Open Access Highly Accessed Research article

Phylogenomic analyses of malaria parasites and evolution of their exported proteins

Christian Pick1, Ingo Ebersberger2, Tobias Spielmann3, Iris Bruchhaus3 and Thorsten Burmester1*

Author Affiliations

1 Institute of Zoology and Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany

2 Center of Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, University of Veterinary Medicine Vienna, Dr.-Bohrgasse 9, 1030 Vienna, Austria

3 Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, D-20359 Hamburg, Germany

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BMC Evolutionary Biology 2011, 11:167  doi:10.1186/1471-2148-11-167

Published: 15 June 2011

Additional files

Additional file 1:

218 P. falciparum proteins with orthologs present in P. reichenowi, P. vivax, P. knowlesi, P. gallinaceum, P. chabaudi, P. yoelii, and P. berghei, as well as the four outgroup taxa (T. gondii, C. parvum, T. annulata, and B. bovis).

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Additional file 2:

Alignment with 135,360 aa positions. Total amount of missing data was 10.2%; amount of missing data per species was 7.1% for T. gondii, 14.8% for C. parvum, 12.2% for T. annulata, 12.5% for B. bovis, 0.5%; for P. falciparum, 35.4% for P. reichenowi; 25.4% for P. gallinaceum, 0.7% for P. knowlesi, 0.6% for P. vivax, 0.8% for P. chabaudi, 4.0% for P. yoelii, and 14.2% for P. berghei.

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Additional file 3:

Alignment with 49,521 aa positions. Total amount of missing data was none.

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Additional file 4:

Likelihood ratio tests for 104 different tree topologies (with and without rate heterogeneity), including their expected likelihood weights (ELW) and probabilities in the approximately unbiased (AU) test. User specified test trees, as well as TREE-PUZZLE and CONSEL output files are given.

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Additional file 5:

Sum of the expected substitutions per site for each of the 218 proteins used for phylogenetic inference. Note that only the proteins of primer taxa (P. falciparum, P. vivax, P. knowlesi, P. yoelii, P. berghei, P. chabaudi, T. gondii, and B. bovis) were considered.

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Additional file 6:

Split network analyses of Plasmodium phylogeny, as reconstructed from the 65 slow-evolving proteins in our dataset. The network was calculated with SplitsTree v. 4.11.3 [71], considering only splits with frequencies of at least 10%. Notably, a sister group position of P. gallinaceum to all mammalian Plasmodium species is not supported.

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Additional file 7:

102 paralog-free P. falciparum proteins that are exported into the host cell and information on the presence or absence of orthologs in other Plamodium species.

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Additional file 8:

Phylogeny of exported P. falciparum proteins with orthologs present in all Plasmodium species; corresponding amino acid alignments and information on the amount of missing data; P. falciparum PEXEL motifs and orthologous sequences of the other Plasmodium species.

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