As a preliminary approach to understand vkr gene evolution, we have analysed the conservation of intron positions throughout the diverse animal groups.
To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS.
To gain a better understanding about G-protein evolution in Pinaceae we analysed sequence divergence within the following phylogenetic clusters: i) Fabaceae Brassicaceae, ii) Fabaceae, iii) Brassicaceae, iv) Pinaceae, v) Picea and vi) Pinus, if the cluster contained more than three different species.
Since standard statistical methods are not designed to capture system features and evolution, we used principal component analyses on two types of pre-processed data: contrasts and group averages.
To gain insight into the Ugt evolution, we performed comprehensive comparative analyses of the Ugt repertoire in teleosts and lower tetrapods.
Because such results could potentially be sensitive to the ortholog pairs compared, the quality of the gene models, and peculiarities of human/mouse evolution, we also repeated such analyses using a variety of other mammals [see Additional file 10].
To assess which forces governed its evolution, we carried out selection analyses of all 43 sequences containing an intact Zn ribbon DNA-binding domain, using the GAbranch method (Kosakovsky Pond and Frost 2005) and the tree presented in figure 3 as a reference.
Because an accurate phylogenetic framework is essential to track the suite of cpDNA changes that took place during prasinophyte evolution, we will present our phylogenomic analyses of concatenated cpDNA-encoded proteins before elaborating further on the structural features of the newly sequenced prasinophyte genomes.
To further investigate the evolution of distinct lineages, we analysed the nucleotide changes that induced gene disruption and genome size reduction.
To get better insight into the evolution of this protein, we analysed the genetic variability of its surface exposed region in 27 M. hominis isolates recovered from the genital tract of Tunisian patients with infertility disorders.
