Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array.

Kawakami T, Backström N, Burri R, Husby A, Olason P, Rice AM, Ålund M, Qvarnström A, Ellegren H

Mol Ecol Resour 14 (6) 1248-1260 [2014-11-00; online 2014-05-03]

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.

NGI Uppsala (SNP&SEQ Technology Platform)

National Genomics Infrastructure

PubMed 24784959

DOI 10.1111/1755-0998.12270

Crossref 10.1111/1755-0998.12270

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dbSNP: SS_974711471
dbSNP: SS_974711472
dbSNP: SS_974711473
dbSNP: SS_974711474
dbSNP: SS_974711475
dbSNP: SS_974711476
dbSNP: SS_974711477
dbSNP: SS_974711478
dbSNP: SS_974711479
dbSNP: SS_974711480
dbSNP: SS_974711481
dbSNP: SS_974711482
dbSNP: SS_974711483
dbSNP: SS_974711484
dbSNP: SS_974711485
dbSNP: SS_974711486
dbSNP: SS_974711487
dbSNP: SS_974711488
dbSNP: SS_974711489
dbSNP: SS_974711490
dbSNP: SS_974711491
dbSNP: SS_974711492
dbSNP: SS_974711493
dbSNP: SS_974711494
dbSNP: SS_974711495
dbSNP: SS_974711496
dbSNP: SS_974711497
dbSNP: SS_974711498
dbSNP: SS_974711499
dbSNP: SS_974711500
dbSNP: SS_974711501
dbSNP: SS_974711502
dbSNP: SS_974711503
dbSNP: SS_974711504
dbSNP: SS_974711505
dbSNP: SS_974711506
dbSNP: SS_974711507
dbSNP: SS_974711508
dbSNP: SS_974711509
dbSNP: SS_974711510
dbSNP: SS_974711511
dbSNP: SS_974711512
dbSNP: SS_974711513
dbSNP: SS_974711514
dbSNP: SS_974711515
dbSNP: SS_974711516
dbSNP: SS_974711517
dbSNP: SS_974711518
dbSNP: SS_974711519
dbSNP: SS_974711520
dbSNP: SS_974711521
dbSNP: SS_974711522
dbSNP: SS_974711523
dbSNP: SS_974711524
dbSNP: SS_974711525
dbSNP: SS_974711526
dbSNP: SS_974711527
dbSNP: SS_974711528
dbSNP: SS_974711529
dbSNP: SS_974711530
dbSNP: SS_974711531
dbSNP: SS_974711532
dbSNP: SS_974711533
dbSNP: SS_974711534
dbSNP: SS_974711535
dbSNP: SS_974711536
dbSNP: SS_974711537
dbSNP: SS_974711538
dbSNP: SS_974711539
dbSNP: SS_974711540
dbSNP: SS_974711541
dbSNP: SS_974711542
dbSNP: SS_974711543
dbSNP: SS_974711544
dbSNP: SS_974711545
dbSNP: SS_974711546
dbSNP: SS_974711547
dbSNP: SS_974711548
dbSNP: SS_974711549
dbSNP: SS_974711550
dbSNP: SS_974711551
dbSNP: SS_974711552
dbSNP: SS_974711553
dbSNP: SS_974711554
dbSNP: SS_974711555
dbSNP: SS_974711556
dbSNP: SS_974711557
dbSNP: SS_974711558
dbSNP: SS_974711559
dbSNP: SS_974711560
dbSNP: SS_974711561
dbSNP: SS_974711562
dbSNP: SS_974711563
dbSNP: SS_974711564
dbSNP: SS_974711565
dbSNP: SS_974711566
dbSNP: SS_974711567
dbSNP: SS_974711568
dbSNP: SS_974711569
dbSNP: SS_974711570
dbSNP: SS_974711571
dbSNP: SS_974711572
dbSNP: SS_974711573
dbSNP: SS_974711574
dbSNP: SS_974711575
dbSNP: SS_974711576
dbSNP: SS_974711577
dbSNP: SS_974711578
dbSNP: SS_974711579
dbSNP: SS_974711580
dbSNP: SS_974711581
dbSNP: SS_974711582
dbSNP: SS_974711583
dbSNP: SS_974711584
dbSNP: SS_974711585
dbSNP: SS_974711586
dbSNP: SS_974711587
dbSNP: SS_974711588
dbSNP: SS_974711589
dbSNP: SS_974711590
dbSNP: SS_974711591
dbSNP: SS_974711592
dbSNP: SS_974711593
dbSNP: SS_974711594
dbSNP: SS_974711595
dbSNP: SS_974711596
dbSNP: SS_974711597
dbSNP: SS_974711598
dbSNP: SS_974711599
dbSNP: SS_974711600
dbSNP: SS_974711601
dbSNP: SS_974711602
dbSNP: SS_974711603
dbSNP: SS_974711604
dbSNP: SS_974711605
dbSNP: SS_974711606
dbSNP: SS_974711607
dbSNP: SS_974711608
dbSNP: SS_974711609
dbSNP: SS_974711610
dbSNP: SS_974711611
dbSNP: SS_974711612
dbSNP: SS_974711613
dbSNP: SS_974711614
dbSNP: SS_974711615
dbSNP: SS_974711616
dbSNP: SS_974711617
dbSNP: SS_974711618
dbSNP: SS_974711619
dbSNP: SS_974711620
dbSNP: SS_974711621
dbSNP: SS_974711622
dbSNP: SS_974711623
dbSNP: SS_974711624
dbSNP: SS_974711625
dbSNP: SS_974711626
dbSNP: SS_974711627
dbSNP: SS_974711628
dbSNP: SS_974711629
dbSNP: SS_974711630
dbSNP: SS_974711631
dbSNP: SS_974711632
dbSNP: SS_974711633
dbSNP: SS_974711634
dbSNP: SS_974711635
dbSNP: SS_974711636
dbSNP: SS_974711637
dbSNP: SS_974711638
dbSNP: SS_974711639
dbSNP: SS_974711640
dbSNP: SS_974711641
dbSNP: SS_974711642
dbSNP: SS_974711643
dbSNP: SS_974711644
dbSNP: SS_974711645
dbSNP: SS_974711646
dbSNP: SS_974711647
dbSNP: SS_974711648
dbSNP: SS_974711649
dbSNP: SS_974711650
dbSNP: SS_974711651
dbSNP: SS_974711652
dbSNP: SS_974711653
dbSNP: SS_974711654
dbSNP: SS_974711655
dbSNP: SS_974711656
dbSNP: SS_974711657
dbSNP: SS_974711658
dbSNP: SS_974711659
dbSNP: SS_974711660
dbSNP: SS_974711661
dbSNP: SS_974711662
dbSNP: SS_974711663
dbSNP: SS_974711664
dbSNP: SS_974711665
dbSNP: SS_974711666
dbSNP: SS_974711667
dbSNP: SS_974711668
dbSNP: SS_974711669
dbSNP: SS_974711670
dbSNP: SS_974711671
dbSNP: SS_974711672
dbSNP: SS_974711673
dbSNP: SS_974711674
dbSNP: SS_974711675
dbSNP: SS_974711676
dbSNP: SS_974711677
dbSNP: SS_974711678
dbSNP: SS_974711679
dbSNP: SS_974711680
dbSNP: SS_974711681
dbSNP: SS_974711682
dbSNP: SS_974711683
dbSNP: SS_974711684
dbSNP: SS_974711685
dbSNP: SS_974711686
dbSNP: SS_974711687
dbSNP: SS_974711688
dbSNP: SS_974711689
dbSNP: SS_974711690
dbSNP: SS_974711691
dbSNP: SS_974711692
dbSNP: SS_974711693
dbSNP: SS_974711694
dbSNP: SS_974711695
dbSNP: SS_974711696
dbSNP: SS_974711697
dbSNP: SS_974711698
dbSNP: SS_974711699
dbSNP: SS_974711700
dbSNP: SS_974711701
dbSNP: SS_974711702
dbSNP: SS_974711703
dbSNP: SS_974711704
dbSNP: SS_974711705
dbSNP: SS_974711706
dbSNP: SS_974711707
dbSNP: SS_974711708
dbSNP: SS_974711709
dbSNP: SS_974711710
dbSNP: SS_974711711
dbSNP: SS_974711712
dbSNP: SS_974711713
dbSNP: SS_974711714
dbSNP: SS_974711715
dbSNP: SS_974711716
dbSNP: SS_974711717
dbSNP: SS_974711718
dbSNP: SS_974711719
dbSNP: SS_974711720
dbSNP: SS_974711721
dbSNP: SS_974711722
dbSNP: SS_974711723
dbSNP: SS_974711724
dbSNP: SS_974711725
dbSNP: SS_974711726
dbSNP: SS_974711727
dbSNP: SS_974711728
dbSNP: SS_974711729
dbSNP: SS_974711730
dbSNP: SS_974711731
dbSNP: SS_974711732
dbSNP: SS_974711733
dbSNP: SS_974711734
dbSNP: SS_974711735
dbSNP: SS_974711736
dbSNP: SS_974711737
dbSNP: SS_974711738
dbSNP: SS_974711739
dbSNP: SS_974711740
dbSNP: SS_974711741
dbSNP: SS_974711742
dbSNP: SS_974711743
dbSNP: SS_974711744
dbSNP: SS_974711745
dbSNP: SS_974711746
dbSNP: SS_974711747
dbSNP: SS_974711748
dbSNP: SS_974711749
dbSNP: SS_974711750
dbSNP: SS_974711751
dbSNP: SS_974711752
dbSNP: SS_974711753
dbSNP: SS_974711754
dbSNP: SS_974711755
dbSNP: SS_974711756
dbSNP: SS_974711757
dbSNP: SS_974711758
dbSNP: SS_974711759
dbSNP: SS_974711760
dbSNP: SS_974711761
dbSNP: SS_974711762
dbSNP: SS_974711763
dbSNP: SS_974711764
dbSNP: SS_974711765
dbSNP: SS_974711766
dbSNP: SS_974711767
dbSNP: SS_974711768
dbSNP: SS_974711769
dbSNP: SS_974711770
dbSNP: SS_974711771

Publications 9.5.0