Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees
Wallberg, Andreas, Uppsala University
Schöning, Caspar, Institute for Bee Research
Webster, Matthew T., Uppsala University
Hasselmann, Martin, University of Hohenheim
Published May 04, 2018 on Dryad.
https://doi.org/10.5061/dryad.jn630
Cite this dataset
Wallberg, Andreas; Schöning, Caspar; Webster, Matthew T.; Hasselmann, Martin (2018). Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees [Dataset]. Dryad. https://doi.org/10.5061/dryad.jn630
Abstract
Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies.
Usage notes
SNP dataset for 39 Kenyan honey bees (part 0)
This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split > 39_kenyan_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
39_kenyan_honeybees.vcf.gz.0.split
SNP dataset for 39 Kenyan honey bees (part 1)
This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split > 39_kenyan_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
39_kenyan_honeybees.vcf.gz.1.split
SNP dataset for 39 Kenyan honey bees (part 2)
This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split > 39_kenyan_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
39_kenyan_honeybees.vcf.gz.2.split
SNP dataset for 39 Kenyan honey bees (part 3)
This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split > 39_kenyan_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
39_kenyan_honeybees.vcf.gz.3.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 0)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.0.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 1)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.1.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 2)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.2.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 3)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.3.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 4)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.4.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 5)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.5.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 6)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.6.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 7)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.7.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 8)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.8.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 9)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.9.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 10)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.10.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 11)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.11.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 12)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.12.split
SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 13)
This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.
The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split > 148_honeybees.vcf.gz
The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
148_honeybees.vcf.gz.13.split