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UID:1927@i2m.univ-amu.fr
DTSTART;TZID=Europe/Paris:20171009T153000
DTEND;TZID=Europe/Paris:20171009T163000
DTSTAMP:20170924T133000Z
URL:https://www.i2m.univ-amu.fr/evenements/likelihood-of-tree-topologies-w
 ith-fossils-and-diversification-rate-estimation/
SUMMARY: (...): Likelihood of tree topologies with fossils and  diversifica
 tion rate estimation
DESCRIPTION:: Since the diversification process cannot be directly observed
  at the human scale\, it has to be studied from the information available\
 , namely the extant taxa and the fossil record. In this sense\, phylogenet
 ic trees including both extant taxa and fossils are the most complete repr
 esentations of the diversification process that one can get. Such phylogen
 etic trees can be reconstructed from molecular and morphological data\, to
  some extent. Among the temporal information of such phylogenetic trees\, 
 fossil ages are by far the most precisely known (divergence times are infe
 rences calibrated mostly with fossils). We propose here a method to comput
 e the likelihood of a phylogenetic tree with fossils in which the only kno
 wn time information is the fossil ages\, and apply it to the estimation of
  the diversification rates from such data. Since it is required in our com
 putation\, we provide a method for determining the probability of a tree t
 opology under the standard diversification model.Testing our approach on s
 imulated data shows that the maximum likelihood rate estimates from the ph
 ylogenetic tree topology and the fossil dates are almost as accurate as th
 ose obtained by taking into account all the data\, including the divergenc
 e times. Moreover\, they are substantially more accurate than the estimate
 s obtained only from the exact divergence times (without taking into accou
 nt the fossil record).We also provide an empirical example composed of 50 
 Permo-carboniferous eupelycosaur (early synapsid) taxa ranging in age from
  about 315 Ma (Late Carboniferous) to 270 Ma (shortly after the end of the
  Early Permian). Our analyses suggest a speciation (cladogenesis\, or birt
 h) rate of about 0.1 per lineage and per My\, an extinction rate marginall
 y lower\, and a considerable hidden paleobiodiversity of early synapsids.W
 ebpage
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