Exact(5)
Because the plants have already diversified, the order of colonization by the insects should be independent of the order of speciation in the plants.
The similarity of chickpea unigenes with other legume species is in general agreement with legume phylogenetic tree displaying relative order of speciation [ 30, 31].
The order of speciation of the yeasts belonging to the CTG complex adopted in this work was based on the order used in previous phylogenetic studies on Hemiascomycetes [ 58- 61].
An important difference of TreeFix-DTL compared with the other methods considered here, is that it does not use information of the time order of speciation events in the species tree (note that AnGST can also run without information on time ordering).
Bayesian phylogenetic trees for the 106 arachnid gene families with a mygalomorph homolog, a scorpion homolog, and a paralog pair with a duplication node assigned to the older duplication peak tended to have low support for determining relative branching order of speciation and duplication nodes.
Similar(55)
Some parsimony methods (e.g. Bansal et al., 2012) do not need information on the order of speciations in time.
Nonetheless, we ran TERA with 10 random time orderings of the species tree and this resulted in statistically identical n-R-F values when using the correct time order of speciations (Wilcoxon rank sum test P = 0.6).
Accurate independent measurements of duplication order can help validate branch lengths and also estimate the relative ordering of speciation events.
In order for speciation to occur, a group of individuals must become reproductively isolated from the remainder of their species (the ancestral species).
In-paralogs and out-paralogs are defined based on the relative order of duplication and speciation events.
Incidentally, although it is interesting to note that the number of chromosomal rearrangements is roughly of the same order as the number of speciation steps on the presumed path between Nakalipithecus and the two modern species, it does not prove in any way that each of those rearrangements was necessarily correlated to a phenomenon of speciation.
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