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

PLoS Genet. 2019 Nov 14;15(11):e1008449. doi: 10.1371/journal.pgen.1008449. eCollection 2019 Nov.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromosome Mapping
  • Genetic Variation / genetics
  • Genome, Human / genetics*
  • Hominidae / genetics*
  • Humans
  • Markov Chains
  • Metagenomics*
  • Neanderthals / genetics
  • Paleontology / trends
  • Phylogeny
  • Recombination, Genetic / genetics*

Associated data

  • figshare/10.6084/m9.figshare.7182776
  • figshare/10.6084/m9.figshare.7182785
  • figshare/10.6084/m9.figshare.7182809
  • figshare/10.6084/m9.figshare.7182794
  • figshare/10.6084/m9.figshare.8269703
  • figshare/10.6084/m9.figshare.9943856

Grant support

JYD acknowledges funding from the Max Planck Society. This work was supported by a grant from the German Research Foundation (Deutsche Forschungsgemeinschaft) attributed to JYD, within the priority program (SPP) 1590 “probabilistic structures in evolution”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.