Genomics of Gene Gain and Gene Loss in Eukaryotes

Evolution has often been perceived as a process driving species toward greater complexity at both biological (organismal) and genomic level. However, this view has repeatedly been challenged through writings of authors like Stephen J. Gould and Eugene V. Koonin, rendering the current evidence inadequate for any strong, trend-like (progressive in particular) claims. The current state of this problem is an agreement that despite the diversity of individual case-study evidence, it is still difficult to make any unequivocal conclusion regarding patterns and trends associated to complexity changes without a sufficiently accurate evolutionary reconstruction of ancestral genomes across numerous evolutionary lineages. Such reconstruction in return would provide valuable source of information regarding the change in the number of genes as a function of time and serve as an adequate proxy for monitoring genomic and consequently organismal complexity patterns. Here I propose a novel method for ancestral genome reconstruction in terms of gene families, revealing a consistent, across all investigated lineages, bell-shaped pattern of change in genomic complexity, with complexity periodically increasing throughout Proterozoic eon, followed by a more systematic decrease prevailing the Phanerozoic. Moreover, a global inverse relationship between gain and loss of gene families appears to be a general rule. Furthermore, some evolutionary periods exhibit specific profiles with exceptionally high gene family gain (or loss) rates coinciding with known key evolutionary transition events.


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