3.3.1 ) using a phylogenetic clustering approach , which progressively examined reciprocal best scoring blast hits at decreasing phylogenetic nodes of a reference animal tree . we recovered 1,235 gene families with orthologous members in all genomes . to assess the effect of fast and slow evolving characters on the tree topology , several phylogenetic approaches were taken ( see supplementary note 5 ) . gene families were considered to be ancestral bilaterian gene families when an orthologous group had at least two protostome and two deuterostome representatives ( in - group ) or two sequences from either in - group and two from basal ( that is , non - bilaterian ) metazoans ( out - group ) . draft genome scaffolds were clustered into ancestral linkage groups ( algs ) based on the locations of orthologous genes in other metazoan genomes , as described previously we iteratively constructed a parsimonious scenario of chromosome evolution , and ancestral genes were assigned to ancestral algs when any other assignment would imply more hops between algs in the history of that gene family ( supplementary note 6 ) . if another set of orthologous genes is identified within a maximal distance of 10 genes of the previous set , both sets were merged together into a microsyntenic block . only syntenic blocks with at least three orthologues per species were considered . gene families with a maximum of 2 missing species ( out of 22 ) were included . intron and indel positions were detected using conserved flanking sites ( 3 out of 8 amino acids ) , no gaps were allowed to flank introns . for indels , phylogenetic inference based on presence or absence was computed with mrbayes as described in supplementary note 5.3 . 3.3.1 ) using a phylogenetic clustering approach , which progressively examined reciprocal best scoring blast hits at decreasing phylogenetic nodes of a reference animal tree . we recovered 1,235 gene families with orthologous members in all genomes . to assess the effect of fast and slow evolving characters on the tree topology , several phylogenetic approaches were taken ( see supplementary note 5 ) . gene families were considered to be ancestral bilaterian gene families when an orthologous group had at least two protostome and two deuterostome representatives ( in - group ) or two sequences from either in - group and two from basal ( that is , non - bilaterian ) metazoans ( out - group ) . draft genome scaffolds were clustered into ancestral linkage groups ( algs ) based on the locations of orthologous genes in other metazoan genomes , as described previously we iteratively constructed a parsimonious scenario of chromosome evolution , and ancestral genes were assigned to ancestral algs when any other assignment would imply more hops between algs in the history of that gene family ( supplementary note 6 ) . if another set of orthologous genes is identified within a maximal distance of 10 genes of the previous set , both sets were merged together into a microsyntenic block . only syntenic blocks with at least three orthologues per species were considered . gene families with a maximum of 2 missing species ( out of 22 ) were included . intron and indel positions were detected using conserved flanking sites ( 3 out of 8 amino acids ) , no gaps were allowed to flank introns . for indels , phylogenetic inference based on presence or absence was computed with mrbayes as described in supplementary note 5.3 .
current genomic perspectives on animal diversity neglect two prominent phyla , the molluscs and annelids , that together account for nearly one - third of known marine species and are important both ecologically and as experimental systems in classical embryology13 . here 
 we describe the draft genomes of the owl limpet ( lottia gigantea ) , a marine polychaete ( capitella teleta ) and a freshwater leech ( helobdella robusta ) , and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective . 
 we find that the genome organization , gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes ( for example , amphioxus and sea urchin ) than those of other protostomes that have been sequenced to date ( flies , nematodes and flatworms ) . 
 the conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor , establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short - range genetic linkages across metazoans . 
 superimposed on this broadly conserved pan - bilaterian background we find examples of lineage - specific genome evolution , including varying rates of rearrangement , intron gain and loss , expansions and contractions of gene families , and the evolution of clade - specific genes that produce the unique content of each genome .