Besides, careful phylogenies of gene families with multiple representatives in many species can yield interesting results concerning the molecular evolution of genes, in particular with regard to gene duplication events.
Apart from these differences, our tree showed very similar relationships in comparison with previous publications utilizing mitogenomes (fig. 3) and the two samples of the two species with multiple representatives in the phylogeny (Hector's dolphin: C. hectori; bottlenose dolphin: T. truncatus) grouped together with high confidence.
The expression of SoxB orthologues has also been linked to early neurogenesis in Nematostella, with multiple representatives of the SoxB family being expressed either in broad patterns or localised to single cells, in the ectoderm and endoderm prior to the overt differentiation of neurons in these layers (Magie et al., 2005).
Success in securing multiple representatives for each genus varied because the material could not be obtained for few taxa characterized by cryptic life habit and presumed low species diversity.
We included multiple representatives from well supported amoebal lineages in our analysis to (a) look for congruence between our results and other amoebozoan phylogenies and (b) test whether any or all organisms described as protosteloid amoebae fell into a clade of amoebozoans that also included the myxogastrids and dictyostelids, i.e. Eumycetozoa sensu Olive [1].
To determine whether WSP sequences were significantly associated with host genera, we sub-sampled the initial dataset to comprise only one host species per wsp allele, that is, the dataset included multiple representatives of the same species only in case they carried distinct wsp alleles.
In addition to GCN5, filamentous fungi possess multiple representatives of distinct HAT families (Borkovich et al., 2004).
In total 18 mitogenome sequences were generated for this study, including multiple representatives per species.
However, before assessing the possibility of multiple representatives, the reasons for non-identification of any of the family member by its representative profile, were analysed in detail.
In the example given here, some GST families are represented by multiple representative nodes, whereas other representative nodes contain multiple SwissProt families (HSP26, Phi and Tau), obscuring how sequence similarity tracks with annotation.
Based on the computational results, the distribution characteristics of vorticity and velocity in multiple representative special structures are analysed, such as the channel formed by two pellets, similar triangle area formed by compact spherical walls and channel.
