If the paralogous pairs in A. oryzae were in fact the products of recent (species-specific) gene duplications, but one gene copy subsequently underwent rapid sequence divergence, the ensuing asymmetry of evolutionary rates could cause phylogenetic methods to infer an incorrect tree due to the phenomenon of long-branch attraction between the accelerated branch and the outgroup [8], [9].
We demonstrate, using a root mean squared deviation statistic, how the removal of the fastest evolving sites aids in the minimisation of the effect of long branch attraction and the generation of a highly supported phylogeny.
Asymmetric or ladder-shape trees were excluded because such tree topologies are often a signal of long branch attraction or lack of phylogenic information [ 29].
Thus, the sequences of C i. intestinalis used in this report are indeed encoded in its genome, and most likely cluster with those of arthropods as a consequence of the phenomenon of long branch attraction (reviewed in Bergsten 2005).
We compared these two sets of genes, with respect to rates of evolution and amino-acid composition, to see whether one signal is the result of a long branch attraction or of a compositional bias.
Believing that the apparent lack of resolution is the result of long branch attraction coupled with large evolutionary distances, we removed all Sec23 sequences from the analysis (fig. 3 B).
Not only do the very high A + T content sequences represent very long branches, raising the possibility of long-branch attraction, but also the presence of very high A + T content in protein coding genes necessitates an emphasis on A + T rich codons.
We also conclude that NORs are indeed closely related with C Type enzymes than with the other types of HCOs and exclude the possibility of Long Branch attraction.
Firstly, the addition of more taxa to the dataset: denser sampling of species can reduce the effect of long branch attraction (LBA) by reducing the overall distances between taxa.
For example, biologists may be concerned by the taxonomic range of sequences, reduction of long-branch attraction effect, presence of paralogues, orthologues, pseudo-genes and/or multi-domain proteins, etc.
