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Metazoa evolution: the relation between molecular evolution of orthologous protein groups and aromorphoses K.V. Gunbin, D.A. Afo nnikov
Institute of Cytology and Genetics SB RAS, Novosibirsk State University, Novosibirsk, Russia, genkvg@bionet.nsc.ru, ada@bionet.nsc.ru

The mo lecular evo lution o f more than 139 000 compact orthologous protein groups (COPGs) containing about 2 000 000 unique proteins fro m 100 fully sequenced organisms belo nging to 25 Metazoa species groups (Figure 1) were analyzed. Orthology relat ions were taken from OrthoDB 6 database [1]. To select ortho logous proteins highly related with eac h other we define COPGs as a parts of diffuse orthologous protein groups (OPGs) containing proteins belonging to minimum 5 species groups wit h mo nophylet ic origin. For example OPG composed of Tunicata, Agnata, Act inopterigii, Sarcopterigii, Amphibia, Dinosauria, and Afrotheria species groups contained only o ne COPG wit h 6 species groups (without Afrotheria). The ancestral protein reconstruction in each internal tree node of COPG was made using RAXML 7.4.2 on the basis of best COPG protein alignment (selected by AQU A 1.1) containing only co lumns with limited variation (selected using NOISY 1.5.12), the COPG tree (FASTTREE 2.1) corrected by species tree (using TREEFIX [2]) and calculated amino acid replacement matrices (via MODELESTIMATOR 1.1). These ancestral sequence s were used to calculate the number of observed amino acid subst itutions. For each observed well confirmed amino acid replacement type (by the RAXML ancestral state reconstruction probabilit ies) we co mpared the observed number of changes wit h expected ones under the assumpt ion of a stationary Markov process of protein evolut ion. Expected replacement numbers were calculated using 1000 simulations of COPGs mo lecular evo lut ion by the INDELible 1.03, taking into account the peculiarities of the invest igated COPGs (alignment length, phylogenet ic tree, amino acid replaceme nt matrix and frequencies of occurrence) . Comparison o f expected and observed numbers of each replacement type was performed using new highly co mputationally optimized permutation test [3].


Primates Glires L au rasiatheria Afroth eria M ar su pialia M onot rem at a D in osau ria Amph ib ia S arcop terygii Act in opt erygii Agn at ha Tu nicat a Ceph aloch ordata Echino der mat a L oph otroc hozoa Nematoda Arach nida Cru st ac ea Paraneopt era H ymen optera Coleop tera L ep ido ptera D ip tera Cn idaria Placozoa

Fig. 1. Phylogenet ic tree of Metazoa species groups under analys is. Bo ld tree branches denote cases with statist ical excess of COPGs containing at ypical, statist ically rare (p0.01) types of amino acid replacements. We showed that internal tree branches o f Metazoa, containing excess o f COPGs wit h at ypical (p <0.01) amino acid replacement t ypes strict ly correspond to aromorphoses in the vertebrate and invertebrate evo lut ion: 1) the full geno me duplicat ions in early stages of vertebrate evolut ion, 2) the adaptation o f vertebrates to terrestrial environments, 3 ) the origin o f Amniota, 4) the divergence of primit ive mammals

and placental mammals; 5) the divergence of Pancrustacea and Insecta; 6) the divergence of Nematoda. We also conducted the funct ional enrichment permutation test of COPGs containing at ypical amino acid replacement at each inner tree branch. This test allows us to uncover various features of Metazoan gene networks evolut ion r elated wit h Vertebrate and Invertebrate aromorphoses. This work was supported by RFBR grant s No. 11-04-01771 and 13-04-01008, RAS programs "Biosphere Origin and Evo lution" and .II.6.8, SB RAS Integration projects 39 and 130. 1. R.M. Waterhouse et al. (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs, Nucl. Acids Res., 41:D358-D365. 2. Y.C. Wu (2013) TreeFix: statistically informed gene tree error correction using species trees, Syst. Biol., 62:110-120. 3. K.V. Gunbin, A. Ruvinsky (2013) Evolut ion of general transcription factors, J. Mol. Evol., 76:28-47.