Consistency of the Neighbor-Net Algorithm

Bryant, David; Moulton, Vincent; Spillner, Andreas

doi:10.1186/1748-7188-2-8

Cited by 36 publications

(39 citation statements)

References 18 publications

(18 reference statements)

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“…The split (NeighborNet) network [24]–[26] from the masked alignment obviously showed less conflict than the split network from the unmasked alignment, especially within subfamilies of formicoids. Nevertheless, conflicting signal is obvious, e.g.…”

Section: Resultsmentioning

confidence: 93%

Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life

et al. 2011

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Martialinae are pale, eyeless and probably hypogaeic predatory ants. Morphological character sets suggest a close relationship to the ant subfamily Leptanillinae. Recent analyses based on molecular sequence data suggest that Martialinae are the sister group to all extant ants. However, by comparing molecular studies and different reconstruction methods, the position of Martialinae remains ambiguous. While this sister group relationship was well supported by Bayesian partitioned analyses, Maximum Likelihood approaches could not unequivocally resolve the position of Martialinae. By re-analysing a previous published molecular data set, we show that the Maximum Likelihood approach is highly appropriate to resolve deep ant relationships, especially between Leptanillinae, Martialinae and the remaining ant subfamilies. Based on improved alignments, alignment masking, and tree reconstructions with a sufficient number of bootstrap replicates, our results strongly reject a placement of Martialinae at the first split within the ant tree of life. Instead, we suggest that Leptanillinae are a sister group to all other extant ant subfamilies, whereas Martialinae branch off as a second lineage. This assumption is backed by approximately unbiased (AU) tests, additional Bayesian analyses and split networks. Our results demonstrate clear effects of improved alignment approaches, alignment masking and data partitioning. We hope that our study illustrates the importance of thorough, comprehensible phylogenetic analyses using the example of ant relationships.

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Section: Resultsmentioning

confidence: 93%

Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life

et al. 2011

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“…In the present study the effect of recombination cannot be properly assessed because of the limited sampling. However, we cannot rule out the possibility of recombination, which can lead to evolutionary histories that are non-tree-like with reticulate patterns (Bryant & al., 2007), such as those found in the NN analysis ( Figs. 3 & 4).…”

Section: Discussionmentioning

confidence: 99%

Revisiting monophyly in Haworthia Duval (Asphodelaceae): Incongruence, hybridization and contemporary speciation

Ramdhani

Barker

Cowling

2011

TAXON

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Molecular phylogenetic reconstructions have indicated that Haworthia is not monophyletic. Here we show, using considerably expanded datasets of both chloroplast (trnL-trnF and psbA-trnH intergenic spacers) and nuclear (ITS1) markers that the issue of a polyphyletic Haworthia is more complicated than previously reported. Both parsimony and bayesian analyses of cpDNA and ITS1 produced poorly resolved phylogenies, with little or no support for deeper nodes. Species of Haworthia are placed in three of the four main lineages in the cpDNA phylogeny, while in the ITS1 phylogeny Haworthia species were placed in two of the four main lineages retrieved. The cpDNA phylogeny was incongruent with that obtained from the ITS1 data, and the topology of the combined dataset reflected that obtained from the ITS1 dataset. As species of H. subg. Hexangulares and subg. Robustipedunculares have been reportedly involved in intergeneric hybridizations with other Alooideae, it is postulated that a history of ancient hybridization may account for a polyphyletic Haworthia. Hybridization is also ongoing between species within H. subg. Haworthia, and may be responsible for results indicating that some species in this subgenus are not monophyletic. This hybridization may be facilitated by the lack of effective reproductive barriers. We hypothesize that Haworthia is undergoing a contemporary and explosive radiation in southern Africa, driven in part by local adaptation to relatively fine-grained ecological heterogeneity of soils and microclimate. OutgroupAloe plicatilis Haworthia II True Aloes Tree-like Aloes Haworthia I Haworthia subg. Haworthia (n = 13) Outgroup Haworthia II Tree-like Aloes Aloe plicatilis Haworthia I True AloesHaworthia subg. Haworthia (n = 4) Aloe ciliaris Aloe aristata Gasteria Haworthia subg. Hexangulares (n = 10) Haworthia subg. Haworthia (n = 2) Gasteria (n = 3) Aloe aristata (n = 2) Astrolaba spiralis (n = 2) Haworthia subg. Hexangulares (n = 18)

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“…Then the agglomerated nodes are expanded to produce the planar splits graph that represents the desired phylogenetic network. The aggregation procedure of the Nnet algorithm implicitly defines a circular split system, which can be shown to be consistent in the sense that for any distance matrix that is a linear combination of split metrics deriving from a circular split system, Nnet recovers the original circular split system, see [19] for the mathematical details. It has been observed that phylogenetic distance data are often circular or at most mildly non-circular, see e.g.…”

Section: Methodsmentioning

confidence: 99%