10.5061/DRYAD.9432P
González-Quevedo, Catalina
University of East Anglia
University of Antioquia
Spurgin, Lewis G.
University of East Anglia
Illera, Juan Carlos
University of East Anglia
Richardson, David S.
University of East Anglia
Data from: Drift, not selection, shapes toll-like receptor variation among
oceanic island populations
Dryad
dataset
2015
Natural Selection and Contemporary Evolution
Anthus campestris
Anthus berthelotii
2015-10-28T16:05:27Z
2015-10-28T16:05:27Z
en
https://doi.org/10.1111/mec.13437
1704440 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Understanding the relative role of different evolutionary forces in
shaping the level and distribution of functional genetic diversity among
natural populations is a key issue in evolutionary and conservation
biology. To do so accurately genetic data must be analyzed in conjunction
with an unambiguous understanding of the historical processes that have
acted upon the populations. Here we focused on diversity at toll-like
receptor (TLR) loci, which play a key role in the vertebrate innate immune
system and, therefore, are expected to be under pathogen-mediated
selection. We assessed TLR variation within and among 13 island
populations (grouped into three archipelagos) of Berthelot's pipit,
Anthus berthelotii, for which detailed population history has previously
been ascertained. We also compared the variation observed with that found
in its widespread sister species, the tawny pipit, Anthus campestris. We
found strong evidence for positive selection at specific codons in TLR1LA,
TLR3 and TLR4. Despite this, we found that at the allele frequency level,
demographic history has played the major role in shaping patterns of TLR
variation in Berthelot's pipit. Levels of diversity and
differentiation within and across archipelagos at all TLR loci
corresponded very closely with neutral microsatellite variation, and with
the severity of the bottlenecks that occurred during colonization. Our
study shows that despite the importance of TLRs in combating pathogens,
demography can be the main driver of immune gene variation within and
across populations, resulting in patterns of functional variation that can
persist over evolutionary timescales.
TLR1LA_All AberthelotiiThis fasta file contains the TLR1LA genotypes of
all Berthelot's pipits sampledTLR1LA_All AcampestrisThis file
contains all the TLR1LA genotypes of tawny pipits sampledTLR1LB_All
AberthelotiiThis file contains the TLR1LB genotypes of all
Berthelot's pipits sampledTLR1LB_All AcampestrisThis file contains
the TLR1LB genotypes of all tawny pipits sampled.TLR3_All AberthelotiiThis
file contains the TLR3 genotypes of all Berthelot's pipits
sampledTLR3_All AcampestrisThis file contains the TLR3 genotypes of all
tawny pipits sampledTLR4_All AberthelotiiThis file contains the TLR4
genotypes of all Berthelot's pipits sampledTLR4 _All AcampestrisThis
file contains the TLR4 genotypes of all tawny pipits sampledTLR21_All
AberthelotiiThis file contains the TLR21 genotypes of all Berthelot's
pipits sampledTLR21_All AcampestrisThis file contains the TLR21 genotypes
of all tawny pipits sampledPipit TLR FSTThis file contains the pairwise
Fst calculated for TLRsPipit pairwise FST per msat locusThis file contains
the pairwise Fst calculated with microsatellitescode to get pairwise
bottleneck distance between islandsThis file contains an R code to get
pairwise bottleneck distancesCO1_Anthus_alignedThis file contains the
alignment of the Cytochrome Oxidase subunit 1 haplotypes from Anthus
campestris and Anthus berthelotiiTLR1LA_All_genotypes2015This is the
output file with Phase results for TLR1LA in Berthelot's pipits. This
is a fasta file but should be opened using a text editor such as
NotepadTLR1LB_All_genotypes2015This is the output file with Phase results
for TLR1LB in Berthelot's pipits. This is a fasta file but should be
opened using a text editor such as NotepadTLR3_All_genotypes2015This is
the output file with Phase results for TLR3 in Berthelot's pipits.
This is a fasta file but should be opened using a text editor such as
NotepadTLR4_All_genotypes2015This is the output file with Phase results
for TLR4 in Berthelot's pipits. This is a fasta file but should be
opened using a text editor such as NotepadTLR21_All_genotypes2015This is
the output file with Phase results for TLR21 in Berthelot's pipits.
This is a fasta file but should be opened using a text editor such as
NotepadTLR1LA_ TREE SESSION 2015Tree file for the TLR1LA
phylogenyTLR1LB_tree session 2015Tree file for the TLR1LB
phylogenyTLR3_TREE SESSION 2015Tree file for the TLR3 phylogenyTLR4_new
tree sessionTree file for the TLR4 phylogenyTLR21_new tree sessionTree
file for the TLR21 phylogeny
Canary Islands
Selvagens
Madeira
Canary Island