Phylostratigraphy: dating origin of new genes

27 May 2016

Sean Eddy
Molecular and Cellular Biology Department
Harvard University


Where do new genes come from? Most genes arise by duplication and divergence, and thus have homologs in many species. Some genes are "orphans" that are found only in narrow clades of species. Orphan genes &ndashp clade-specific gene families – may represent de novo origins of new genes at the base of their clades. Systematic study of de novo gene origins might reveal patterns of molecular evolution over deep time, perhaps including bursts of evolutionary innovation at key events like the origin of neural circuits in animals. These appealing ideas have been called "phylostratigraphy", by analogy to studying fossils over time in geological strata. However, phylostratigraphic approaches are confounded by the fact that computational methods for sequence homology detection are not all-powerful. Apparent "orphans" may merely be rapidly evolving genes that escape our ability to detect homologs. I will discuss a new project in our lab, in which we aim to statistically distinguish fast-evolving genes from putative de novo origin events, using predictive mathematical models of protein sequence evolution.

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