More advanced analyses, but not without flaws

Even if phylogenomics has allowed a leap forward in the understanding of the evolutionary relationships between species, it is not a panacea. ‘This approach also has disadvantages. It is not enough to increase the number of genes to be compared to obtain a reliable tree,’ explains Denis Baurain. ‘You still need to use carefully checked data and sophisticated analysis methods,’ insists the researcher. It is precisely that which Denis Baurain, working together with a Canadian team at the University of Montreal, underlines in an article published in PLoS Biology (1). What did the common ancestor of all animals in existence look like? That is, before the Cambrian explosion over the course of which the major current branches sprang to light. It is to this question that three concurrent phylogenomic studies have tried to answer (2, 3, and 4). ‘And yet the latter came to three different conclusions, only one of which is correct,’ (Fig.below) adds Denis Baurain. With his trans-Atlantic colleagues, he thus critically re-examined the data and the analysis methods used in the two studies which had reached erroneous conclusions. ‘We either corrected the data or used a more appropriate analysis method, and in both cases we came to the right solution,’ continues Denis Baurain. ‘The problem within these two studies had arisen from an accumulation of errors in the data combined with bad analysis techniques.’

(1) Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Wörheide G, Baurain D (2011) Resolving difficult phylogenetic questions: Why more sequences are not enough. PLoS Biol 9:e1000602
(2) Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R (2009) Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. PLoS Biol 7:e20
(3) Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sorensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749.
(4) Philippe H, Derelle R, Lopez P, Pick K, Borchiellini C, Boury-Esnault N, Vacelet J, Renard E, Houliston E, Queinnec E, Da Silva C, Wincker P, Le Guyader H, Leys S, Jackson DJ, Schreiber F, Erpenbeck D, Morgenstern B, Worheide G, Manuel M (2009) Phylogenomics revives traditional views on deep animal relationships. Curr Biol 19:706-712.