As a kind of off-thread elaboration on a thread on protein evolution, here is a Science news article on the evolution of mammalian chromosomes. By using full genome sequences, they are trying to trace back the evolution of mammalian genomes to their ancestral set of chromosomes. They only looked at placental mammals (19 species), not marsupials (opossums, kangaroos) or monotremes (egg layers like the platypus), starting from about 105 million years ago. Interesting findings: ancestral condition 21 pairs of chromosomes few chromosomes stayed intact found 162 breakpoints which lead to shuffling pieces of DNA around within and between different chromosomes rates of surviving breakpoints were between 8 and 10 breakpoints per 10 million years (these are the mutations that could survive and prosper competitively) The proliferation of repetitive sequences from proliferating mobile genetic elements with in a genome (like transposons) may have increased the rates of these shuffling events by putting very similar sequences all over the place. In correct sequence matching during DNA repair of breakpoint mutations can lead to scrambling things around. On a longer timescale, duplications of whole genomes have occurred several times in vertebrate evolution, leading to the doubling of all the genes in the genome at once (see first figure for a clear graphic of this concept). This creates a lot of redundant well organized sequence (sequence encoding functional proteins and other things) for evolution to mess around with. Thus evolution can proceed more rapidly.