Reconstruction of Reticulate Networks from Gene Trees

Huson, Daniel H.; Klöpper, Tobias H.; Lockhart, P. J.; Steel, Mike

doi:10.1007/11415770_18

Cited by 127 publications

(131 citation statements)

References 23 publications

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“…Most of these methods work by computing a split system 2 on the taxa (except T-Rex which reconstructs reticulograms directly from a distance matrix 3 ). After filtering some splits 4,5 , it is represented by a split network 6,7,8,9 , or by a galled network 10,11 . These indirect reconstruction approaches, which first compute an abstract representation of the data, and then try to deduce an explicit phylogenetic network of a restricted subclass of phylogenetic networks, have drawbacks.…”

Section: Introductionmentioning

confidence: 99%

Quartets and Unrooted Phylogenetic Networks

Gambette

Berry

Paul

2012

J. Bioinform. Comput. Biol.

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Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data.In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analogue of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.

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Section: Introductionmentioning

confidence: 99%

Quartets and Unrooted Phylogenetic Networks

Gambette

Berry

Paul

2012

J. Bioinform. Comput. Biol.

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“…This problem was proved to be NP-hard [5]. Various special cases with additional hypotheses on the networks have also been studied, such as [24], [9], [13], [14].…”

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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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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“…2007). We expect to see progress in the near future as novel phylogenetic methods to detect hybridisation, both current and historical (Huson et al 2005;Winkworth et al 2005;Barom et al 2006;McBreen & Lockhart 2006;Holland et al 2008; in press a), are applied to more species. Technical advances in multilocus genotyping methods and pyrosequencing make many more markers available, and expectations of molecular phylogenetic datasets will correspondingly increase dramatically.…”

Section: Future Directionsmentioning

confidence: 99%

“…The arrival of exotic species has been well documented and geological studies give us some ability to date the fragmentation, expansion and hybridisation of our native species. New Zealand mathematicians who are developing novel methods to study hybridisation will continue to give us impact in the international scientific community (for example Huson 2005;Winkworth et al 2005;Barom et al 2006;McBreen & Lockhart 2006;Bordewich & Semple 2007;Joly et al 2007, in press a; Holland et al 2008).…”

Section: Introductionmentioning

confidence: 99%

A review of genetic analyses of hybridisation in New Zealand

Morgan‐Richards

Smissen

Shepherd

et al. 2009

Journal of the Royal Society of New Zealand

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Hybridisation between related taxa has a range of possible biological consequences, ranging from the production of sterile offspring, through introgression of alleles into populations, to the formation of new species. Examples of plant and animal species hybridising with related taxa abound in the New Zealand region. We review New Zealand examples of hybridisation that have been verified with chromosomal, protein or DNA data. Contemporary hybridisation has been studied at hybrid zones where distinct populations meet and mate in a defined and stable zone of contact. The role of human habitat modification is highlighted with examples of recent range changes that have led to hybridisation and subsequent conservation problems. Hybridisation can result in the swamping of endangered species, although it can also act as a bridge for the transfer of adaptations among lineages. Historical hybridisation in New Zealand has been examined with phylogenetics and there are many examples of organelle introgression or capture. The origin of new species of New Zealand stick insects, ferns and daisies via hybridisation has been demonstrated with cytogenetic and DNA sequence evidence. Thus the importance of hybridisation in the evolution of New Zealand's flora and fauna is highlighted.

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Reconstruction of Reticulate Networks from Gene Trees

Cited by 127 publications

References 23 publications

Quartets and Unrooted Phylogenetic Networks

Quartets and Unrooted Phylogenetic Networks

Regular Networks Can be Uniquely Constructed from Their Trees

A review of genetic analyses of hybridisation in New Zealand

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