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We present lower and upper bounds on the minimum number of reticulation events in the minimum reticulate network (and infer an approximately parsimonious reticulate network).
More importantly, the lower and upper bounds match for many datasets (especially when the number of trees is small or reticulation level is low), and this allows us to solve the minimum reticulate network problem exactly for these datasets.
Such a network is called the minimum reticulate network.
The general minimum reticulate network (GMRN) problem: Given a set of phylogenetic trees T={ T1,…, T K }, reconstruct the minimum reticulate network 𝒩min for T1, T2,…, T K.
Results: We present novel results on the minimum reticulate network problem.
The central computational problem on reticulate networks, the minimum reticulate network problem, is: given a set of gene trees, reconstruct the minimum reticulate network that displays these gene trees.
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Even in the case where additional simplifications are reasonable, one may still want to compare with the unconstrained minimum reticulate networks.
There are several existing approaches for reconstructing the exact minimum reticulate networks when there are only two gene trees (Bordewich et al., 2007; Linz and Semple, 2009; Wu, 2009; Wu and Wang, 2010).
In fact, for many simulated datasets of this type, the lower and upper bounds often match, which means our methods can reconstruct the exact minimum reticulate networks for these datasets.
By exhaustively searching through the set of all 885 refinements of these 6 trees, we find that only 9 of them give rise to a reticulate network with the minimum number of 4 hypothesized allopolyploidization events.
Now we investigate whether there exists a reticulate network with d1+ e reticulation nodes for these three trees.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com