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. 2024 Mar 13;3(3):pgae107. doi: 10.1093/pnasnexus/pgae107

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© The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences.

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Fig. 1. — A) WT and blue Agapornis fischeri and A. personatus. Photos © Dirk Van den Abeele. B) Genome-wide differentiation (F_ST) between WT and blue individuals, single nucleotide polymorphism (SNP) associations with the color, and RND values between blue and WT individuals across the genome were shown for A. fischeri. The same peak of F_ST and SNP association in scaffold 2 was identified for A. personatus (results are not shown). Points indicate overlapping sliding window F_ST and RND values in 200 kb windows. Red horizontal lines indicate the 99.9th percentile for F_ST, Bonferroni-corrected P value for genome-wide association studies (GWAS), and 99.9th percentile for RND values, respectively. Chromosome-level scaffold identities for the reference A. roseicollis genome are shown at the bottom. C) F_ST, SNP associations, and Fisher's exact test P values of the highly differentiated region in A. fischeri (top) and A. personatus (bottom). Annotated genes in this region are depicted by blocks at the top. The red line indicates the position of the R644W substitution. The blue and pink solid dots indicate the association and Fisher's exact test P value of the R644W substitution. D) Signatures of selective sweep in the blue A. fischeri and blue A. personatus but not WT individuals. The red line indicates the position of the R644W substitution. CLR, composite likelihood ratio values. E) Alignment of MuPKS sequences from different avian species showing the region with the R644W substitution. Bottom table shows the nonsynonymous substitution of arginine (R) by tryptophan (W) segregates completely with the color difference in both A. fischeri (left) and A. personatus (right), based on both Sanger sequencing and whole-genome data. F) Genotypes at SNPs between WT and blue A. fischeri and A. personatus in the MuPKS region (scaffold 2, 18−21 Mb), indicating the blue-associated region with the signature of selective sweep is highly similar in both species. Each row represents one individual. Green, light blue, and yellow indicate positions homozygous for the allele that was the same as the reference genome, homozygous for the allele different from the reference, and heterozygous for both alleles, respectively. Annotated genes in this region are depicted by blocks at the bottom. G) Relationship between haplotypes of the divergent region from WT and blue A. fischeri and A. personatus, showing a high level of blue-associated haplotypes (residue 644: W) sharing but little overlaps in the WT haplotypes (residue 644: R) between the two species.