The variable branching concerned terminal branches which did not affect the main observations of this tree.
Microarray analysis showed that among the genes (adhE1, ctfA, ctfB, adhE2, adc, bdhA and bdhB) concerned with branch pathways of solvents formation, only sol operon genes showed differential expression after ccpA inactivation.
The phylogenetic relationships are unresolved concerning the branching pattern among Thaliacea and Phlebobranchia, but suggest a paraphyly of the Phlebobranchia with respect to Thaliacea, with Doliolum appearing as the sister taxon of Rhodosoma (Corellidae).
In contrast, all phylogenies of charophycean green algae previously inferred from a smaller number of genes failed to provide any conclusive results concerning the branching order of the charophycean green algae and their relationships with land plants [ 15, 16].
We were particularly interested to obtain further information concerning the branching pattern among papionin genera and among all seven species groups of the genus Macaca and to provide comprehensive data for further comparative molecular studies.
In the context of the debate concerning the branching order of the UTC lineages, the predicted architecture of the chloroplast genome of the earliest members of the Ulvophyceae strengthens the notion that this lineage is sister to the Chlorophyceae [ 5, 6].
Levels of incongruence were generally low, the three exceptions being the internodes concerned with the branching of Anopheles christyi, with the branching of the subgenus Anopheles as well as the already reported incongruence within the Anopheles gambiae species complex.
However, the GSF and IC values of the internodes concerned with the branching of the subgenus Anopheles, the branching of A. christyi, as well as with branchings within the A. gambiae species complex, were still lower even for the strictest filters.
Even though the GSF and IC values of the internodes concerned with the branching of the subgenus Anopheles, with the branchings within the A. gambiae species complex, and with the branching of A. christyi, increased as the stringency of the BS and TC filters increased, the values themselves were still lower even for the strictest filters (supplementary table S2, Supplementary Material online).
The second important difference concerns the branch length: form A cystatins exhibit higher overall branch lengths than form B, suggesting different rates of evolution for these two cystatin forms.
