Journal Article


Jeroni Galmés
Domingo Sancho-Knapik
Jairo Rocha
José Javier Peguero-Pina
Arántzazu Molins
Arnau Mir
Maxim V Kapralov
Eustaquio Gil-Pelegrín
Ángel Fernández
Mario A Fares
and 1 others


Agriculture & Food Science

environmental conditions enzyme decision model amino acid trees ecological maximum likelihood decision tree

Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations. (2017)

Abstract 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.
Collections Ireland -> Trinity College Dublin -> PubMed

Full list of authors on original publication

Jeroni Galmés, Domingo Sancho-Knapik, Jairo Rocha, José Javier Peguero-Pina, Arántzazu Molins, Arnau Mir, Maxim V Kapralov, Eustaquio Gil-Pelegrín, Ángel Fernández, Mario A Fares and 1 others

Experts in our system

Mario Ali Fares
Trinity College Dublin
Total Publications: 43