Fig. 2.

Distribution of paralogs descending from gene duplications across six eukaryotic supergroups. (a) The figure shows the distribution of paralogs resulting from gene duplications in eukaryotic-specific genes (E-O) and eukaryotic genes with prokaryotic homologs (E-P) (see Materials and Methods for details). Duplicated genes refer to the numbers of gene trees with at least one duplication event with descendant paralogs across the supergroups (filled circles in the center). Number of duplication events refers to the total number of gene duplications. The red row circles indicate gene duplications with descendant paralogs in species from all six supergroups and, thus, tracing to LECA regardless of the eukaryotic phylogeny. An early study assigned 4,137 duplicated gene families to LECA but attributed all copies present in any two major eukaryotic groups to LECA (Makarova et al. 2005). In the present sample, we find 2,869 gene duplication events that trace to the common ancestor of at least two supergroups. Our stringent criterion requiring paralog presence in all six supergroups leaves 713 duplications in 475 gene families in LECA. (b) Rooted phylogeny of eukaryotic supergroups that maximizes compatibility with gene duplications. Gene duplications mapping to five edges are shown (b₁, b₂, … , b₅). The tree represents almost exactly all edges containing the most duplications, the exception is the branch joining Hacrobia and SAR because the alternative branch joining SAR and Opisthokonta is better supported. However, the resulting subtree ((Opisthokonta, SAR),(Archaeplastida, Hacrobia)) accounts for 249 duplications, fewer than the (Opisthokonta,(Archaeplastida,(SAR, Hacrobia))) subtree shown (262 duplications). The position of the root identifies additional gene duplications tracing to LECA (table 1 and supplementary table 4).