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

2019; Public Library of Science; Volume: 15; Issue: 11 Linguagem: Inglês

10.1371/journal.pgen.1008449

1553-7404

Gustavo Valadares Barroso, Nataša Puzović, Julien Y. Dutheil,

Genetic Mapping and Diversity in Plants and Animals

Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. 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 ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.