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41. Gomez R, Mendez-Vigo B, Marcer A et al
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42. Kawakatsu T, Huang SC, Jupe F et al (2016)
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Nucleic Acids Res 46:D1150–D1156
44. Seren U, Vilhjalmsson BJ, Horton MW et al
(2012) GWAPP: a web application for
genome-wide association mapping in Arabidopsis. Plant Cell 24:4793–4805
45. Grimm DG, Roqueiro D, Salome PA et al
(2017) easyGWAS: a cloud-based platform for
comparing the results of genome-wide association studies. Plant Cell 29:5–19
46. Seren U, Grimm D, Fitz J, Weigel D,
Nordborg M, Borgwardt K, Korte A (2017)
AraPheno: a public database for Arabidopsis
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complex traits in diverse samples. Bioinformatics 23:2633–2635
48. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC
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49. Kumar S, Stecher G, Li M et al (2018) MEGA
X: molecular evolutionary genetics analysis
across computing platforms. Mol Biol Evol
35:1547–1549
50. Leigh J, Bryant D (2015) PopART: full-feature
software for haplotype network construction.
Methods Ecol Evol 6:1110–1116
51. Goodstein DM, Shu S, Howson R et al (2012)
Phytozome: a comparative platform for green
plant genomics. Nucleic Acids Res 40:
D1178–D1186
52. Madeira F, Park YM, Lee J et al (2019) The
EMBL-EBI search and sequence analysis tools
APIs in 2019. Nucleic Acids Res 47:
W636–W641.
https://doi.org/10.1093/
nar/gkz268
53. Nicholas KB, Nicholas HBJ, Deerfield DW
(1997) GeneDoc: analysis and visualization of
genetic variation. EMBNETWNEWS 4:1–4
54. Wang Y, Lu J, Yu J et al (2013) An integrative
variant analysis pipeline for accurate genotype/
haplotype inference in population NGS data.
Genome Res 23:833–842
55. Danecek P, Auton A, Abecasis G et al (2011)
The variant call format and VCFtools. Bioinformatics 27:2156–2158
56. Ferrero-Serrano A, Assmann SM (2019) Phenotypic and genome-wide association with the
local environment of Arabidopsis. Nat Ecol
Evol 3:274–285
57. Frichot E, Schoville SD, Bouchard G et al
(2013) Testing for associations between loci
and environmental gradients using latent factor
mixed models. Mol Biol Evol 30:1687–1699
58. Gunther T, Coop G (2013) Robust identification of local adaptation from allele frequencies.
Genetics 195:205–220
59. Rangel TF, Diniz-Filho JAF, Bini LM (2010)
SAM: a comprehensive application for spatial
analysis in macroecology. Ecography 33:46–50
60. Nordborg M, Hu TT, Ishino Y et al (2005)
The pattern of polymorphism in Arabidopsis
thaliana. PLoS Biol 3:e196
61. Clewer AG, Scarisbrick DH (2008) Practical
statistics and experimental design for plant
and crop science. John Wiley & Sons Ltd,
West Sussex
62. Pico ´ FX (2012) Demographic fate of Arabidopsis thaliana cohorts of autumn- and
spring-germinated plants along an altitudinal
gradient. J Ecol 100:1009–1018
63. Duncan S, Holm S, Questa J et al (2015) Seasonal shift in timing of vernalization as an adaptation to extreme winter. elife 4:e06620
64. Donohue K (2009) Completing the cycle:
maternal effects as the missing link in plant
Analyses of Natural Variation
111
(2014) Lagging adaptation to warming climate
in Arabidopsis thaliana. Proc Natl Acad Sci U S
A 111:7906–7913
37. Hu J, Lei L, de Meaux J (2017) Temporal
fitness fluctuations in experimental Arabidopsis
thaliana populations. PLoS One 12:e0178990
38. Taylor MA, Cooper MD, Sellamuthu R et al
(2017) Interacting effects of genetic variation
for seed dormancy and flowering time on phenology, life history, and fitness of experimental
Arabidopsis thaliana populations over multiple
generations in the field. New Phytol
216:291–302
39. Exposito-Alonso M, Brennan AC, AlonsoBlanco C et al (2018) Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana. Evolution
72:157–1586
40. Frachon L, Libourel C, Villoutreix R et al
(2017) Intermediate degrees of synergistic
pleiotropy drive adaptive evolution in ecological time. Nat Ecol Evol 1:1551–1561
41. Gomez R, Mendez-Vigo B, Marcer A et al
(2018) Quantifying temporal change in plant
population attributes: insights from a resurrection approach. AoB Plants 10:ply063
42. Kawakatsu T, Huang SC, Jupe F et al (2016)
Epigenomic diversity in a global collection of
Arabidopsis
thaliana
accessions.
Cell
166:492–505
43. Togninalli M, Seren U, Meng D et al (2017)
The AraGWAS catalog: a curated and standardized Arabidopsis thaliana GWAS catalog.
Nucleic Acids Res 46:D1150–D1156
44. Seren U, Vilhjalmsson BJ, Horton MW et al
(2012) GWAPP: a web application for
genome-wide association mapping in Arabidopsis. Plant Cell 24:4793–4805
45. Grimm DG, Roqueiro D, Salome PA et al
(2017) easyGWAS: a cloud-based platform for
comparing the results of genome-wide association studies. Plant Cell 29:5–19
46. Seren U, Grimm D, Fitz J, Weigel D,
Nordborg M, Borgwardt K, Korte A (2017)
AraPheno: a public database for Arabidopsis
thaliana phenotypes. Nucleic Acids Res 45:
D1054–D1059
47. Bradbury PJ, Zhang Z, Kroon DE et al (2007)
TASSEL: software for association mapping of
complex traits in diverse samples. Bioinformatics 23:2633–2635
48. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC
et al (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol
34:3299–3302
49. Kumar S, Stecher G, Li M et al (2018) MEGA
X: molecular evolutionary genetics analysis
across computing platforms. Mol Biol Evol
35:1547–1549
50. Leigh J, Bryant D (2015) PopART: full-feature
software for haplotype network construction.
Methods Ecol Evol 6:1110–1116
51. Goodstein DM, Shu S, Howson R et al (2012)
Phytozome: a comparative platform for green
plant genomics. Nucleic Acids Res 40:
D1178–D1186
52. Madeira F, Park YM, Lee J et al (2019) The
EMBL-EBI search and sequence analysis tools
APIs in 2019. Nucleic Acids Res 47:
W636–W641.
https://doi.org/10.1093/
nar/gkz268
53. Nicholas KB, Nicholas HBJ, Deerfield DW
(1997) GeneDoc: analysis and visualization of
genetic variation. EMBNETWNEWS 4:1–4
54. Wang Y, Lu J, Yu J et al (2013) An integrative
variant analysis pipeline for accurate genotype/
haplotype inference in population NGS data.
Genome Res 23:833–842
55. Danecek P, Auton A, Abecasis G et al (2011)
The variant call format and VCFtools. Bioinformatics 27:2156–2158
56. Ferrero-Serrano A, Assmann SM (2019) Phenotypic and genome-wide association with the
local environment of Arabidopsis. Nat Ecol
Evol 3:274–285
57. Frichot E, Schoville SD, Bouchard G et al
(2013) Testing for associations between loci
and environmental gradients using latent factor
mixed models. Mol Biol Evol 30:1687–1699
58. Gunther T, Coop G (2013) Robust identification of local adaptation from allele frequencies.
Genetics 195:205–220
59. Rangel TF, Diniz-Filho JAF, Bini LM (2010)
SAM: a comprehensive application for spatial
analysis in macroecology. Ecography 33:46–50
60. Nordborg M, Hu TT, Ishino Y et al (2005)
The pattern of polymorphism in Arabidopsis
thaliana. PLoS Biol 3:e196
61. Clewer AG, Scarisbrick DH (2008) Practical
statistics and experimental design for plant
and crop science. John Wiley & Sons Ltd,
West Sussex
62. Pico ´ FX (2012) Demographic fate of Arabidopsis thaliana cohorts of autumn- and
spring-germinated plants along an altitudinal
gradient. J Ecol 100:1009–1018
63. Duncan S, Holm S, Questa J et al (2015) Seasonal shift in timing of vernalization as an adaptation to extreme winter. elife 4:e06620
64. Donohue K (2009) Completing the cycle:
maternal effects as the missing link in plant
Analyses of Natural Variation
111