Abstract
Recombination maps of ancestral species can be constructed from comparative analyses of genomes from closely related species, exemplified by a recently published map of the human-chimpanzee ancestor. Such maps resolve differences in recombination rate between species into changes along individual branches in the speciation tree, and allow identification of associated changes in the genomic sequences. We describe how coalescent hidden Markov models are able to call individual recombination events in ancestral species through inference of incomplete lineage sorting along a genomic alignment. In the great apes, speciation events are sufficiently close in time that a map can be inferred for the ancestral species at each internal branch - allowing evolution of recombination rate to be tracked over evolutionary time scales from speciation event to speciation event. We see this approach as a way of characterizing the evolution of recombination rate and the genomic properties that influence it.
Highlights
Recombination is required for proper segregation of homologous chromosomes during the first division of meiosis [1]
Comparison of the human map, the ancestral gibbon map and the ancestral human-gibbon map should allow the effect of chromosomal context of the very similar genomic sequence to be quantified in great detail, and this may reveal residual variation controlled by other factors
If recombination rate has changed recently, the GC content will not be at equilibrium, and it will not reflect the potential effect of GC-biased gene conversion (gBGC)
Summary
Recombination is required for proper segregation of homologous chromosomes during the first division of meiosis [1]. The majority of recombination is confined to small parts of the genome, in that 60% of crossovers occur in 6% of the genome distributed over roughly 30,000 so-called “hotspots” [11] These recombination hotspots are less than five thousand bases wide, and exhibit recombination rates that are one to three orders of magnitude larger than that in the surrounding sequence. A fine-scale recombination map based on genetic diversity in western chimpanzees shows that the locations of hotspots in chimpanzees and humans are entirely different [22]. Apart from the distribution of hotspots the factors producing observed differences in fine-scale patterns of recombination rate between individuals and species are largely unknown. In this review we outline how inference of recombination rate in ancestral species provides such information, and how this may progress our understanding of cause and effect of recombination on the evolution of genomes
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