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Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

(2020) G3-GENES GENOMES GENETICS. 10(8). p.2683-2696
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Abstract
Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity inPinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. MakingP. sylvestrisan even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.
Keywords
Genetics(clinical), Genetics, Molecular Biology, adaptation, population genetics - empirical, landscape genetics, gymnosperms, Pinus sylvestris, Local adaptation, Targeted DNA Sequencing, Structural Variation, QUANTITATIVE TRAIT LOCI, POPULATION-STRUCTURE, LINKAGE DISEQUILIBRIUM, NUCLEOTIDE DIVERSITY, CLIMATIC ADAPTATION, SCOTS PINE, POPULUS-TRICHOCARPA, MOLECULAR MARKERS, COMPLEX TRAITS, SELECTION

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MLA
Tyrmi, Jaakko S., et al. “Genomics of Clinal Local Adaptation in Pinus Sylvestris under Continuous Environmental and Spatial Genetic Setting.” G3-GENES GENOMES GENETICS, vol. 10, no. 8, 2020, pp. 2683–96, doi:10.1534/g3.120.401285.
APA
Tyrmi, J. S., Vuosku, J., Acosta, J. J., Li, Z., Sterck, L., Cervera, M. T., … Pyhäjärvi, T. (2020). Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting. G3-GENES GENOMES GENETICS, 10(8), 2683–2696. https://doi.org/10.1534/g3.120.401285
Chicago author-date
Tyrmi, Jaakko S., Jaana Vuosku, Juan J. Acosta, Zhen Li, Lieven Sterck, Maria T. Cervera, Outi Savolainen, and Tanja Pyhäjärvi. 2020. “Genomics of Clinal Local Adaptation in Pinus Sylvestris under Continuous Environmental and Spatial Genetic Setting.” G3-GENES GENOMES GENETICS 10 (8): 2683–96. https://doi.org/10.1534/g3.120.401285.
Chicago author-date (all authors)
Tyrmi, Jaakko S., Jaana Vuosku, Juan J. Acosta, Zhen Li, Lieven Sterck, Maria T. Cervera, Outi Savolainen, and Tanja Pyhäjärvi. 2020. “Genomics of Clinal Local Adaptation in Pinus Sylvestris under Continuous Environmental and Spatial Genetic Setting.” G3-GENES GENOMES GENETICS 10 (8): 2683–2696. doi:10.1534/g3.120.401285.
Vancouver
1.
Tyrmi JS, Vuosku J, Acosta JJ, Li Z, Sterck L, Cervera MT, et al. Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting. G3-GENES GENOMES GENETICS. 2020;10(8):2683–96.
IEEE
[1]
J. S. Tyrmi et al., “Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting,” G3-GENES GENOMES GENETICS, vol. 10, no. 8, pp. 2683–2696, 2020.
@article{8688508,
  abstract     = {Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity inPinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. MakingP. sylvestrisan even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.},
  author       = {Tyrmi, Jaakko S. and Vuosku, Jaana and Acosta, Juan J. and Li, Zhen and Sterck, Lieven and Cervera, Maria T. and Savolainen, Outi and Pyhäjärvi, Tanja},
  issn         = {2160-1836},
  journal      = {G3-GENES GENOMES GENETICS},
  keywords     = {Genetics(clinical),Genetics,Molecular Biology,adaptation,population genetics - empirical,landscape genetics,gymnosperms,Pinus sylvestris,Local adaptation,Targeted DNA Sequencing,Structural Variation,QUANTITATIVE TRAIT LOCI,POPULATION-STRUCTURE,LINKAGE DISEQUILIBRIUM,NUCLEOTIDE DIVERSITY,CLIMATIC ADAPTATION,SCOTS PINE,POPULUS-TRICHOCARPA,MOLECULAR MARKERS,COMPLEX TRAITS,SELECTION},
  language     = {eng},
  number       = {8},
  pages        = {2683--2696},
  title        = {Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting},
  url          = {http://dx.doi.org/10.1534/g3.120.401285},
  volume       = {10},
  year         = {2020},
}

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