10.5061/DRYAD.JN630
Wallberg, Andreas
Uppsala University
Schöning, Caspar
Institute for Bee Research
Webster, Matthew T.
Uppsala University
Hasselmann, Martin
University of Hohenheim
Data from: Two extended haplotype blocks are associated with adaptation to
high altitude habitats in East African honey bees
Dryad
dataset
2018
Haplotypes
Populations
2018-05-04T00:00:00Z
2018-05-04T00:00:00Z
en
https://doi.org/10.1371/journal.pgen.1006792
17300382100 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.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 >
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 >
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 >
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 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > 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 > 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