Chromosome and Large Scale Genome Evolution

[BillTre]

As a kind of off-thread elaboration on a thread on protein evolution, http://www.sciencemag.org/news/2017...ily_2017-06-19&et_rid=33537079&et_cid=1393464
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.

 

[Ygggdrasil]

Neat! Here's a link to the scientific publication:

Kim et al 2017 Reconstruction and evolutionary history of eutherian chromosomes. Proc Natl Acad Sci USA. Published online before print June 19, 2017, doi: 10.1073/pnas.1702012114
http://www.pnas.org/content/early/2017/06/13/1702012114.full

Abstract:

Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over ∼105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first ∼60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases.

The finding that the rate of rearrangements was significantly lower further back into the past is a strange result and could suggest issues with the reconstruction (reconstruction and identification of rearrangements becomes harder the further back in time one goes, so the difference in rate could simply reflect the increased difficulty of reconstructing more ancient rearrangements or insufficient sampling of taxa representing earlier branchpoints (because the authors focused on human evolution, they sampled more taxa closer to humans). In the paper, the authors speculate that this difference in rate could represent the diversification of mammals that occurred at the K-P boundary (the mass extinction leading to the switch from dinosaurs to mammals as the dominant land animals), which is another plausible explanation.