Concept component analyses
1b, d, f, h, concept part loadings: Most document 1: Rates S2–S5). The three autosomal inversions had a couple head homozygote haplotype groups (for the heterozygous some one in between) while the sex chromosome divided in to around three chief homozygote haplotype groups (on heterozygous someone in-between). Brand new groups was in fact well-defined towards autosomes but towards chromosome TguZ minimum of common haplotype (haplotype C inside Fig. 1h) appeared to allow it to be some recombination with every of the two other haplotypes, making the clusters significantly more diffuse. not, both low mediocre heterozygosity within this per class from homozygotes opposed in order to heterozygotes (Dining table 2) and you will median-joining networking sites (playing with Network v4.six.1.step one with standard configurations ) toward phased SNP research on inversion breakpoint (using Beagle v3.step three.2 ; Additional file step one: Contour S6) next support the interpretation the LD places portray inversion polymorphisms. It should be men looking for women ads also detailed one to chromosomes Tgu5 and you will TguZ got been prior to now receive cytogenetically to take pericentric inversions and also the breakpoints match precisely for the LD region limits [45, 48–50].
Regarding the most recent analyses we do not learn with confidence and therefore plan try ancestral and we also therefore label her or him predicated on the allele regularity (Good = significant haplotype, B = minor haplotype, C = least common haplotype for the chromosome TguZ; Fig. 1b, d, f, h; Table dos). The major alleles of all the five inversion polymorphisms demonstrated remarkably equivalent wavelengths varying ranging from 0.53 and 0.sixty (Desk dos). To your chromosome TguZ, minimum of preferred allele (haplotype C) are unusual (volume 0.074; Desk dos). Most of the inversion polymorphisms was during the Robust–Weinberg equilibrium (HWE; Desk 2) so there is zero LD among them, which means that it segregate separately (Even more file dos: Desk S1).
Pooled heterozygosity and you can lesser allele matters during the 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