Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

Kawakami, Takeshi, Mugal, Carina F., Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992, Nater, Alexander, Burri, Reto, Smeds, Linnéa and Ellegren, Hans (2017) Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds. Molecular Ecology, 26 (16). pp. 4158-4172. ISSN 0962-1083

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Abstract

Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400–3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.

Item Type: Article
Additional Information: Funding Information: This work was supported by Swedish Research Council (grant numbers 2007-8731, 2010-5650 and 2013-8271 to HE, and 2014-6325 to TK), Marie Sklodowska Curie Actions, Co-fund Project INCA (grant number 600398 to TK) and the Knut and Alice Wallenberg Foundation (grant type Wallenberg Scholar to HE). We thank Sébastien Renaut and three anonymous reviewers for their constructive comments on an earlier version of the manuscript. Computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). Publisher Copyright: © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd
Uncontrolled Keywords: cpg island,gc-biased gene conversion,linked selection,population genomics,recombination,transposon,ecology, evolution, behavior and systematics,genetics ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 16 Sep 2022 15:35
Last Modified: 24 Sep 2022 07:15
URI: https://ueaeprints.uea.ac.uk/id/eprint/88408
DOI: 10.1111/mec.14197

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