Message - 7th IAL Symposium

The 7 th International Association for Lichenology Symposium 2012
(2A-1-P4) Submission ID: IAL0103-00002
PHENOTYPE-BASED PHYLOGENETIC BINNING - A QUICK TUTORIAL
Lücking R. 1 , Berger S. 2 , Stamatakis A. 2 , Rivas Plata E. 3 , Caceres M. E. 4
1 Department of Botany, The Field Museum, Chicago, Illinois, United States
2 The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
3 Department of Biology, Duke University, Durham, North Carolina, United States
4 Departamento de Biociencias, Universidade Federal de Sergipe, Itabaiana, Brazil
Despite the potential shortcomings of phenotype (morphological) data for phylogenetic inference, there
are scenarios where only morphological data is available for systematic classification, such as phylogenetic
placement of fossils or analysis of large taxonomic groups in which only a subset of species has been sequenced.
Because of the frequently incongruent phylogenetic signal between morphological and molecular
data, computational methods are required to (1) determine morphological site patterns that are congruent with
the molecular tree (which represents the reference tree relative to any topology inferred from morphological data
alone) and to (2) downweight incongruent sites, in order to improve accuracy of the phylogenetic classification
of taxa for which only morphological data exist. A quick tutorial is presented here regarding a novel method
called “phylogenetic binning”. We used molecular site weight calibration as implemented in the software RAxML
to weight morphological characters based on their distribution on a maximum likelihood tree inferred from molecular
data. We subsequently assigned morphologically defined taxa that lack molecular data to branches of
the molecular reference tree, based on the morphology of the taxa included in the reference tree by means of
molecular evidence. Bootstrapping was conducted to estimate support for the placement of individual taxa. We
demonstrate this methodology using the lichen genera Graphis s.lat. and Stegobolus s.lat. (Ascomycota: Ostropales:
Graphidaceae), which were recently shown to represent two separate, distantly related lineages each. As
an example, of the 313 species of Graphis s.lat. included, 16 were represented by molecular and morphological
data and 297 by morphology only. Using maximum likelihood and maximum parsimony site weight calibration
and morphology-based phylogenetic binning, 290 of the 297 species represented by morphological data only
were assigned to either Graphis s.str. or the segregate genus Allographa, with strong support (90–100%). Our
results showed that assignment of taxa to clades based on morphological data substantially improved with molecular
site weight calibration. Both molecular site weight calibration and branch assignment to the molecular
reference tree are implemented in the RAxML 7.2.6 Windows executable and the RAxML 7.2.8 open-source
code available at http://www.exelixis-lab.org/software.html
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