Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array
Article first published online: 26 MAY 2014
© 2014 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.
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Molecular Ecology Resources
Volume 14, Issue 6, pages 1248–1260, November 2014
How to Cite
Kawakami, T., Backström, N., Burri, R., Husby, A., Olason, P., Rice, A. M., Ålund, M., Qvarnström, A. and Ellegren, H. (2014), Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array. Molecular Ecology Resources, 14: 1248–1260. doi: 10.1111/1755-0998.12270
- Issue published online: 10 OCT 2014
- Article first published online: 26 MAY 2014
- Accepted manuscript online: 30 APR 2014 09:13AM EST
- Manuscript Accepted: 25 APR 2014
- Manuscript Revised: 14 APR 2014
- Manuscript Received: 21 JAN 2014
- European Research Council. Grant Number: 249976
- Knut and Alice Wallenberg Foundation
- Swedish Research Council. Grant Number: 2010-5650
- collared flycatcher;
- GWAS ;
- pied flycatcher;
- single-nucleotide polymorphism genotyping;
With the access to draft genome sequence assemblies and whole-genome resequencing data from population samples, molecular ecology studies will be able to take truly genome-wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb collared flycatcher genome assembly and identified 13 million single-nucleotide polymorphism (SNP)s in population resequencing of this species and its sister species, pied flycatcher. Here, we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. Using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity = 0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. Linkage disequilibrium declined quickly to the background level at an average distance of 17 kb, but the extent of LD varied markedly within the genome and was more than 10-fold higher in ‘genomic islands’ of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F1 hybrids but no later-generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1 Ma, this suggests strong selection against F1 hybrids and unusually rapid evolution of reproductive incompatibility in an avian system.