Open AccessPositively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations
Author(s) -
Carmen Hermida-Carrera,
Mario A. Fares,
Agustina Fernández Fernández,
Eustaquio GilPelegrín,
Maxim V. Kapralov,
Arnau Mir,
Arántzazu Molins,
José Javier PegueroPina,
Jairo Rocha,
Domingo SanchoKnapik,
Jeroni Galmés
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0183970
Subject(s) - rubisco , biology , phylogenetic tree , photosynthesis , botany , phylogenetics , amino acid , adaptation (eye) , evolutionary biology , gene , biochemistry , neuroscience
Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks ( Quercus ). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML.