Publicação
Population genomics and landscape genetics of the Iberian honey bee (Apis mellifera iberiensis)
| Resumo: | The goal of this study was to disentangle the complex variation patterns of the Iberian honey bee ( Apis mellifera iberiensis) hybrid zone using the highly polymorphic tRNAleu-cox2 mitochondrial region and nuclear genome-wide Single Nucleotide Polymorphisms (SNPs). Initially, a maternal analysis was performed using a PCR-RFLP marker, known as the DraI test, in the tRNAleu-cox2 intergenic region of colonies sampled in Portugal (N=950). Using this test, 16 novel haplotypes of African ancestry, 15 belonging to sub-lineage AIII and 1 to sub-lineage AI, were identified. This result suggests that the Atlantic side of the Iberian Peninsula is an important reservoir of maternal diversity that has been missed out because of under-sampling in previous studies. To obtain a fuller picture of maternal diversity patterns in the Iberian honey bee, 711 drones, sampled across three north-south Iberian transects, were screened for tRNAleu-cox2 variation using sequence data. The tRNAleu-cox2 sequence revealed a more complex diversity pattern of haplotypes in the Iberian honey bee than previously thought when using only the DraI test, which is reflected by detection of 164 novel haplotypes of African (lineage A) and Western European (lineage M) ancestry. At the same time, the distribution of haplotypes A and M reported in this study has further refined the well-defined Southwestern-Northeastern clinal pattern previously described, and also has rescued and reinforced the hypothesis of a hybrid origin for the Iberian honey bee. The distribution pattern of both lineages suggests the presence of two glacial refuges located in the Northeastern and Southern of Iberia. Nonetheless, the confined distribution of sub-lineage AIII to the North Atlantic side of Iberia suggests a putative third refuge, an hypothesis that deserves further investigation. A phylogenetic tree representing over 281 haplotypes, of which 8 exhibited intermediate A and M characteristics, resolved that the AI, AII, AIII cluster and lineage M are sister groups, which have probably diverged from a common ancestor similar to sub-lineage Z. These findings suggest that lineage M might have a more ancestral African origin, not from North African populations but from Northeastern African and Near East populations where haplotypes of sub-lineage Z have been reported. The low number of colonies (only 1) carrying haplotypes of Eastern European ancestry (lineage C) indicates that importation of commercial honey bees is residual in Iberia, which contrasts with other regions of Western Europe where C-lineage honey bees are replacing the native subspecies. Analysis of selection was carried out to find out if this evolutionary force has been shaping the complex patterns of Iberian honey bees. The 711 drones were screened for 1536 SNPs using the GoldenGate Assay of Illumina, of which only 383 revealed polymorphic. While a total of 69 outlier SNPs were identified using two coalescent and two Bayesian methods, only 17 were crossvalidated by the four methods. Additionally, a spatial method identified 33 outlier SNPs of which 28 coincided with the previous four methods. Among the 17 outliers, 10 exhibited the strongest signal of selection (9 directional and 1 balancing). 71 outlier SNPs were located in or near genes involved in putative functions as signaling, structural, metabolism, regulation, transport, and immunity. Vision, xenobiotic detoxification and immune response mechanisms were well represented by several genes under selection. For the vision mechanism, five genes are responsible for neural development, synapse formation, axon guidance, regeneration and production of chromophore (formation of rhodopsin). For xenobiotic detoxification, three genes are responsible for tolerance to plant toxins and insecticide resistance. Finally, the two genes related with innate immune response participate in the phagocytosis process. The spatial analysis corroborated that selection is an underlying force shaping a latitudinal and longitudinal gradient. Population structure was inferred from both maternal (tRNAleu-cox2 intergenic region) and biparental (SNPs) markers using spatial and non-spatial methods. The geographical distribution of lineages A and M revealed a sharp southwestern-northeastern maternal cline. Congruent with the mtDNA, population structure inferred from SNPs indicates the presence of two clusters that remarkably overlap the distribution of A and M maternal lineages. These results support a process of secondary contact between divergent honey bee populations in Iberia. Further support for the secondary contact hypothesis comes from (i) geographic cline analysis, which revealed the existence of multiple coincident clines, (ii) elevated values of linkage disequilibrium and of diversity towards the center of the cline. The previous findings suggest the existence of two putative refuges located in Northeastern (between Iberian Mountain Range and Pyrenees) and Southern (Betic Ranges in Spain) Iberia, as proposed for a growing list of other Iberian taxa. In summary, the complex diversity patterns exhibited by Iberian honey bees has seemingly been shaped by a process of secondary contact between two highly divergent groups (A and M), together with selective forces producing local adaptation to a very heterogeneous area as the Iberian Peninsula. |
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| Autores principais: | Chávez Galarza, Julio César |
| Assunto: | Ciências Naturais::Ciências Biológicas |
| Ano: | 2016 |
| País: | Portugal |
| Tipo de documento: | tese de doutoramento |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | português |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | The goal of this study was to disentangle the complex variation patterns of the Iberian honey bee ( Apis mellifera iberiensis) hybrid zone using the highly polymorphic tRNAleu-cox2 mitochondrial region and nuclear genome-wide Single Nucleotide Polymorphisms (SNPs). Initially, a maternal analysis was performed using a PCR-RFLP marker, known as the DraI test, in the tRNAleu-cox2 intergenic region of colonies sampled in Portugal (N=950). Using this test, 16 novel haplotypes of African ancestry, 15 belonging to sub-lineage AIII and 1 to sub-lineage AI, were identified. This result suggests that the Atlantic side of the Iberian Peninsula is an important reservoir of maternal diversity that has been missed out because of under-sampling in previous studies. To obtain a fuller picture of maternal diversity patterns in the Iberian honey bee, 711 drones, sampled across three north-south Iberian transects, were screened for tRNAleu-cox2 variation using sequence data. The tRNAleu-cox2 sequence revealed a more complex diversity pattern of haplotypes in the Iberian honey bee than previously thought when using only the DraI test, which is reflected by detection of 164 novel haplotypes of African (lineage A) and Western European (lineage M) ancestry. At the same time, the distribution of haplotypes A and M reported in this study has further refined the well-defined Southwestern-Northeastern clinal pattern previously described, and also has rescued and reinforced the hypothesis of a hybrid origin for the Iberian honey bee. The distribution pattern of both lineages suggests the presence of two glacial refuges located in the Northeastern and Southern of Iberia. Nonetheless, the confined distribution of sub-lineage AIII to the North Atlantic side of Iberia suggests a putative third refuge, an hypothesis that deserves further investigation. A phylogenetic tree representing over 281 haplotypes, of which 8 exhibited intermediate A and M characteristics, resolved that the AI, AII, AIII cluster and lineage M are sister groups, which have probably diverged from a common ancestor similar to sub-lineage Z. These findings suggest that lineage M might have a more ancestral African origin, not from North African populations but from Northeastern African and Near East populations where haplotypes of sub-lineage Z have been reported. The low number of colonies (only 1) carrying haplotypes of Eastern European ancestry (lineage C) indicates that importation of commercial honey bees is residual in Iberia, which contrasts with other regions of Western Europe where C-lineage honey bees are replacing the native subspecies. Analysis of selection was carried out to find out if this evolutionary force has been shaping the complex patterns of Iberian honey bees. The 711 drones were screened for 1536 SNPs using the GoldenGate Assay of Illumina, of which only 383 revealed polymorphic. While a total of 69 outlier SNPs were identified using two coalescent and two Bayesian methods, only 17 were crossvalidated by the four methods. Additionally, a spatial method identified 33 outlier SNPs of which 28 coincided with the previous four methods. Among the 17 outliers, 10 exhibited the strongest signal of selection (9 directional and 1 balancing). 71 outlier SNPs were located in or near genes involved in putative functions as signaling, structural, metabolism, regulation, transport, and immunity. Vision, xenobiotic detoxification and immune response mechanisms were well represented by several genes under selection. For the vision mechanism, five genes are responsible for neural development, synapse formation, axon guidance, regeneration and production of chromophore (formation of rhodopsin). For xenobiotic detoxification, three genes are responsible for tolerance to plant toxins and insecticide resistance. Finally, the two genes related with innate immune response participate in the phagocytosis process. The spatial analysis corroborated that selection is an underlying force shaping a latitudinal and longitudinal gradient. Population structure was inferred from both maternal (tRNAleu-cox2 intergenic region) and biparental (SNPs) markers using spatial and non-spatial methods. The geographical distribution of lineages A and M revealed a sharp southwestern-northeastern maternal cline. Congruent with the mtDNA, population structure inferred from SNPs indicates the presence of two clusters that remarkably overlap the distribution of A and M maternal lineages. These results support a process of secondary contact between divergent honey bee populations in Iberia. Further support for the secondary contact hypothesis comes from (i) geographic cline analysis, which revealed the existence of multiple coincident clines, (ii) elevated values of linkage disequilibrium and of diversity towards the center of the cline. The previous findings suggest the existence of two putative refuges located in Northeastern (between Iberian Mountain Range and Pyrenees) and Southern (Betic Ranges in Spain) Iberia, as proposed for a growing list of other Iberian taxa. In summary, the complex diversity patterns exhibited by Iberian honey bees has seemingly been shaped by a process of secondary contact between two highly divergent groups (A and M), together with selective forces producing local adaptation to a very heterogeneous area as the Iberian Peninsula. |
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