Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 100; no. 23; pp. 13407 - 13412
• Main Authors: Martinez-Castilla, L.P, Alvarez-Buylla, E.R
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 11.11.2003; National Acad Sciences
• Subjects: Adaptation; Amino acids; Arabidopsis - genetics; Arabidopsis thaliana; Bayes Theorem; Biological Sciences; Chromosomes; Divergent evolution; DNA, Complementary - metabolism; duplicate genes; Evolution; Evolution, Molecular; Gene duplication; Genes; Genomes; Genomics; MADS Domain Proteins - chemistry; MADS Domain Proteins - genetics; Multigene Family; natural selection; nucleotide sequences; Phenotype; Phylogeny; Plants; Positive selection; Protein Structure, Tertiary; Proteins; regulator genes; sequence alignment; transcription factors; Transcription, Genetic; Trees
• DOI: 10.1073/pnas.1835864100
• ISSN: 0027-8424

Gene duplication is a substrate of evolution. However, the relative importance of positive selection versus relaxation of constraints in the functional divergence of gene copies is still under debate. Plant MADS-box genes encode transcriptional regulators key in various aspects of development and have undergone extensive duplications to form a large family. We recovered 104 MADS sequences from the Arabidopsis genome. Bayesian phylogenetic trees recover type II lineage as a monophyletic group and resolve a branching sequence of monophyletic groups within this lineage. The type I lineage is comprised of several divergent groups. However, contrasting gene structure and patterns of chromosomal distribution between type I and II sequences suggest that they had different evolutionary histories and support the placement of the root of the gene family between these two groups. Site-specific and site-branch analyses of positive Darwinian selection (PDS) suggest that different selection regimes could have affected the evolution of these lineages. We found evidence for PDS along the branch leading to flowering time genes that have a direct impact on plant fitness. Sites with high probabilities of having been under PDS were found in the MADS and K domains, suggesting that these played important roles in the acquisition of novel functions during MADS-box diversification. Detected sites are targets for further experimental analyses. We argue that adaptive changes in MADS-domain protein sequences have been important for their functional divergence, suggesting that changes within coding regions of transcriptional regulators have influenced phenotypic evolution of plants.