University of Tsukuba
HEAD：CCS 名称／ CCS・筑波大ロゴ

HPC for Phylogenetic Tree Inference
Phylogenetic Inference on the Universal Tree of LifeThe central focus of our research is to gain insights into the origin and early evolution of eukaryotes. This requires i) to reconstruct the Universal Treeof Life including diverse organisms on Earth based on large-scale sequence datasets, and ii) to apply parameter-rich models to obtain appropriate
evaluation of complex evolution in a disparate range of species.

Phylogeneitc position of a newly identified protist, Palpitomonas bilix,
inferred from a large-scale multigene dataset
Introduction: Palpitomonas bilix is a recently identified single-cell
protist and considered to provide key information regarding the early
evolution of major groups of photosynthetic eukaryotes. However, thephylogenetic position of Palpitomonas has yet to be resolved withconfidence.
Results: We conducted massive expressed sequence tag analyses on
Palpitomonas bilix using 454 pyrosequencing technology, and prepareda 159-gene dataset including 69 taxa and 42,744 amino acid positions. In the 159-gene analyses,
Palpitomonas was robustly placed at the ancestral position of the clade of cryptophytes andGonionmonas. Interestingly, our result showed that two photosynthetic groups, haptophytes andcryptophytes were NOT monophyletic, which was contradictory to the hypothesis proposed prior to
our analyses.
Discussion: Our 159-gene analyses successfully provided the first clues for the putative phylogenetic
position of Palpitomonas. In addition, our phylogenetic analysis disfavored the hypothesis assuming
the intimate relationship between cryptophytes and haptophytes.
Methods: The 159-gene dataset was analyzed by RAxML with LG+Γ+F model. Maximum-likelihoodbootstrap values were presented on nodes. Branch lengths indicate the average number ofsubstitutions per position.
Reference: Yabuki et al. “Palpitomonas bilix gen. et sp. nov.: A novel deep-branching Heterotroph
possibly related to Archaeplastida or Hacrobia.” Protist. 2010. 161:523-538.

Parallelization of the phylogenetic inference with the non-homogeneous substitution models
Introduction: The nucleotide and amino acid sequences in distantly related species certainly
evolve under different evolutionary processes (non-homogeneous evolution). Thus, to inferphylogenetic trees from real-world sequence data, non-homogeneous (NH) models, in which
allocate different model parameters on each node of the tree to evaluate, are more realistic
than homogeneous models which enforce a single set of model parameters to all branches inthe tree. However, the analyses with NH models can be computationally intense, as enormous
amount of model parameters need to be optimized.
Results: We applied two approaches for parallel computing, OpenMP and MPI, for estimating
the parameters in the maximum-likelihood (ML) method with a NH model. This HYBRIDparallel programming enabled to finish the likelihood calculation of single phylogenetic tree in 8~ 9 times faster than the control. However, the analyses using more than 16 cores showed nocontribution for the likelihood calculation.
Discussion: In this study, we only parallelized the parameter estimation of the NH model on asingle tree. However, ML phylogenetic inferences in general require the likelihood calculationsof a numerous number of tree topologies during heuristic tree search. Therefore, we need toachieve the higher level of parallel computing on the likelihood calculation of multiple trees
than that presented here.
Methods: We simulated two nucleotide sequence data, i) 40 taxa and 50,000 positions, and ii)
200 taxa and 10,000 positions, based on different model trees. Each sequence dataset was
subjected to the likelihood calculation of the corresponding model tree with the NH model.
Data analyses on multiple processors were run on T2K Tsukuba (~ 4 nodes/64 cores; eachnode is composed of 4 quad-core CPUs).
Reference: Galtier and Gouy. “Inferring pattern and process: maximum-likelihood
implementation of a nonhomogeneous model of DNA sequence evolution for phylogeneticanalysis.” Molecular Biology and Evolution. 1998. 15:871-9.

FOOT：連絡先／ CCS のアドレス

http://www.ccs.tsukuba.ac.jp/