Principle parts analyses
1b, d, f, h, concept component loadings: Most file step 1: Data S2–S5). The 3 autosomal inversions had a couple of chief homozygote haplotype clusters (into heterozygous individuals around) and gender chromosome put into around three main homozygote haplotype clusters (to your heterozygous some body in-between). The brand new groups was basically well defined with the autosomes but toward chromosome TguZ the least preferred haplotype (haplotype C inside the Fig. 1h) seemed to succeed particular recombination with every of these two other haplotypes, putting some clusters far more diffuse. Although not, both the lowest mediocre heterozygosity within this for each and every group away from homozygotes opposed so you’re able to heterozygotes (Desk dos) and you may median-joining channels (having fun with Community v4.6.1.1 having standard options ) into the phased SNP study at the inversion breakpoint (playing with Beagle v3.3.2 ; More document 1: Profile S6) then secure the interpretation that the LD countries matchbox ne demek show inversion polymorphisms. It should also be indexed one to chromosomes Tgu5 and you will TguZ had started before located cytogenetically to carry pericentric inversions and also the breakpoints meets correctly on the LD region limits [forty-five, 48–50].
About current analyses we really do not discover with certainty and this arrangement are ancestral and we also therefore term them centered on its allele regularity (A great = big haplotype, B = small haplotype, C = the very least popular haplotype to the chromosome TguZ; Fig. 1b, d, f, h; Table dos). The major alleles of the many five inversion polymorphisms displayed remarkably comparable frequencies varying anywhere between 0.53 and you can 0.60 (Dining table dos). Towards chromosome TguZ, the least well-known allele (haplotype C) try uncommon (volume 0.074; Desk 2). The inversion polymorphisms was within the Sturdy–Weinberg balance (HWE; Desk dos) so there is actually no LD among them, and thus they segregate separately (Extra file 2: Desk S1).
Pooled heterozygosity and slight allele counts within inversion breakpoints
We calculated pooled heterozygosity (ZHp) in 50-kb non-overlapping sliding windows along each chromosome (Fig. 2a). Low values of ZHp are indicative of regions with a high degree of fixation, for example, due to positive selection ; high values of ZHp are expected, for example, in regions of local population structure (like inversions) or under balancing selection . We found pronounced peaks in ZHp at the presumed breakpoints of the inversions on chromosomes Tgu5, Tgu11, and Tgu13, whereas ZHp dropped to almost genome-wide average values in the interior of the inversions. Chromosome Tgu11 had only one such peak, suggesting that the proximal breakpoint is missing in the current genome assembly. Diversity (SNPs per site in a 50-kb window; Additional file 1: Figure S7) was slightly reduced at the presumed breakpoints of every inversion compared to the inversion’s interior (mean SNPs per site ± standard deviation at breakpoints versus interior of 0.017 ± 0.005 versus 0.020 ± 0.005 for Tgu5, 0.0057 ± 0.0036 versus 0.018 ± 0.004 for Tgu11, and 0.016 ± 0.006 versus 0.022 ± 0.004 for Tgu13; 0.021 ± 0.007 collinear autosomal genome-wide average SNPs per site). On chromosome TguZ, the entire inversion interior had high ZHp values, which only dropped to the genome-wide average outside the inverted region. Further, diversity on TguZ was markedly reduced all along the inverted region, including the presumed breakpoints, and increased to the genome-wide average only outside the inversion (0.0021 ± 0.0015 versus 0.022 ± 0.009, respectively).
a Pooled heterozygosity (ZHp) in 50-kb windows along each chromosome in the zebra finch genome. b–e For the highlighted areas in a, which are the presumed inversion breakpoints on the autosomes and the entire inversion interior on the sex chromosome, the minor allele count frequency (MAC) spectra are shown for chromosome Tgu5 with a local maximum at 0.34–0.36 and a frequency of the minor (B) haplotype in the sample of 0.35 (b), Tgu11 with a local maximum at 0.48–0.50 and a frequency of minor (B) haplotype in the sample of 0.47 (c), Tgu13 with a local maximum at 0.48–0.50 and a frequency of minor (B) haplotype in the sample of 0.50 (d), and TguZ with two local maxima at 0.28–0.30 and 0.42–0.44 and a frequency of the B haplotype in the sample of 0.30 and frequency of the major (A) haplotype in the sample of 0.63 (e). f For comparison, the MAC of all remaining SNPs peaks at an allele frequency of around 0.1 because SNPs with a lower frequency were not unambiguously called
