1b, d, f, h, concept part loadings: look at this now More file step 1: Data S2–S5). The 3 autosomal inversions got a couple head homozygote haplotype groups (towards heterozygous somebody between) while the intercourse chromosome divided in to around three main homozygote haplotype groups (into the heterozygous individuals in the middle). The latest groups was basically well defined on autosomes but into chromosome TguZ at least preferred haplotype (haplotype C when you look at the Fig. 1h) did actually succeed particular recombination with every of the two most other haplotypes, deciding to make the groups a whole lot more diffuse. But not, the lowest mediocre heterozygosity within this each group regarding homozygotes compared so you’re able to heterozygotes (Dining table dos) and you will average-joining companies (having fun with Community v4.6.step 1.step 1 which have important setup ) towards phased SNP study during the inversion breakpoint (playing with Beagle v3.3.2 ; Extra file 1: Contour S6) after that secure the interpretation your LD countries represent inversion polymorphisms. It should additionally be noted that chromosomes Tgu5 and TguZ got already been before found cytogenetically to create pericentric inversions and the breakpoints match truthfully into LD part limitations [forty five, 48–50].
Regarding newest analyses we really do not discover with certainty and that arrangement is actually ancestral and in addition we thus identity them considering their allele regularity (An excellent = major haplotype, B = small haplotype, C = minimum well-known haplotype towards the chromosome TguZ; Fig. 1b, d, f, h; Table 2). The big alleles of all the four inversion polymorphisms exhibited remarkably comparable frequencies ranging anywhere between 0.53 and you can 0.sixty (Desk dos). To your chromosome TguZ, at least prominent allele (haplotype C) was unusual (regularity 0.074; Table dos). All inversion polymorphisms was for the Robust–Weinberg equilibrium (HWE; Table 2) there is no LD between them, which means they separate individually (More document 2: Table S1).
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