This old paper from 2007 was just brought to my attention by a netter discussing the MGD and the latest Science paper on high mutation rate of small genomes. This 2007 paper shows that large genomes show higher rate of large DNA segment duplications, insertions, rearrangments, etc, so called high rate of genome evolution in large genomes. These events are in fact both genetic and epigenetic, and are in fact stated in my MGD paper as epigenetic. Inserting a gene encoding an epigenetic enzyme is more of an epigenetic event. So, large genomes mainly use DNA indels and rearrangements, rather than point mutations, to adapt and evolve. This is the opposite of small genomes or simple organisms. This is entirely predicted by the MGD that large genomes or complex organisms use mainly epigenetic mechanisms rather than point mutations to evolve. Genetic diversity defined in the MGD paper is about neutral point mutations (some neutral indels may be included as well).
The mode and tempo of genome size evolution in eukaryotes
Matthew J. Oliver1,5, Dmitri Petrov2, David Ackerly3, Paul Falkowski1,4, and Oscar M. Schofield1
1 Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901, USA;
2 Department of Biology, Stanford University, Stanford, California 93405, USA;
3 Department of Integrative Biology, University of California Berkeley, Berkeley, California 94720, USA;
4 Department of Geological Sciences, Rutgers University, Piscataway, New Jersey 08854, USA
Eukaryotic genome size varies over five orders of magnitude; however, the distribution is strongly skewed toward small values. Genome size is highly correlated to a number of phenotypic traits, suggesting that the relative lack of large genomes in eukaryotes is due to selective removal. Using phylogenetic contrasts, we show that the rate of genome size evolution is proportional to genome size, with the fastest rates occurring in the largest genomes. This trend is evident across the 20 major eukaryotic clades analyzed, indicating that over long time scales, proportional change is the dominant and universal mode of genome-size evolution in eukaryotes. Our results reveal that the evolution of eukaryotic genome size can be described by a simple proportional model of evolution. This model explains the skewed distribution of eukaryotic genome sizes without invoking strong selection against large genomes.