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Genomics of Gene Gain and Gene Loss in Eukaryotes


Bakarić,  Robert
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Bakarić, R. (2016). Genomics of Gene Gain and Gene Loss in Eukaryotes. PhD Thesis, Kiel University, Kiel.

Cite as: https://hdl.handle.net/11858/00-001M-0000-002D-28B9-7
Evolution is often perceived as a process driving species toward greater complexity at both biological (organismal) and genomic level. However, this concept has repeatedly been challenged over the years 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 supporting the competing views. The current state of this problem is an agreement that despite the diversity of individual case-study evidence, it is still impossible to make any unequivocal conclusion without a sufficiently accurate evolutionary reconstruction of ancestral genomes across numerous evolutionary lineages. Such reconstruction would provide 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. The reconstruction consists of a detailed mapping of gain and loss of genes and gene families over a large number of taxonomically diverse groups. In terms of computational difficulty, this task is seen as exceptionally hard, even in the case when a fast and a well-established heuristic sequence similarity search algorithm like BLAST is used. To address this problem I propose a novel, sequence identity based pre-filtering solution for homology detection, utilizing high dimensional index based similarity search algorithm, thousand times faster than BLAST. I implement this solution in a gene gain computation tool I call QphyloStrat and conduct the analysis by mapping the gene family gain and loss events across 383 Eukaryote lineages. The resulting reconstruction reveals 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 xii gene families appears to be a general rule. Aside from these global trends, some evolutionary periods exhibit specific profiles with exceptionally high gene family gain or loss rates mostly associated to known key evolutionary transition events.