First, average levels of sequence identity could be reduced by preferentially adding sequences from the lower end of the sequence identity distribution.
A second sequence alignment was created by adding 12 sequences from GenBank with known dates of collection to the original Nigerian sequences.
We tested this hypothesis through outgroup analysis by adding 72 sequences from 23 other poeciliid lineages retrieved from GenBank into our phylogenetic alignments [ Belonesox belizanus; Gambusia affinis; Limia dominicensis, L. melanogaster, L. tridens, and L. vittata; Pamphorichthys hollandi; Pseudoxiphophorus (15 lineages); and Xiphophorus helleri; Additional file 1: Table S1].
In this study, we reanalyzed the above-mentioned genome quartets by adding homologous sequences from sixty reference genomes to each QuartOP creating what we call "extended datasets".
Here we simulated this situation by adding orthologs to a set of coregulated reference genes, but assuming that all added sequences derived from one species did not contain the motif site.
We increased the gene sample of Wiegmann et al. [29] from six to nine and nearly doubled the number of nucleotide positions by adding DNA sequence data from EF-1α, 18S and 28S.
While our current hypothesis still reveals a few branches lacking in robustness – a problem that will most likely be solved by adding more sequence data from currently under-represented species – our analysis nonetheless puts forward several well corroborated hypotheses concerning seed plant phylogeny, namely: Gymnosperms are a monophyletic group, sister to the angiosperms.
Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely related blue catfish.
It is likely that the coalescence time of the P node will be soon further reassessed, not only by adding complete mtDNA sequences from additional ancient aurochs remains, but also from additional modern samples, at least four reported, whose mtDNA sequence data clearly indicate an affiliation within P [28] [30].
The TCM barcode database will become permanent data that can be improved by adding new research sequences from taxonomists.
