A Comparison of Phylogenetic Network Methods Using Computer Simulation

Woolley, Steven M.; Posada, David; Crandall, Keith A.

doi:10.1371/journal.pone.0001913

Cited by 107 publications

(99 citation statements)

References 40 publications

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“…A phylogenetic network was constructed using the software Network version 4.5.1.0 (http://www.fluxus-engineering.com) with a medianjoining algorithm based on maximum parsimony and a 'greedy' method (Bandelt et al, 1999). Under the circumstances of closely related sequences, there are advantages in using a median-joining network to depict relationships (Posada and Crandall, 2001) and simulation studies have demonstrated that this method provides reliable estimates of the true genealogy (Cassens et al, 2005;Woolley et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

Colonization of Ireland: revisiting ‘the pygmy shrew syndrome’ using mitochondrial, Y chromosomal and microsatellite markers

et al. 2011

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There is great uncertainty about how Ireland attained its current fauna and flora. Long-distance human-mediated colonization from southwestern Europe has been seen as a possible way that Ireland obtained many of its species; however, Britain has (surprisingly) been neglected as a source area for Ireland. The pygmy shrew has long been considered an illustrative model species, such that the uncertainty of the Irish colonization process has been dubbed 'the pygmy shrew syndrome'. Here, we used new genetic data consisting of 218 cytochrome (cyt) b sequences, 153 control region sequences, 17 Y-intron sequences and 335 microsatellite multilocus genotypes to distinguish between four possible hypotheses for the colonization of the British Isles, formulated in the context of previously published data. Cyt b sequences from western Europe were basal to those found in Ireland, but also to those found in the periphery of Britain and several offshore islands. Although the central cyt b haplotype in Ireland was found in northern Spain, we argue that it most likely occurred in Britain also, from where the pygmy shrew colonized Ireland as a human introduction during the Holocene. Y-intron and microsatellite data are consistent with this hypothesis, and the biological traits and distributional data of pygmy shrews argue against long-distance colonization from Spain. The compact starburst of the Irish cyt b expansion and the low genetic diversity across all markers strongly suggests a recent colonization. This detailed molecular study of the pygmy shrew provides a new perspective on an old colonization question.

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Section: Discussionmentioning

confidence: 99%

Colonization of Ireland: revisiting ‘the pygmy shrew syndrome’ using mitochondrial, Y chromosomal and microsatellite markers

et al. 2011

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“…A potential avenue could be the use of explicit phylogenetic networks (Huson and Bryant 2006), where one could do the ASR integrating over the different trees embedded in the network, as in Bayesian phylogenetics (Huelsenbeck and Bollback 2001). However, this might be quite challenging given the impact of recombination on the accuracy of phylogenetic networks (Woolley et al 2008) and potential problems identifying the GMRCA (Castelloe and Templeton 1994). An alternative could be the reconstruction of rooted ancestral recombination graphs (Song and Hein 2005;Minichiello and Durbin 2006;Parida et al 2008).…”

Section: Discussionmentioning

confidence: 99%

The Effect of Recombination on the Reconstruction of Ancestral Sequences

Arenas

Posada

2010

Genetics

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While a variety of methods exist to reconstruct ancestral sequences, all of them assume that a single phylogeny underlies all the positions in the alignment and therefore that recombination has not taken place. Using computer simulations we show that recombination can severely bias ancestral sequence reconstruction (ASR), and quantify this effect. If recombination is ignored, the ancestral sequences recovered can be quite distinct from the grand most recent common ancestor (GMRCA) of the sample and better resemble the concatenate of partial most recent common ancestors (MRCAs) at each recombination fragment. When independent phylogenetic trees are assumed for the different recombinant segments, the estimation of the fragment MRCAs improves significantly. Importantly, we show that recombination can change the biological predictions derived from ASRs carried out with real data. Given that recombination is widespread on nuclear genes and in particular in RNA viruses and some bacteria, the reconstruction of ancestral sequences in these cases should consider the potential impact of recombination and ideally be carried out using approaches that accommodate recombination.

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“…The search for the 'perfect' phylogenetic tree construction algorithm, based on distance matrices, is still ongoing (Woolley et al, 2008). In the fu- for both methods and all 698 species pairs (i, j).…”

Section: Discussionmentioning

confidence: 99%

PROTEIN DOMAIN PHYLOGENIES - Information Theory and Evolutionary Dynamics

Hamacher¹

2010

Proceedings of the First International Conference on Bioinformatics

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Abstract:The ever-increasing wealth of whole-genome information prompts for phylogenies based on entire genomes. The quest for a good distance measure, however, poses a big challenge; e.g. because of large-scale evolutionary events such as genomic rearrangements or inversions. We introduce here an information theory driven measure that for the encoded protein domain composition of genomes as protein domains are key evolutionary entities. Thus the new method focuses on selective advantageous events. As evolving different protein domain compositions is more complex than single point mutations, the method makes longer evolutionary times accessible. Illustrating the new methodology we extract several phylogenetic trees for some 700 genomes, e.g. the separation of the three kingdoms of life, trees for mammals and bacillales, and a speculative result for plants (monocotyledons and dicotyledons). The method itself is shown to be robust against incomplete genome sampling. It has a consistent interpretation in both, information space at the sequence/information level and at the level of stochastic, evolutionary dynamics. In contrast to established protocols it becomes more accurate as more organisms are taken into account. Finally we show the equivalence to a (simplified) model of evolutionary dynamics of proteomes.

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A Comparison of Phylogenetic Network Methods Using Computer Simulation

Cited by 107 publications

References 40 publications

Colonization of Ireland: revisiting ‘the pygmy shrew syndrome’ using mitochondrial, Y chromosomal and microsatellite markers

Colonization of Ireland: revisiting ‘the pygmy shrew syndrome’ using mitochondrial, Y chromosomal and microsatellite markers

The Effect of Recombination on the Reconstruction of Ancestral Sequences

PROTEIN DOMAIN PHYLOGENIES - Information Theory and Evolutionary Dynamics

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