The latest five chromosomes found in the LD check always including presented inversion-regular habits on PCA (Fig

The latest five chromosomes found in the LD check always including presented inversion-regular habits on PCA (Fig

Idea parts analyses

1b, d, f, h, principle component loadings: Extra document step 1: Figures S2–S5). The three autosomal inversions had a couple of main homozygote haplotype groups (on heterozygous anyone in the middle) and gender chromosome split into three chief homozygote haplotype clusters (into the heterozygous someone among). The latest groups was in fact well defined on the autosomes but towards the chromosome TguZ minimum of popular haplotype (haplotype C for the Fig. 1h) did actually create particular recombination with each of the two other haplotypes, deciding to make the clusters significantly more diffuse. Although not, both reduced mediocre heterozygosity contained in this for each and every team away from homozygotes opposed so you can heterozygotes (Desk 2) and you will median-signing up for networks (playing with Network v4.6.step 1.step one with fundamental setup ) to your phased SNP analysis at inversion breakpoint (playing with Beagle v3.step three.2 ; Additional file 1: Figure S6) after that keep the interpretation that LD regions portray inversion polymorphisms. It has to be also indexed you to definitely chromosomes Tgu5 and you may TguZ got already been prior to now receive cytogenetically to take pericentric inversions and also the breakpoints match accurately towards the LD part borders [forty five, 48–50].

About current analyses we do not learn with confidence hence arrangement are ancestral and now we hence title her or him based on its allele regularity (An excellent = big haplotype, B = minor haplotype, C = the very least prominent haplotype towards the chromosome TguZ; Fig. 1b, d, f, h; Table 2). The big alleles of the many four inversion polymorphisms exhibited interestingly equivalent frequencies starting anywhere between 0.53 and 0.sixty (Table 2). Towards chromosome TguZ, the least prominent allele (haplotype C) try rare (regularity 0.074; Desk dos). The inversion polymorphisms was inside Robust–Weinberg equilibrium (HWE; Dining table 2) so there try zero LD among them, and thus it segregate by themselves (Extra document 2: Dining table S1).

Pooled heterozygosity and small allele matters at 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

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