DOI: 10.5061/dryad.jn630
title: Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees

description: 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.
description: 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 &gt;
 39_kenyan_honeybees.vcf.gz The VCF file can then be unzipped using the
 UNIX command: gunzip 39_kenyan_honeybees.vcf.gz39_kenyan_honeybees.vcf.gz.0.splitSNP 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 &gt; 39_kenyan_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz39_kenyan_honeybees.vcf.gz.1.splitSNP 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 &gt; 39_kenyan_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz39_kenyan_honeybees.vcf.gz.2.splitSNP 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 &gt; 39_kenyan_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz39_kenyan_honeybees.vcf.gz.3.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.0.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.1.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.2.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.3.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.4.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.5.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.6.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.7.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.8.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.9.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.10.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.11.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.12.splitSNP 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 &gt; 148_honeybees.vcf.gz The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz148_honeybees.vcf.gz.13.split