4. Prune taxon 6, which does not participate in any quartet, and all duplicate taxa at the pendant nodes.
Our final matrix with duplicate taxa removed consisted of 13,533 tips and 1401 nucleotide sites with 4.6238% of the matrix consisting of gaps.
On the trees in our data set, the combined taxon loss between the MRF computation and the postprocessing was much lower than it would have been had we simply removed all duplicate taxa from the original trees.
Duplicate sites were merged with the MergeDuplicateSNPsPlugin (options: -callHets, -misMat 0.05), and duplicated taxa were merged with the MergeIdenticalTaxaPlugin (options: -hetFreq 0.8).
In order to reduce the redundancy of the database and improve the data quality and integrity, we adopted relational database normalization to parse the raw data table into a second normal form schema. Through the normalization process, potential errors such as duplicate entries, misplaced taxa, etc., could be eliminated efficiently.
If so, these data also suggest that the categories of genes which remain duplicated in different taxa following large scale genome duplication events could be subject to comparable selective pressures in each taxa reflecting a similarity in environmental forces applied to each species.
Analyses of whole-genome sequence data from newly published genomes since the late 1990s has confirmed the ubiquitous presence of gene duplicates in diverse taxa (reviewed in [ 1]).
The importance of concerted evolution has been demonstrated through whole genome comparisons of gene duplicates, across diverse taxa [ 36- 39], but in most detail for yeast [ 31, 40, 41].
The few examples of non-cluster genes grouping within the cluster clades (e.g. peptide synthetase (P) from T. reesei; cytochrome P450 monooxygenase (C) from A. flavus and N. fischeri) may indicate relics of former clusters or cluster duplicates in these taxa that have since disassembled.
We found evidence of gene duplication in four taxa, but phylogenetic analysis suggested that duplicate genes have generally not persisted through multiple speciation events.
Some of these genes may also be duplicated in several specific taxa and thus, have the potential of being phylogenetically discrepant [13], [14], [15], [16], [17], [18].
