Funding for the collection of sediments and participation of VPE and JMB

in this research was provided by the US National Science Foundation grant MCB-060484. We also acknowledge the constructive Ponatinib cost feedback from four anonymous reviewers. Electronic supplementary material Additional file 1: Maximum likelihood (ML) analysis of 29 taxa focusing on the position of Calkinsia aureus within the Euglenozoa clade. Two jakobids, Andalucia incarcerata and A. godoyi, are used as outgroups in this analysis. The short environmental sequences are excluded from the dataset used in Figure 11 and fast-evolve euglenids sequences, Ploeotia, Menoidium and Astasia, are included. ML bootstrap values greater than 50% are shown. Thick branches indicate Bayesian posterior probabilities over 0.95. Ba, bacteriotroph; click here Eu, eukaryotroph; Os, osmotroph; Ph, phototroph. GenBank accession numbers of the sequences analyzed are shown in parentheses. (EPS 405 KB) Additional file 2: Maximum likelihood (ML) analysis of 25 taxa focusing on the position of Calkinsia aureus within the Euglenozoa clade. Two jakobids, Andalucia incarcerata and A. godoyi, are used as outgroups in this analysis. The short environmental sequences are removed from the dataset used in Figure 11 and fast-evolve euglenids sequences, Dinema, Ploeotia, Menoidium and Astasia, are excluded. ML bootstrap values greater than 50% are shown. Thick branches

indicate Bayesian posterior probabilities over 0.95. PIK3C2G Ba, bacteriotroph; Eu, eukaryotroph; Ph, phototroph. GenBank accession numbers of the sequences analyzed are shown in parentheses. (EPS 400 KB) References 1. Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, Roger AJ, Gray MW: The tree of eukaryotes. Trends Ecol

Evol 2005, 20:670–676.CrossRefPubMed 2. Yoon HS, Grant J, Tekle YI, Wu M, Chaon BC, Cole JC, Logsdon JM Jr, Patterson DJ, Bhattacharya D, Katz LA: Broadly sampled multigene trees of eukaryotes. BMC Evol Biol 2008, 8:14.CrossRefPubMed 3. Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S, James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L, Moestrup Ø, Mozley-Standridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW, Taylor MF: The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 2005, 52:399–451.CrossRefPubMed 4. Adl SM, Leander BS, Simpson AGB, Archibald JM, Anderson OR, Bass D, Bowser SS, Brugerolle G, Farmer MA, Karpov S, Kolisko M, Lane CE, Lodge DJ, Mann DG, Meisterfeld R, Mendoza L, Moestrup Ø, Mozley-Standridge SE, Smirnov AV, Spiegel F: Diversity, nomenclature, and taxonomy of protists. Syst Biol 2007, 56:684–689.CrossRefPubMed 5. Cavalier-Smith T: Kingdom protozoa and its 18 phyla. Microbiol Rev 1993, 57:953–994.PubMed 6.