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Response to Nelson-Sathi et al. (Nature 517, 77-80) Origins of major archaeal clades do not correspond to gene acquisitions from bacteria Mathieu Groussin1 , Bastien Boussau2,3,4 , Gergely J. Szöllősi5 , Laura Eme6 , Manolo Gouy2,3,4 , Céline Brochier-Armanet2,3,4 , Vincent Daubin2,3,4 1 – Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA 2 3 4 – Université Lyon 1, 69622 Villeurbanne, France – CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France 5 6 – Université de Lyon, 69361 Lyon, France – ELTE-MTA “Lendület” Biophysics Research Group, Pázmány, Budapest, Hungary – Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada 1 b) 5 + + + + + + + + + + + + 2 4 6 8 10 10 + 8 2 1 2 + 3 4 + 5 6 + 7 2 4 + + 6 + + + 8 Maximum Likelihood expectations (Total = 25) 25 10 15 20 + + + + + 4 + + + 6 + + + + 8 10 + + + 12 14 10 200 Nelson-Sathi et al. estimates (Total = 1047) + + + +++++ + ++++++ ++++ + + 5 Number of genomes in which the family is found Maximum Likelihood expectations (Total = 215) 100 150 + 50 Number of gene families inferred at the root + + 10 Haloarchaea 0 150 100 Maximum Likelihood expectations (Total = 15) 50 0 Number of gene families inferred at the root + 8 Nelson-Sathi et al. estimates (Total = 100) f) Nelson-Sathi et al. estimates (Total = 338) + 6 + Number of genomes in which the family is found Methanosarcinales + + Methanococcales 2 8 Number of genomes in which the family is found e) + 5 0 Number of gene families inferred at the root 70 60 50 40 30 20 10 + + 0 Number of gene families inferred at the root Maximum Likelihood expectations (Total = 23) + + + 4 d) Nelson-Sathi et al. estimates (Total = 128) + + Number of genomes in which the family is found Methanobacteriales + + + + 12 Number of genomes in which the family is found c) Maximum Likelihood expectations (Total = 4) 6 10 Maximum Likelihood expectations (Total = 5) Nelson-Sathi et al. estimates (Total = 40) 4 + Desulfurococcales 2 Number of gene families inferred at the root 15 Nelson-Sathi et al. estimates (Total = 59) 0 Thermoproteales 0 Number of gene families inferred at the root a) 10 15 + 20 Number of genomes in which the family is found Figure 1: Family size and gene gains for the “import” set at the origin of archaeal phyla. The 6 phyla for which Nelson-Sathi et al. (2015) [NS] claim a strong signal for HGTs from bacteria at their origins are shown. NS estimates are represented in purple. Maximum Likelihood expectations of gains at the origin for the same datasets are represented by red crosses. Expectations of gains were calculated from branch-specific rates of gene gain and loss estimated from the 25,762 gene families of NS, but we report only the results for the 2,264 genes from the “import” set of NS. Most of the families inferred to be gained at the origin of each phylum by NS are distributed over 2 or 3 archaeal genomes only. ML estimates show that only a small fraction of gene families were actually acquired at the origin of each phylum. 2 1000 800 Parsimony estimates 200 400 600 Maximum Likelihood estimates les ea ca Th er mo p oc oc ur ulf De s ro t les s ale lob les lfo ca Su oc mo c Th er ac ter ial es les ca ob an th Me th an oc oc les ata sm Me Th er mo og ae ch Ar pla lob ale s es ial ob icr om an th Me Me th an oc ell ale s ale a ar cin ae os rc h Me th an loa Ha s 0 Number of gene gains at the origin of archaeal phyla Nelson-Sathi et al. estimates Figure 2: Consistency of gene family ancestral gain estimations on the “import” gene set. Along the archaeal reference tree provided by Nelson-Sathi et al. (2015) [NS], both Parsimony (green) and Maximum Likelihood (blue) inferences of ancestral gains were computed with Count (Csurs and Miklos, 2006; Csurs, 2010), and compared with the estimates of NS. Wagner parsimony with a large range of gain/loss costs combinations were tested, yielding similar estimations. Here are represented the results with a gain cost of 2 and 4, from left to right respectively. In ML, ancestral branch-specific gain expectations were computed from rates of gene gain and loss estimated either from the 2,264, 3,315 or 25,762 gene family sets defined by NS, from left to right respectively. All analyses are consistent and strongly contradict the scenario of massive gene acquisitions among these 2,264 families at the origin of archaeal phyla, claimed by NS 3 References Csurs M. 2010. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26:1910–1912. Csurs M and Miklos I. 2006. A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. In Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB) Vol. 3909 of Springer Lecture Notes in Bioinformatics, Heidelberg:206–220. Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chvez N, Thiergart T, Janssen A, Bryant D, Landan G, Schnheit P, Siebers B, McInerney JO, and Martin WF. 2015. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517:77–80. 4