might be the result of nonadaptive demographical processes,
such as bottlenecks [71].
40. Phylogenetic networks can be reconstructed using software
packages such as Network or POP ART (see Table 1).
41. Orthologue gene sequences can be obtained for A. lyrata and
other related Brassicaceae species from specific genome databases or from Phytozome webpage (see Table 1). Integrating
A. lyrata sequences in your analyses requires previous alignment with the available A. thaliana sequences, which can be
done with Clustal Omega (see Note 31).
42. Depending on the number of haplotypes and their nucleotide
differentiation, phylogenetic networks can be rather complex
and difficult to interpret. Network complexity can be reduced
by removing very low frequency haplotypes, or discarding
some recombinant haplotypes that can be previously inferred
by recombination analysis using DnaSP. In addition, for genes
with a large number of missense mutations, networks and trees
can be reconstructed from data files including only
non-synonymous polymorphisms or protein sequences, which
can be generated with DnaSP (see Table 1).
43. The geographic information (latitude, longitude, and altitude)
of Arabidopsis accessions can be obtained from the 1001 genomes or CLIMtools databases. Climatic information can be
downloaded from the CLIMtools database or from the World
climate web site using the R package raster. Soil and landscape
data can be extracted from the corresponding public databases
(see Table 1; [72]).
44. The geographic distribution of SNPs can be visualized using
basic graphical options of spreadsheets, software packages like
SAM (see Table 1), or with the R package maps. Information
on climatic variables can be visualized using the R package
raster, including the distribution of accessions according to
SNP alleles.
45. Nucleotide alignments or vcf files can be filtered with software
packages such as TASSEL, VCFtools, or SNPtools (see
Table 1).
46. Very low frequency polymorphisms have a higher probability of
showing false associations with quantitative variables due to the
small sample size of accessions with the rare allele. To reduce
the number of such false positives, a minimum number of five
accessions should carry the minor allele for each polymorphism. Depending on the total number of accessions selected
for your gene, the filtering of polymorphisms can be done at
different minor allele frequencies. Polymorphisms with a minor
allele frequency lower than 5% should be removed when analyzing less than 100 accessions, but this frequency could be
Analyses of Natural Variation
107
such as bottlenecks [71].
40. Phylogenetic networks can be reconstructed using software
packages such as Network or POP ART (see Table 1).
41. Orthologue gene sequences can be obtained for A. lyrata and
other related Brassicaceae species from specific genome databases or from Phytozome webpage (see Table 1). Integrating
A. lyrata sequences in your analyses requires previous alignment with the available A. thaliana sequences, which can be
done with Clustal Omega (see Note 31).
42. Depending on the number of haplotypes and their nucleotide
differentiation, phylogenetic networks can be rather complex
and difficult to interpret. Network complexity can be reduced
by removing very low frequency haplotypes, or discarding
some recombinant haplotypes that can be previously inferred
by recombination analysis using DnaSP. In addition, for genes
with a large number of missense mutations, networks and trees
can be reconstructed from data files including only
non-synonymous polymorphisms or protein sequences, which
can be generated with DnaSP (see Table 1).
43. The geographic information (latitude, longitude, and altitude)
of Arabidopsis accessions can be obtained from the 1001 genomes or CLIMtools databases. Climatic information can be
downloaded from the CLIMtools database or from the World
climate web site using the R package raster. Soil and landscape
data can be extracted from the corresponding public databases
(see Table 1; [72]).
44. The geographic distribution of SNPs can be visualized using
basic graphical options of spreadsheets, software packages like
SAM (see Table 1), or with the R package maps. Information
on climatic variables can be visualized using the R package
raster, including the distribution of accessions according to
SNP alleles.
45. Nucleotide alignments or vcf files can be filtered with software
packages such as TASSEL, VCFtools, or SNPtools (see
Table 1).
46. Very low frequency polymorphisms have a higher probability of
showing false associations with quantitative variables due to the
small sample size of accessions with the rare allele. To reduce
the number of such false positives, a minimum number of five
accessions should carry the minor allele for each polymorphism. Depending on the total number of accessions selected
for your gene, the filtering of polymorphisms can be done at
different minor allele frequencies. Polymorphisms with a minor
allele frequency lower than 5% should be removed when analyzing less than 100 accessions, but this frequency could be
Analyses of Natural Variation
107