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

View ORCID ProfileGustavo Valadares Barroso, Natasa Puzovic, View ORCID ProfileJulien Dutheil
doi: https://doi.org/10.1101/452268
Gustavo Valadares Barroso
Max Planck Institute for Evolutionary Biology
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  • For correspondence: gvbarroso@gmail.com
Natasa Puzovic
Max Planck Institute for Evolutionary Biology
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Julien Dutheil
Max Planck Institute for Evolutionary Biology
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Abstract

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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 25, 2018.
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Inference of recombination maps from a single pair of genomes and its application to archaic samples
Gustavo Valadares Barroso, Natasa Puzovic, Julien Dutheil
bioRxiv 452268; doi: https://doi.org/10.1101/452268
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Inference of recombination maps from a single pair of genomes and its application to archaic samples
Gustavo Valadares Barroso, Natasa Puzovic, Julien Dutheil
bioRxiv 452268; doi: https://doi.org/10.1101/452268

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