters
Northern - simpler and shorterSouthern - 13,000 stanzas longer
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Sanskrit Texts
North-West(Kashmiri)
North-East
South
Sarada (Z)Devanagari version of Sarada (K)
Telugu (T)Grantha (G)Malayalam (M)
Devanagari (D)Bengali (B)Nepali (J)Maithili (V)Devanagari version of vulgate (Dn)
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NeighborNet of complete data
Kashmiri
North-East
South
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NeighborNet of Section 1
D6 and Dn1 closely related
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NeighborNet of Section 2
D6 and Dn1 closely related
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NeighborNet of Section 3
D6 and D5 closely related
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Manuscripts D6 and D5
Max chi-squared value = 71.0Chr no. (max chi-squared) = 3735
P = 1.5 x 10-8
(significance threshold = 8.0 x 10-4)
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Manuscripts D6 and Dn1
Max chi-squared value = 57.8Chr no. (max chi-squared) = 3757
P = 2.7 x 10-6
(significance threshold = 8.0 x 10-4)
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Predicted break-point D6/D5 = chr 3735 (end Ch51)
Predicted break-point D6/Dn1 = chr 3757(Start Ch59)
(52-58 not included in analysis)
Start of chapter 59 is a key part of the narrative where the protagonists begin a dicing match, staking their brothers, their wives and eventually their kingdoms.
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Phylogenetic methods offer a powerful tool for studying the copying history of manuscripts.
Conclusions are consistent with those reached by conventional scholarship. Results can be obtained much faster.
We can identify situations where scribes used more than one version in making their copy.• Canterbury Tales• Mahabharata
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Parchment is, in effect, dried animal skin, often with minimal chemical treatment (unlike tanning).
It is likely to contain DNA from the organism used to make it.
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Between species:
• What species was used? Cow, sheep, rabbit, seal?
• Mitochondrial DNA
Within species:
• Manuscript of uncertain origin was written on parchment genetically indistinguishable from a manuscript of known origin
• Mediaeval husbandry
• Nuclear DNA
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QuickTime™ and aTIFF (Uncompressed) decompressor
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Mitochondrial DNA analysis of 1763, 1829 & modern parchments
(D-loop, primers1F, 2R)
Siz
e st
and
ards
176
3
182
9
Mod
ern
Bla
nks
Expected size
Successful amplification of mitochondrial DNA
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QuickTime™ and aTIFF (Uncompressed) decompressor
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QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Successful amplification of a nuclear microsatellite
Siz
e st
and
ards
176
3
182
9
Mod
ern
Note size difference
Microsatellite INRA005 allows differentiation between source of modern parchment and 1763, 1829 sources
Composite figure
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We can successfully isolate mitochondrial and nuclear DNA from parchment.
Need to develop less (or non-) destructive methods
Offers:
• unambiguous identification of source species
• insights into medieval animal breeding
• identification of close relationships between different parchments
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Textual Analysis
Heather Windram, Wendy Phillips-Rodriguez, Adrian Barbrook
University of Cambridge
Matt Spencer
University of Liverpool
Peter Robinson, Barbara Bordalejo
University of Birmingham
Linne Moooney
University of York
Parchment DNA
Mim Bower, Michael Campana & colleagues
University of Cambridge
Christopher de Hamel
Corpus Christi College, Cambridge
Funding
Leverhulme Trust
Arts & Humanities Research Council