DOI: 10.1101/452268Oct 24, 2018Paper

Inference of recombination maps from a single pair of genomes and its application to archaic samples

BioRxiv : the Preprint Server for Biology
Gustavo Valadares BarrosoJulien Dutheil


Understanding the causes and consequences of recombination rate evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Since statistical inference of recombination maps typically depends on large samples, reaching out studies to non-model organisms requires alternative tools. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the variation in recombination along a pair of genomes. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios, remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of archaic hominids. We report that the evolution of the recombination landscape follows the established phylogeny of Neandertals, Denisovans and modern human populations, as expected if the genomic distribution of cross-overs in hominids is largely neutral.

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