Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny

Holland, Barbara R.

doi:10.1093/molbev/msh145

Cited by 152 publications

(114 citation statements)

References 11 publications

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“…These facts are internal evidence that the network N is consistent with these data. Moreover, network N bears an intriguing close resemblance to the consensus network found by Holland et al [12], Fig. 1c, for the maximum parsimony trees for the same dataset.…”

Section: Discussionsupporting

confidence: 76%

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Regular Networks Can be Uniquely Constructed from Their Trees

Willson

2011

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Abstract-A rooted acyclic digraph N with labelled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T . Let T r(N ) denote the set of all trees displayed by the network N . In general, there may be many other networks M such that T r(M ) = T r(N ). A network is regular if it is isomorphic with its cover digraph. If N is regular and D is a collection of trees displayed by N , this paper studies some procedures to try to reconstruct N given D. If the input is D = T r(N ), one procedure is described which will reconstruct N . Hence if N and M are regular networks and T r(N ) = T r(M ), it follows that N = M , proving that a regular network is uniquely determined by its displayed trees. If D is a (usually very much smaller) collection of displayed trees that satisfies certain hypotheses, modifications of the procedure will still reconstruct N given D.

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Section: Discussionsupporting

confidence: 76%

“…The collection of 106 maximum-parsimony trees and 106 maximum-likelihood trees included more than 20 different robustly supported topologies. While [20] concatenated the data to try to achieve resolution, [12] employed consensus networks to display the incompatibilities that existed among the trees.…”

Section: Introductionmentioning

confidence: 99%

Regular Networks Can be Uniquely Constructed from Their Trees

Willson

2011

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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“…These methods visualize incompatibilities of sequence patterns or tree topologies as reticulation cycles in a network (14)(15)(16). Only the subfield of evolutionary networks is amenable to reticulate detection.…”

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confidence: 99%

Topology of viral evolution

Chan

Carlsson

Rabadán

2013

Proc. Natl. Acad. Sci. U.S.A.

218

188

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The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees. Drawing from algebraic topology, we present a unique evolutionary framework that comprehensively captures both clonal and reticulate evolution. We show that whereas clonal evolution can be summarized as a tree, reticulate evolution exhibits nontrivial topology of dimension greater than zero. Our method effectively characterizes clonal evolution, reassortment, and recombination in RNA viruses. Beyond detecting reticulate evolution, we succinctly recapitulate the history of complex genetic exchanges involving more than two parental strains, such as the triple reassortment of H7N9 avian influenza and the formation of circulating HIV-1 recombinants. In addition, we identify recurrent, large-scale patterns of reticulate evolution, including frequent PB2-PB1-PA-NP cosegregation during avian influenza reassortment. Finally, we bound the rate of reticulate events (i.e., 20 reassortments per year in avian influenza). Our method provides an evolutionary perspective that not only captures reticulate events precluding phylogeny, but also indicates the evolutionary scales where phylogenetic inference could be accurate. n On the Origin of the Species in 1859, Darwin first proposed the phylogenetic tree as a structure to describe the evolution of phenotypic attributes. Since then, the advancement of modern sequencing has spurred development of a number of phylogenetic inference methods (1, 2). The tree structure effectively models vertical or clonal evolution, mediated by random mutations over multiple generations (Fig. 1A). Phylogenetic trees, however, cannot capture horizontal, or reticulate, events, which occur when distinct clades merge together to form a new hybrid lineage ( Fig. 1B and SI Appendix, Fig. S1). In nature, horizontal evolution can occur through species hybridization in eukaryotes, lateral gene transfer in bacteria, recombination and reassortment in viruses, viral integration in eukaryotes, and fusion of genomes of symbiotic species (e.g., mitochondria). These horizontal genetic exchanges create incompatibilities that mischaracterize the species tree (3). Doolittle (4) argued that molecular phylogeneticists have failed to identify the "true tree of life" because the history of living organisms cannot be understood as a tree. One may wonder what other mathematical structures beyond phylogeny can capture the richness of evolutionary processes.Current techniques that detect reticulate events can be divided into phylogenetic and nonphylogenetic methodologies. Phylogenetic methods detect incongruence in the tree structure of different segments (5-8). Nonphylogenetic methods probe for homoplasies (shared character traits independently arising in different lineages by convergent or parallel evolution) or similar inconsistencies in sequence alignment (9-...

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“…On the other hand, character methods include joining networks (Median-joining network, Bandelt et al, 1999;median network, Bandelt et al, 2000) and, especially, the widely used statistical parsimony (Templeton et al, 1992), which represents each change between two haplotypes as a mutational step (Clement et al, 2000;TCS software). Networks may be also reconstructed from phylogenetic trees, such as with consensus networks (Holland et al, 2004(Holland et al, , 2006 or super-networks (Huson et al, 2004).…”

Section: Reconstruction Of Genealogical Relationships Using Dna Sequementioning

confidence: 99%

Biogeography of Flowering Plants: A Case Study in Mignonettes (Resedaceae) and Sedges (Carex, Cyperaceae)

Martín‐Bravo¹

2012

Global Advances in Biogeography

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Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny

Cited by 152 publications

References 11 publications

Regular Networks Can be Uniquely Constructed from Their Trees

Regular Networks Can be Uniquely Constructed from Their Trees

Topology of viral evolution

Biogeography of Flowering Plants: A Case Study in Mignonettes (Resedaceae) and Sedges (Carex, Cyperaceae)

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