Darwin’s Abominable Mystery: DNA Replication Timing, Genome Stability and Biodiversity

Both adaptive and non-adaptive theories of evolution have been proposed to explain the process of speciation: how natural selection operates on individuals and populations. Non-adaptive theories emphasize the force of genetic drift in driving speciation while adaptive theories emphasize the force of ecological selection. Both types of theory focus on genetic variation in the organism’s genotype, the set of all genes in the genome. The repeatedly observed correlation between amino acid substitution (non-synonymous nucleotide substitutions in codons, dN) and mutation rates (synonymous nucleotide substitutions in genes, dS) has remained something of a mystery since it was first observed and subsequently confirmed in multiple organisms. The following will examine the interaction between the forces of genetic drift and ecological selection in the context of two separate but interacting molecular clocks: the well established gene specific molecular clock and the largely overlooked karyotype specific or “junk” DNA clock.