Nov 19, 2008 — We often hear about the similarities between genomes, but what about the differences?  There’s a growing realization that groups of animals have genetic orphans – genes that are unique to that line.  These genes have no evolutionary homology or kinship to genes from other lineages.  How did they arise?  And what do they do?

A German team examined orphan genes, also called “taxonomically restricted genes” (TRGs) in two species of hydra.  They found that the hydra-specific Hym301 genes do something: they affect tentacle formation.  Knockout experiments and alteration of expression of Hym301 genes clearly caused changes in tentacle length and arrangement.  Their work was published in PLoS Biology1 and was summarized by Science Daily.  They felt their experiments demonstrate that orphan genes are not baggage but are involved in the specific morphological character of the organism…

Maybe this is just a little problem for Darwin, though – if orphan genes are very rare.  How common are they?  The author’s summary states that “every group of animals also has a small proportion of genes that are extremely variable among closely related species or even unique.”  They elaborated on that “small proportion” in paragraph two: it is a “substantial fraction” of the genome –

There is, however, one much less appreciated source for the creation of morphological novelties.  All genome and expressed sequence tag (EST) projects to date in every taxonomic group studied so far have uncovered a substantial fraction of genes that are without known homologs.  These “orphans” or “taxonomically restricted genes” (TRGs) are defined as being exclusively restricted to a particular taxonomic group.  For example, analysis of the phylum Nematoda [roundworms] has identified more than 20% of genes that were nematode-unique TRGs.  The draft genome of Ciona intestinalis revealed that nearly one-fifth of the genes were orphans.  A comparison between the genome sequences of Schizosaccharomyces pombe and Saccharomyces cerevisiae [yeast] showed about 14% of the predicted proteins to be unique to Sc. pombe and 19% unique to Sa. cerevisiae.  In Drosophila, [fruit fly] TRGs include indispensable regulators of development such as bicoid and spatzle.  Recent comparative data on the genomes of 12 Drosophila species revealed that about 2.5% of genes are not present outside of the genus Drosophila and, therefore, have most likely arisen de novo.  An even larger proportion of lineage-specific genes have been detected in the genome of Tribolium [a beetle].  In bacteria, the cumulative number of orphans identified does not appear to be leveling off, although hundreds of complete genome sequences have been already analyzed…

The question of the origin of orphan genes was left to others: “Therefore, future research on these species may provide novel insights on how TRGs are involved in the evolution of the corresponding adaptive traits…. Discovering not only the similarities but also the molecular differences between different organisms might yield intriguing clues in the mechanisms responsible for evolutionary changes.”  Science Daily was no help, either.  The article also just hoped that the finding will be “pointing the way to a new, more complete understanding of how evolution works at the level of a particular group of animals.”  It concluded, “Emergence of ‘novel’ genes may reflect evolutionary processes which allow animals to adapt in the best way to changing environmental conditions and new habitats.”  But how does evolution explain emergence?  Stuff happens?

More… (source)