Gene Loss and Evolution of Surviving Paralogs Figure 8. Consequences of lineage-specific gene loss on functional evolution of surviving paralogs. (A) Evolutionary model reconstructing the evolution of Aldh1a gene subfunctions in the developing retina. Mechanisms of early subfunctionalization, late subfunction partitioning, and acquisition or modification of ancestral subfunctions associated to events of gene duplication or gene loss (dotted lines) are indicated in the horizontal plane of a three-dimensional tree, in which events of vertebrate diversification are indicated in the vertical plane. A schematic retina at the stage of complete cup invagination represents dorso ventral (DV) expression domains of Aldh1a genes in different colors is indicated for present species and inferred for ancestral conditions. Bars indicate co-expression in the same dorso-ventral domains (or expression of ancestral genes), and dots refer to weak or remaining expression from earlier developmental stages. Aldh1a1: red, Aldh1a2: blue and Aldh1a3: green. Aldh1a expression data have been obtained from [58,65,69,77,79,80,84–87,111–120] and this work Figure 6B). (B) Evolutionary mechanistic model to explain how the ancestral developmental program can remain unaltered after gene loss. This general model, extrapolated from our findings on the evolution of the expression of Aldh1a paralogs during eye development, is based on how heterochronic expression could facilitate the loss of a paralog, while leading to an apparent shuffling of functions between a lost paralog and a surviving paralog without the gain of new regulatory elements, but the loss of negative regulators. doi:10.1371/journal.pgen.1000496.g008 PLoS Genetics | www.plosgenetics.org 14 May 2009 | Volume 5 | Issue 5 | e1000496