Concept part analyses
1b, d, f, h, principle part loadings: Additional file step 1: Data S2–S5). The 3 autosomal inversions got a couple head homozygote haplotype groups (towards heterozygous some one between) together with sex chromosome split into around three chief homozygote haplotype clusters (on heterozygous some body in the middle). This new groups was indeed well-defined to the autosomes but on chromosome TguZ minimum of well-known haplotype (haplotype C in the Fig. 1h) did actually allow it to be specific recombination with every of the two most other haplotypes, putting some clusters way more diffuse. But not, the lower mediocre heterozygosity inside for every single people from homozygotes opposed so you’re able to heterozygotes (Dining table 2) and you will median-signing up for companies (having fun with System v4.six.1.step one which have simple options ) towards phased SNP research on inversion breakpoint (having fun with Beagle v3.step three.2 ; More file step 1: Profile S6) further support the translation the LD countries portray inversion polymorphisms. It has to additionally be indexed you to definitely chromosomes Tgu5 and you may TguZ had become in the past located cytogenetically to bring pericentric inversions therefore the breakpoints meets accurately towards LD area borders [forty-five, 48–50].
About current analyses we really do not see with confidence and therefore arrangement are ancestral and then we for this reason name him or her predicated on its allele frequency (A good = significant haplotype, B = small haplotype, C = the very least preferred haplotype to the chromosome TguZ; Fig. 1b, d, f, h; Dining table dos). The top alleles of the many five inversion polymorphisms shown amazingly comparable frequencies starting between 0.53 and you can 0.60 (Desk 2). Into chromosome TguZ, minimum of popular allele (haplotype C) is rare (regularity 0.074; Table dos). The inversion polymorphisms was in fact when you look at the Robust–Weinberg equilibrium (HWE; Dining table dos) and there is no LD among them, which means that it segregate by themselves (Even more document 2: Desk S1).
Pooled heterozygosity and you can lesser allele matters in 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 https://datingranking.net/nl/badoo-overzicht/ 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