Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection

Table 1 High diversity genomic regions and associated disease resistance genes

	Smoothing parameters		Number windows showing significantly (p < 0.05) elevated polymorphism
a)
Group^a	Proportion missing data	Window size parameter, σ (Kbp)	Total number of windows	H _e	π	H _e and π	Total	Proportion showing significantly elevated polymorphism
NA-S	0	150	4327	151	165	94	410	0.0948
NA-S	< 50%	150	7256	163	225	154	542	0.0747
EU-N	< 50%	60	16,990	393	190	491	1074	0.0632
NA-O	< 50%	60	14,572	555	307	966	1828	0.1254
ALL-O	< 50%	50	23,465	452	478	917	1847	0.0787
b)
Group^a	Proportion missing data	Number regions of high diversity	Size of regions (Mbp)	Number genes in regions		Number NLR genes in region		Proportion of all NLR genes
NA-S	0	50	24.351600	4355		52		0.250
NA-S	< 50%	43	22.346912	3710		49		0.238
EU-N	< 50%	128	22.903806	3647		64		0.311
NA-O	< 50%	156	31.039876	5575		90		0.437
ALL-O	< 50%	179	28.702652	4406		75		0.364

(a) the number of smoothed high diversity windows with significantly elevated H_e (expected heterozygosity), π (nucleotide diversity) or both for different sample groups; and (b) the number of candidate NLR loci (Nucleotide binding site- Leucine rich repeat genes described in test panel in Additional file 1: Table S5) in genomic regions of significantly elevated diversity. Genomic regions are based on combining smoothed windows of significantly elevated diversity that overlap along a chromosome
^aNA-S = N. American selfing, EU-N = Northern European (Sweden, Iceland and Norway), NA-O = N. American outcrossing, ALL-O = all outcrossing samples i.e. without NA-S samples

ISSN: 1471-2164