@article{fdi:010070058,
  title = {{S}ignatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples},
  author = {{F}ustier, {M}. {A}. and {B}randenburg, {J}. {T}. and {B}oitard, {S}. and {L}apeyronnie, {J}. and {E}guiarte, {L}. {E}. and {V}igouroux, {Y}ves and {M}anicacci, {D}. and {T}enaillon, {M}. {I}.},
  editor = {},
  language = {{ENG}},
  abstract = {{S}patially varying selection triggers differential adaptation of local populations. {H}ere, we mined the determinants of local adaptation at the genomewide scale in the two closest maize wild relatives, the teosintes {Z}ea mays ssp parviglumis and ssp. mexicana. {W}e sequenced 120 individuals from six populations: two lowland, two intermediate and two highland populations sampled along two altitudinal gradients. {W}e detected 8479581 single nucleotide polymorphisms ({SNP}s) covered in the six populations with an average sequencing depth per site per population ranging from 17.0x to 32.2x. {P}opulation diversity varied from 0.10 to 0.15, and linkage disequilibrium decayed very rapidly. {W}e combined two differentiation-based methods, and correlation of allele frequencies with environmental variables to detect outlier {SNP}s. {O}utlier {SNP}s displayed significant clustering. {F}rom clusters, we identified 47 candidate regions. {W}e further modified a haplotype-based method to incorporate genotype uncertainties in haplotype calling, and applied it to candidate regions. {W}e retrieved evidence for selection at the haplotype level in 53% of our candidate regions, and in 70% of the cases the same haplotype was selected in the two lowland or the two highland populations. {W}e recovered a candidate region located within a previously characterized inversion on chromosome 1. {W}e found evidence of a soft sweep at a locus involved in leaf macrohair variation. {F}inally, our results revealed frequent colocalization between our candidate regions and loci involved in the variation of traits associated with plant-soil interactions such as root morphology, aluminium and low phosphorus tolerance. {S}oil therefore appears to be a major driver of local adaptation in teosintes.},
  keywords = {environmental variables ; {F}-{ST} scan ; haplotypes ; linkage disequilibrium ; selective sweeps ; soil ; subspecies differentiation ; {MEXIQUE}},
  booktitle = {},
  journal = {{M}olecular {E}cology},
  volume = {26},
  numero = {10},
  pages = {2738--2756},
  ISSN = {0962-1083},
  year = {2017},
  DOI = {10.1111/mec.14082},
  URL = {https://www.documentation.ird.fr/hor/fdi:010070058},
}