Publicação
Exploring population structure and adaptation in honey bee subspecies from southern glacial refugia: A. M. Iberiensis and A. M. Ligustica
| Resumo: | Glacial refugia harbor populations with complex diversity patterns. In honey bees, the Iberian and Italian Peninsulas served as two of the most important glacial refugia in Europe. Here, we analyzed whole genomes generated from drones to infer population structure, genetic diversity, and the molecular basis of the local adaptation for the two native subspecies of these Peninsulas: A. m. iberiensis (N=86; M-lineage) and A. m. ligustica (N=225; C-lineage). For A. m. iberiensis, Admixture analysis revealed a strong cline between two genetic backgrounds from Southwest to Northeast and no C-lineage introgression was detected. For A. m. ligustica, introgression with A. m. carnica occurred in Central and Southern Italy (median q-valuecarnica=0.069; IQR=0.187), away from the natural hybridization zone in Northeastern Italy where higher admixture proportions were detected (median q-valuecarnica=0.229; IQR=0.262). A. m. mellifera introgression was detected especially in the Northwest (median q-valuemellifera 0.053; IQR=0.030), and with lower values in Central and Southern Italy (median q-valuemellifera 0.014; IQR=0.041). A. m. iberiensis showed higher diversity when compared to A. m. ligustica: π (πiberiensis=0.325, πligustica= 0.245, p-value<0.001); He (Heiberiensis=0.319, Heligustica=0.319; p-value<0.001) but lower relatedness (IBD kinshipiberiensis=0.002, IBD kinshipligustica=0.014; p-value<0.001). Selection signatures were detected and cross-validated using PCAdapt, SAMBADA, and RDA. SNPs with q-adjusted p-values < 0.01 detected by at least two methods were considered strong candidates. For A. m. ligustica, 133 candidate SNPs annotated to 125 genes were detected by all three methods, including dnaJ homolog subfamily C member 9, nephrin, and the diuretic hormone receptor, and these were correlated with precipitation. For A. m. iberiensis, 528 SNPs annotated to 527 genes were detected, and these included proteins related to heat-shock response, such as Cyp40 and rrp45. While no common candidate SNPs were detected between both subspecies, 20 common genes containing candidate SNPs were detected, such as 4-coumarate-CoA ligase 1, CPR9, and alpha-mannosidase 2. |
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| Autores principais: | Yadró Garcia, Carlos A. |
| Outros Autores: | Henriques, Dora; Cilia, Giovanni; Rufino, José; Martín-Hernández, Raquel; Nanetti, Antonio; Pinto, M. Alice |
| Assunto: | Apis mellifera iberiensis Apis mellifera ligustica Population structure Adaptation |
| Ano: | 2024 |
| País: | Portugal |
| Tipo de documento: | documento de conferência |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Instituto Politécnico de Bragança |
| Idioma: | inglês |
| Origem: | Biblioteca Digital do IPB |
| Resumo: | Glacial refugia harbor populations with complex diversity patterns. In honey bees, the Iberian and Italian Peninsulas served as two of the most important glacial refugia in Europe. Here, we analyzed whole genomes generated from drones to infer population structure, genetic diversity, and the molecular basis of the local adaptation for the two native subspecies of these Peninsulas: A. m. iberiensis (N=86; M-lineage) and A. m. ligustica (N=225; C-lineage). For A. m. iberiensis, Admixture analysis revealed a strong cline between two genetic backgrounds from Southwest to Northeast and no C-lineage introgression was detected. For A. m. ligustica, introgression with A. m. carnica occurred in Central and Southern Italy (median q-valuecarnica=0.069; IQR=0.187), away from the natural hybridization zone in Northeastern Italy where higher admixture proportions were detected (median q-valuecarnica=0.229; IQR=0.262). A. m. mellifera introgression was detected especially in the Northwest (median q-valuemellifera 0.053; IQR=0.030), and with lower values in Central and Southern Italy (median q-valuemellifera 0.014; IQR=0.041). A. m. iberiensis showed higher diversity when compared to A. m. ligustica: π (πiberiensis=0.325, πligustica= 0.245, p-value<0.001); He (Heiberiensis=0.319, Heligustica=0.319; p-value<0.001) but lower relatedness (IBD kinshipiberiensis=0.002, IBD kinshipligustica=0.014; p-value<0.001). Selection signatures were detected and cross-validated using PCAdapt, SAMBADA, and RDA. SNPs with q-adjusted p-values < 0.01 detected by at least two methods were considered strong candidates. For A. m. ligustica, 133 candidate SNPs annotated to 125 genes were detected by all three methods, including dnaJ homolog subfamily C member 9, nephrin, and the diuretic hormone receptor, and these were correlated with precipitation. For A. m. iberiensis, 528 SNPs annotated to 527 genes were detected, and these included proteins related to heat-shock response, such as Cyp40 and rrp45. While no common candidate SNPs were detected between both subspecies, 20 common genes containing candidate SNPs were detected, such as 4-coumarate-CoA ligase 1, CPR9, and alpha-mannosidase 2. |
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