Supplementary Table and Figures

Supplementary Table S1-ch.6. OTU (Operational Taxonomic Unit) name and chimera construc-tion. Percentage of missing data per species and per genes. Detailed list of the 127 genes used, describ-ing the amount of missdescrib-ing data per species.

Not shown in this manuscript because of its very large size, but is available upon request.

Supplementary Figure 1-ch.6. Phylogeny summarizing the relationships among the major groups of eukaryotes when T. subtilis and R. contractilis are not included in the analysis. This tree was ob-tained with phylobayes ran under the CAT model (consensus between two independent Markov chains), and subsequently schematized in FigTree (http://tree.bio.ed.ac.uk/software/figtree/) with the “Cartoon” option. Black dots correspond to 1.0 posterior probability (PP) and 100% ML boot-strap (BP), otherwise values at node represent PP (above) and BP (below) when not maximal. Black squares show the constrained bifurcations used in the separate analysis and RELL bootstraps (RBP) are indicated.

Supplementary Figure 2-ch.6. Tree representing a Bayesian phylogeny of eukaryotes when R. con-tractilis is removed, obtained from the consensus between two independent Markov chains, run under the CAT model implemented in phylobayes. The curved dashed lines indicate the alternative branchings recovered in the ML analysis of the same dataset. Black dots correspond to 1.0 posterior probability (PP) and 100% ML bootstrap (BP), otherwise values at node represent PP (above) and BP (below) when not maximal. The white thick bars are the groups that were originally included in the chromalveolates. Assemblages indicated by capitalized names correspond to the hypothetical su-pergroups of eukaryotes. The scale bar represents the estimated number of amino acid substitutions per site.

Supplementary Figure 3-ch.6. Tree representing a Bayesian phylogeny of eukaryotes when T. sub-tilis is removed, obtained from the consensus between two independent Markov chains, run under the CAT model implemented in phylobayes. The curved dashed lines indicate the alternative branchings recovered in the ML analysis of the same dataset. Black dots correspond to 1.0 posterior probability (PP) and 100% ML bootstrap (BP), otherwise values at node represent PP (above) and BP (below) when not maximal. The white thick bars are the groups that were originally included in the chromal-veolates. Assemblages indicated by capitalized names correspond to the hypothetical supergroups of eukaryotes. The scale bar represents the estimated number of amino acid substitutions per site.

Supplementary Figure 4-ch.6. Summary of the AU tests based on the concatenated alignments, showing the alternative branching points that were tested (numbers on branches) and the P-values higher than 0.05. The values in circles correspond to the positions that were not rejected by the AU tests. When both T. subtilis and R. contractilis were present, only one species was moved at a time leaving the other in its inferred position. (A) Bayesian tree as in Figure 1, T. subtilis or R. contractilis were successively placed on alternative branches; (B) ML tree as in Figure 1, T. subtilis or R. contrac-tilis were successively placed on alternative branches; (C) Bayesian tree as in Figure 1, both T. subcontrac-tilis and R. contractilis were successively placed on alternative branches; (D) Bayesian tree as in Supp. Fig-ure 2, T. subtilis was successively placed on alternative branches; (E) Bayesian tree as in Supp. FigFig-ure 2, T. subtilis was successively placed on alternative branches. Ma: Malawimonas; Tr: Trimastix; Di:

Discoba; Re: Red algae; Gr: Green algae; Gl: Glaucophytes; Cr: Cryptomonads; Ha: Haptophytes; Te:

T.subtilis; Ra: R.contractilis; Un: Unikonts.

Chapter 7: General conclusions and perspectives

7.1 Achievements

Our work has explored ancient evolution within the eukaryotic tree of life by means of phylogenomics, a new tool that has allowed biologists to infer phylogenetic relationships and revisit the history of life. As in any approach it has its drawbacks and one needs to remain critical when constructing and analyzing very large datasets, because statistical supports can be high for trees that are not necessarily correct. Yet we believe that the analyses of phylogenomic alignments represents one important way towards the successful reconstruction of the tree of eukaryotes. Compared to phylogenies inferred from much less data, phylogenomics generally allows extraction of the weak signal that is contained in in-dividual genes. Thus it has become possible to address questions that were out of reach not so long ago. I have discussed in this manuscript examples of the early successes of phylo-genomics, many more are to come.

When we started this project four years ago, one of the six supergroups of eukaryotes – Rhizaria– was absent from phylogenomic studies. This was a critical issue because without it discussions about early eukaryote evolution were necessarily missing an important as-pect. Although this major assemblage is still suffering from poor genomic representation in databases compared to all other supergroups, our initial efforts allowed us to include Rhi-zaria in a phylogenomic context (Chapters 2 and 3: [Burki et al. 2006; Burki and Paw-lowski 2006]). Soon after, the inference of the unexpected “SAR” group (chapter 4: [Burki et al. 2007]) and its association with haptophytes, cryptomonads and Plantae into a mono-phyletic mega-clade of eukaryotes (chapter 5: [Burki et al. 2008]) defined a new framework that will certainly have important consequences on our understanding of eukaryote evolu-tion (schematized in Figure 1-ch.7).

The placement of taxa whose phylogenetic affinities to the major groups of eukaryotes are still controversial is a particularly important issue. Indeed these species are often char-acterized by cellular properties that, if reliably placed in a robust evolutionary framework, can shed light on crucial events in evolution. We have investigated the origin of two such

‘orphan’ groups, the enigmatic eukaryotic lineages telonemids and centrohelids (chapter 6).

I have also participated in the phylogenomic study of Breviata anathema, another deeply branching anaerobic amoeboflagellate eukaryote that was also unplaced in the eukaryotic tree ({Minge, 2009, p08461}, see annexes for the article). Importantly, this nomadic species is regarded as crucial for better defining the nature of the last common ancestral eukaryo-tes [Roger and Simpson 2009].

7.2 Origin and spread of chlorophyll-c containing plastids, and