10.5061/DRYAD.HP758SN
Lundregan, Sarah L.
Norwegian University of Science and Technology
Hagen, Ingerid J.
Norwegian Institute for Nature Research
Norwegian University of Science and Technology
Gohli, Jostein
University of Helsinki
Norwegian University of Science and Technology
Niskanen, Alina K.
University of Oulu
Norwegian University of Science and Technology
Kemppainen, Petri
University of Helsinki
Norwegian University of Science and Technology
Ringsby, Thor Harald
Norwegian University of Science and Technology
Kvalnes, Thomas
Norwegian University of Science and Technology
Pärn, Henrik
Norwegian University of Science and Technology
Rønning, Bernt
Norwegian University of Science and Technology
Holand, Håkon
Norwegian University of Science and Technology
Ranke, Peter S.
Norwegian University of Science and Technology
Båtnes, Anna S.
Norwegian University of Science and Technology
Selvik, Linn-Karina
Norwegian University of Science and Technology
Lien, Sigbjorn
Norwegian University of Life Sciences
Sæther, Bernt-Erik
Norwegian University of Science and Technology
Husby, Arild
University of Helsinki
Norwegian University of Science and Technology
Uppsala University
Jensen, Henrik
Norwegian University of Science and Technology
Saether, Bernt-Erik
Norwegian University of Science and Technology
Data from: Inferences of genetic architecture of bill morphology in house
sparrow using a high‐density SNP array point to a polygenic basis
Dryad
dataset
2018
Bill morphology
polygenic
Holocene
Passer domesticus
2018-07-16T21:34:52Z
2018-07-16T21:34:52Z
en
https://doi.org/10.1111/mec.14811
1364767983 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Understanding the genetic architecture of quantitative traits can provide
insights into the mechanisms driving phenotypic evolution. Bill morphology
is an ecologically important and phenotypically variable trait, which is
highly heritable and closely linked to individual fitness. Thus, bill
morphology traits are suitable candidates for gene mapping analyses.
Previous studies have revealed several genes that may influence bill
morphology, but the similarity of gene and allele effects between species
and populations is unknown. Here, we develop a custom 200K SNP array and
use it to examine the genetic basis of bill morphology in 1857 house
sparrow individuals from a large-scale, island metapopulation off the
coast of Northern Norway. We found high genomic heritabilities for bill
depth and length, which were comparable with previous pedigree estimates.
Candidate gene and genome wide association analyses yielded six
significant loci, four of which have previously been associated with
craniofacial development. Three of these loci are involved in bone
morphogenic protein (BMP) signalling, suggesting a role for BMP genes in
regulating bill morphology. However, these loci individually explain a
small amount of variance. In combination with results from genome
partitioning analyses this indicates that bill morphology is a polygenic
trait. Any studies of eco-evolutionary processes in bill morphology are
therefore dependent on methods that can accommodate polygenic inheritance
of the phenotype and molecular-scale evolution of genetic architecture.
All phenotypic measurements for Helgeland house sparrowsFile containing
all phenotypic measurements for Helgeland individuals used in main
analysis (metapopulation location 66°30’N, 12°30’E). Measurements were
taken from all adult birds recorded between 1998-2013. id is individual id
as determined by ring number. Sex is the genetic sex. Hatch island is the
island the bird was first recorded on. Hatch year is the first year
recorded if a bird was measured as a nestling, or the year prior to first
year recorded if first measured as an adult. Year and month refer to the
date the phenotypic measurement was taken. Age is the age of the bird when
the measurement was taken. Island is the same as hatch island if hatch
island is one of the 8 SNP-typed islands, else the island is that on which
the blood sample for SNP typing was
taken.LundreganEtAl_PhenosAll.txtSingle phenotypic measurements for
Helgeland house sparrows adjusted to May 2CYFile containing single
phenotypic measurements for Helgeland individuals used in main analysis
(metapopulation location 66°30’N, 12°30’E). Measurements were taken from
all adult birds recorded between 1998-2013. To give a single value for
each individual, measurements of adult birds (second calendar year (2CY)
and older) were adjusted to May in 2CY using a linear mixed effects model
with age, age2 and month as fixed factors, random intercepts for year,
cohort and ID number, and a random slope for the effect of age within ID
number to account for any between-individual variation. If age and month
effects were significant (P < 0.05) in likelihood ratio tests,
predicted values from the model were used to adjust measurements to May in
2CY before calculation of mean phenotypic values. ID is individual id
determined by ring number. Sex is the genetic sex. Hatchyear is the first
year recorded for birds measured as nestlings or fledged juveniles, or the
year prior to first year recorded for birds ringed as adults. Hatch island
is the island the bird was first recorded on. Island is hatch island if
hatch island was one of the 8 SNP typed islands, else it is the island on
which the blood sample for SNP typing was
taken.LundreganEtAl_PhenosAge1.txt.map file for Helgeland individualsPLINK
.map file containing marker information for Helgeland individuals. File
contains information on chromosome, marker id, and bp position within
chromosome.LundreganEtAl_HelgelandBillData.map.ped file for Helgeland
individualsPLINK .ped file containing genotype information for all
Helgeland individuals used in analysis.LundreganEtAl_HelgelandBillData.ped
64°55' N - 11°00' E
Helgeland
63°55' N - 09°55' E
64°08' N – 29°31' E
64°01' N - 09°54' E
60°10' N – 24°57' E
62°35' N - 6°27' E
63°14' N - 10°16' E
65°40' N - 11°55' E
65°05' N - 11°40' E
66°10' N - 12°44' E
69°27' N - 30°00' E
Northern Norway
66°30' N - 12°06' E
64°43' N – 9°41' E
66°33' N - 12°50' E
69°58' N - 30°23' E
66°30’N - 12°30’E