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Phylogenetic models and MCMC methods for the reconstruction of language history Robin J. Ryder CEREMADE – Paris Dauphine / CREST – INSEE Joint work with Geoff K. Nicholls at the Department of Statistics, University of Oxford www.slideshare.net/robinryder
Carles li reis, nostre emper[er]e magnes Set anz tuz pleins ad estet en Espaigne : Tresqu’en la mer cunquist la tere altaigne. N’i ad castel ki devant lui remaigne ; Mur ne citet n’i est remes a fraindre, Fors Sarraguce, ki est en une muntaigne. Chanson de Roland , 1r (11 th  century)
La plus commune façon d'amollir les coeurs de ceux qu'on a offensez, lors qu'ayant la vengeance en main, ils nous tiennent à leur mercy, c'est de les esmouvoir par submission à commiseration et à pitié. Montaigne,  Essais , I, 1 (1580)
Tes yeux sont si profonds qu'en me penchant pour boire J'ai vu tous les soleils y venir se mirer S'y jeter à mourir tous les désespérés Tes yeux sont si profonds que j'y perds la mémoire Aragon,  Les Yeux d'Elsa  (1942)
Et la piaule swingue au son du ghetto, on tape à la porte Chill c'est trop fort ! baisse le son merde ! j'connais A chaque fois c'est pareil tant pis il faut qu'ça pète Et profite en traître des nouveaux albums qu'Rod m'achète Akhénaton,  Juste une pression  (2005)
What to expect ,[object Object]
Model of language diversification
MCMC for phylogenetic trees
Synthetic studies
Analysis of two data sets
Indo-European languages
Indo-European languages
Language diversification Languages change in a way comparable to biological species Similarities between languages indicate that they may be cousins. Most common model : phylogenetic tree
 
Questions ,[object Object]
Internal ages
Age of the root: 6000-6500 BP or 8000-9500 BP?
(BP=Before Present)
Core vocabulary ,[object Object]
Borrowing is possible (non-tree-like change), but:
“ Easy” to detect
Uncommon
Does not introduce systematic bias
Data coding Old English:  stierfþ Old High German:  stirbit ,  touwit Avestan:  miriiete Old Church Slavonic:  umĭretŭ Latin:  moritur Oscan: ? Cognacy classes: 1.  {stierfþ, stirbit} 2.  {touwit} 3.  {miriiete, umĭretŭ, moritur}
Constraints ,[object Object]
Constraints on some internal ages
We use these constraints to infer rates and other ages
 
Description of the model (1)‏ ,[object Object]
Trait instances die at rate μ
λ and μ are constants
Description of the model (2)‏ ,[object Object]
At a catastrophe, each trait dies with probability κ and Poiss(ν) traits are born.
λ/μ=ν/κ: the number of traits is constant on average.
Description of the model (3)‏ ,[object Object]
Some traits are not observed and are therefore deleted from the data
Registration process
Registration process
Registration process
Registration process
Posterior distribution
Likelihood calculations
Prior distribution on trees ,[object Object]
We would like the marginal prior on the root age to be (approximately) uniform over (say) 5000-15000BP
MCMC moves ,[object Object]
Various moves on the tree (Drummond et al., 2002)
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Checking mixing and convergence ,[object Object]
Need statistics on the tree
Length of the tree
Root age
Presence/Absence of a few subtrees

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Phylogenetic models and MCMC methods for the reconstruction of language history