Data from: Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome

Properly estimating genetic diversity in populations of non-model species
requires a basic understanding of how diversity is distributed across the
genome and among individuals. To this end we analysed whole-genome
re-sequencing data from 20 collared flycatchers (genome size ≈1.1 Gb;
10.13 million single nucleotide polymorphisms detected). Genome-wide
nucleotide diversity was almost identical among individuals (mean =
0.00394, range = 0.00384-0.00401) but diversity levels varied extensively
across the genome (95% confidence interval for 200 kb windows =
0.0013-0.0053). Diversity was related to selective constraint such that in
comparison to intergenic DNA, diversity at fourfold degenerate sites was
reduced to 85%, 3’ UTRs to 82%, 5’ UTRs to 70% and non-degenerate sites to
12%. There was a strong positive correlation between diversity and
chromosome size, probably driven by a higher density of targets for
selection on smaller chromosomes increasing the diversity-reducing effect
of linked selection. Simulations exploring the ability of sequence data
from a small number of genetic markers to capture the observed diversity
clearly demonstrated that diversity estimation from finite sampling of
such data is bound to be associated with large confidence intervals.
Nevertheless, we show that precision in diversity estimation in large
outbred populations benefits from increasing the number of loci rather
than the number of individuals. Simulations mimicking RAD sequencing
showed that this approach gives accurate estimates of genome-wide
diversity. Based on the patterns of observed diversity and the performed
simulations we provide broad recommendations for how genetic diversity
should be estimated in natural populations.