Principle part analyses
1b, d, f, h, idea component loadings: Extra file step one: Figures S2–S5). The three autosomal inversions got a few main homozygote haplotype clusters (into the heterozygous somebody in-between) while the gender chromosome divided into about three head homozygote haplotype clusters (into heterozygous somebody in between). The latest clusters have been well defined towards the autosomes but on the chromosome TguZ at least preferred haplotype (haplotype C into the Fig. 1h) did actually succeed specific recombination with each of the two most other haplotypes, making the clusters far more diffuse. However, both reduced average heterozygosity inside per group regarding homozygotes compared to heterozygotes (Table 2) and you will average-joining networks (playing with Network v4.six.step one.step 1 that have simple configurations ) into phased SNP study at the inversion breakpoint (using Beagle v3.step 3.dos ; More file step 1: Figure S6) then support the interpretation that LD regions depict inversion polymorphisms. It should additionally be indexed one to chromosomes Tgu5 and you will TguZ got already been before discover cytogenetically to bring pericentric inversions and also the breakpoints meets correctly on LD area limits [forty five, 48–50].
About latest analyses we do not discover with confidence and therefore arrangement is actually ancestral and we also for this reason title him or her predicated on its allele regularity (An excellent = biggest haplotype, B = slight haplotype, C = least well-known haplotype toward chromosome TguZ; Fig. 1b, d, f, h; Table 2). The big alleles of the many four inversion polymorphisms showed surprisingly comparable wavelengths ranging between 0.53 and you can 0.60 (Table 2). Into the chromosome TguZ, minimum of preferred allele (haplotype C) is uncommon (frequency 0.074; Desk dos). The inversion polymorphisms were inside Hardy–Weinberg equilibrium (HWE; Desk 2) and there are zero LD among them, and thus it segregate alone (A lot more document 2: Table S1).
Pooled heterozygosity and you can slight allele counts on 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 https://datingranking.net/tr/swapfinder-inceleme 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