First, for the 1-kb analyses, we excluded low-diversity windows because of the expectation that these windows would harbor little information for accurately estimating recombination rates.
The framework is applied on data covering the UK and Ireland at 250 m resolution, evaluating a variety of indicators including mean patch size, edge density and Shannon diversity at window sizes ranging from 2.5 km to 80 km.
Although the data we present here are unweighted means of 50-kb windows, diversity estimates from 20 kb and 100 kb windows are highly consistent, as are results when we weight diversity by the fraction of bases in each window sequenced to a depth of at least two (data not shown).
Diversity in major windows of preservation was highest during the late Langsettian and Duckmantian (> 50 species), lower in the Late Pennsylvanian (25 40 species) and the lowest in the Asselian (~ 20 species).
We do however find that hotspots are significantly closer to the chromosome and have significantly greater nucleotide diversity than nonhotspot windows.
(C ) shows the anti-correlation between the rate of nonsynonymous divergence and synonymous diversity in 1kb windows across the genome (color indicates position on the genome blue→green→yellow→red). (D ) shows the site frequency spectrum of synonymous (blue) and nonsynonymous (green) SNPs.
Using published information on a total of 7.2 million chicken SNPs obtained from re-sequencing of pooled samples [ 25], we derived genome-wide estimates of local (1 Mb windows) diversity level for three chicken populations (red jungle fowl [RJF], broiler and layer) based on non-repetitive and putatively non-functional sites in the genome (see Materials and Methods).
And if diversity descends into window dressing, it isn't diversity at all.
We therefore calculated haplotype diversity for sliding-window analysis using only sites with a minimum coverage of ten reads.
We performed diversity (pi) sliding window analysis for the alignment of full length sequence of each MITE family.
To determine the effect of the segregating inversion on diversity, we performed window-based analyses of π for the three different karyotypes present in NGS and NGS INBRED (fig. 5).
