Brand new four chromosomes found in the LD test plus presented inversion-regular designs about PCA (Fig
Concept component analyses
1b, d, f, h, principle component loadings: A lot more document step 1: Rates S2–S5). The three autosomal inversions had one or two head homozygote haplotype clusters (towards the heterozygous people between) together with gender chromosome split into about three chief homozygote haplotype groups (towards the heterozygous somebody between). The latest groups was in fact well-defined to the autosomes but towards chromosome TguZ minimum of common haplotype (haplotype C for the Fig. 1h) did actually make it some recombination with every of the two most other haplotypes, putting some groups a lot more diffuse. But not, the reduced average heterozygosity inside for every people away from homozygotes opposed so you’re able to heterozygotes (Dining table 2) and you will median-joining networking sites (using System v4.six.step 1.step 1 which have standard settings ) into the phased SNP studies at the inversion breakpoint (playing with Beagle v3.step three.2 ; More file step 1: Figure S6) next contain the interpretation that the LD nations depict inversion polymorphisms. It has to even be detailed you to chromosomes Tgu5 and you may TguZ got become in earlier times receive cytogenetically to take pericentric inversions as well as the breakpoints meets precisely towards LD region limitations [forty five, 48–50].
Regarding latest analyses we do not know confidently and therefore arrangement was ancestral and then we for this reason identity him or her predicated on the allele volume (A great = biggest haplotype, B = slight haplotype, C = minimum popular haplotype towards chromosome TguZ; Fig. 1b, d, f, h; Desk 2). The top alleles of all the four inversion polymorphisms presented remarkably comparable frequencies starting between 0.53 and you will 0.60 (Table dos). To the chromosome TguZ, the least popular allele (haplotype C) are rare (frequency 0.074; Table dos). Most of the inversion polymorphisms was indeed for the Robust–Weinberg equilibrium (HWE; Desk dos) so there try zero LD between the two, meaning that they separate by themselves (Even more file dos: Desk S1).
Pooled heterozygosity and you will lesser allele counts 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 local hookups 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