Phylogenetic Tree Reconstruction in Parallel by mikeholy

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									          Dan Janies

janies-1@medctr.osu.edu


Department of Biomedical Informatics

Parallel Computing in Phylogenetics
   Discovery of common ancestry
    via shared derived features

frog   mouse   robin      alligator



                            gizzard


                       amnion

                   limbs with digits
       Character change over time

frog     mouse   robin   alligator
                                         2 temporal
                                         fenestrae




                                         1 temporal
                                         fenestra


                                     0 temporal
                                     fenestrae
 Discovering relationships among
           organisms

  Historical maps of the changes
between ancestral and descendant
          DNA or anatomy

        Predictive power
                                                                                                                100   Solaster stimpsonii
                                                                                                          99          Crossaster papposus

                                                                                99
                                                                                      99
                                                                                                99
                                                                                                                      Perknaster fuscus
                                                                                                                      Stegnaster inflatus
                                                                                                                      Asterina gibbosa
                                                                                                                                               Solasteridae
Asterozoan                                                       95
                                                                          97



                                                                               94
                                                                                      99
                                                                                                100



                                                                                                99
                                                                                                           100
                                                                                                                      Asterina pectinifera
                                                                                                                      Asterina miniata
                                                                                                                      Patiriella regularis
                                                                                                                      Dermasterias imbricata
                                                                                                                      Mediaster aequalis
                                                                                                                      imbricataaaaaaaaaaaa
                                                                                                                      Benthopecten sp.



combined                                                   69
                                                                                     100
                                                                                                100
                                                                                                               100
                                                                                                                      Culcita novaeguineae
                                                                                                                      Archaster typicus
                                                                                                                      Odontaster validus
                                                                                                                      Odontaster meridionalis
                                                                                                                      Asterodon miliaris
                                                                                                                                                   Valvatida
                                                                           100                  100                   Astrogonium miliarus
                                                                                                                      Asterodon dilotatus
                                                                 70                                                   Acodontaster conspicuus


phylogeny                                       75
                                                     71
                                                                                      69


                                                                                     100
                                                                                                100
                                                                                                      61

                                                                                                           100
                                                                                                                      Caymanostella sp.
                                                                                                                      Asthenactis fisheri
                                                                                                                      Eurygonias hylacanthus
                                                                                                                      Luidia foliolata
                                                                                                                      Luidia clathrata
                                                                                                                      Macroptychaster accrescens
                                                                                                100                   Astropecten paleocanthus
                                                                     99
                                                                                                                      Astropecten articulatus
                                                                                                           100        Pseudarchaster parelii
                                                                                                                      Acanthaster planci
                                                                                                                      Linckia laevigata
Jackknife                                  91
                                                                                      99
                                                                                            100
                                                                                                          98          Leptasterias hexactis
                                                                                                                      Evasterias troschelii
                                                                                                                      Pisaster ochraceus
                                                                                99
values at nodes
                                                                                                                                                   Forcipulatida
                                                                          99                                          Orthasterias koehleri
                                                                99                                                    Asterias forbesi
                                                          99                                                          Rathb unaster californicus
                                      93                                                                              Coscinasterias muricata
                                                 93                                                                   Diplasterias brucei
                                                                                                     96               Heliaster helianthoides
                                                                                      95                              Allostichaster sp



                            99
                                 99                              94
                                                                                                 100
                                                                                                                      Stichaster australis
                                                                                                                      Henricia sp
                                                                                                                      Echinaster sentus
                                                                                                                      Myxoderma platyacanthum
                                                                                                                      Brisingaster robillardi
                                                                                                                                                   Ecinasteridae
                                                                                                                                                   Pterasteridae
                                                                                                          100         Pteraster pulvillus
                                                                                           100                        Pteraster militaris
                                                                               100                                    Pteraster obscurus
                      100                                       99
                                                                                                                      Pteraster tesselatus
                                                100
                                                                                                                      Hymenaster pellucidus
                                                                                                                      Xyloplax turnerae
                                                                                                                      PLATANASTER
                                                                                                           100        Ophiopholis aculeata
                                                                                                     92               Ophiothrix oerstedii
                100                                                                    97
                                                                                                                      Ophionereis reticulata
                                                                                100                                   Ophiocoma echinata
                                                                                                          100         Ophioderma brevispinum
                                                                                           98                         Ophiomyxa flaccida
                                                                      100
                                                                                                                      Ophiopsammus maculata
          100                                             100                                              98         Gorgonocephalus eucnemis
                                                                                     100                              Ophiuroidea 6249
                                                                                                                      Schizostella bifurcata
                                                                                                                      FURCASTER
                                                                                                                      STENASTER
                                                                                                                                               Ophiuroidea
                                                                                                                                              Somasteroids
                                                                                                                      ARCHEGONASTER
                                                                                      100                             VILLEBRUNASTER
                                                                                                                      CHINIANASTER
                                                                                                                      Florometra serratissima
Retrospection <> prediction
                       The number of evolutionary trees
                           expands combinatorially

                        300                                                                                  metazoa
                       10
                  10




                        250
                       10
possible trees log




                        200                                                          protostomes
                       10
                        150
                                                                           arthropods
                       10
                        100
                                                     deuterostomes
                       10
                        50
                       10                       amniotes
                            0
                                3   5   6   7    8   9   10...   20   30   40   50   60   70   80   90 100 110 120 130 140 150
                                                         ..
                                                                 Number of organisms
       Available Parallelism

Spawn various ________to slave processors

       topologies during build

       branch clippings during swapping

       reweightings of data during ratcheting

       pairs of trees during fusion

       parameter sets contributes diversity of trees for fusion
    564 processor
       cluster

     9th fastest
    cluster in the
        world
     June 2001
.
Parallel efficiency depends on
how you divide up the search
      among the cluster.
   Tree
 building:

 speedup
   and
granularity
Parallel   High ratio of
           communication to
building   computation




 Multi     Low ratio of
           communication to
building   computation
 New biological directions
   OSU bioinformatics

Develop predictive tools by
correlating variation across
many genes and taxa with
 evolution of phenotypes

								
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