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

Autoři: Gustavo V. Barroso aff001;  Nataša Puzović aff001;  Julien Y. Dutheil aff001
Působiště autorů: Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemann-Straße , Plön–GERMANY aff001
Vyšlo v časopise: Inference of recombination maps from a single pair of genomes and its application to ancient samples. PLoS Genet 15(11): e32767. doi:10.1371/journal.pgen.1008449
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008449


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.

Klíčová slova:

Gene mapping – Hidden Markov models – Human evolution – Chromosome mapping – Introgression – Paleogenetics – Probability distribution – Markov processes


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2019 Číslo 11

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