On the quirks of maximum parsimony and likelihood on phylogenetic networks

Abstract

Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene transfer that are commonplace in many groups of organisms and result in mosaic patterns of relationships cannot be represented by a single phylogenetic tree. This is why phylogenetic networks, which can display such events, are becoming of more and more interest in phylogenetic research. It is therefore necessary to extend concepts like maximum parsimony from phylogenetic trees to networks. Several suggestions for possible extensions can be found in recent literature, for instance the softwired and the hardwired parsimony concepts. In this paper, we analyze the so-called big parsimony problem under these two concepts, i.e. we investigate maximum parsimonious networks and analyze their properties. In particular, we show that finding a softwired maximum parsimony network is possible in polynomial time. We also show that the set of maximum parsimony networks for the hardwired definition always contains at least one phylogenetic tree. Lastly, we investigate some parallels of parsimony to different likelihood concepts on phylogenetic networks.

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The molecular taxonomy of three endemic Central Asian species of Ranunculus(Ranunculaceae)

“…Maximum Likelihood (ML) [39], Maximum Parsimony (MP) [40], and Neighbor-Joining (NJ) [41] methods were used for the phylogenetic analysis of Ranunculus species in MEGA software [42]. Bootstraps with 100, 500, 1000, 5000, and 10,000 replications were used for each method (S2 Appendix).…”

Molecular identification of the powdery mildew fungus infecting rubber trees in China

“…Sequences were edited using DNAman 6.0 software (Lynnon Biosoft), and consensus sequences were deposited in GenBank. Manual adjustments generated with MEGA 7.0 phylogenetic relationships were estimated by maximum parsimony (MP), neighbour-joining (NJ) and maximum likelihood (ML) analysis (Bryant, Fischer, Linz, & Semple, 2017;Saitou & Nei, 1987) for construction of the phylogenetic tree with 1,000 bootstrap replications by the MEGA 7.0 program (Kumar, Stecher, & Tamura, 2016).…”