In Computational Biology, the notion of phylogeny has become synonymous with tree-like evolution. Recent advances in the Life Sciences have suggested that evolution has a much more diverse course. In this paper we will survey some of the models that have been proposed to overcome the limitations of using phylogenies to represent evolutionary histories.
KeywordsEvolutionary trees Pedigrees Haplotypes Networks
We would like to thank the anonymous referees, whose detailed suggestions have greatly contributed to the paper. GDV and YP have been partially supported by FAR grant “Computational models for phylogenetic analysis of gene variations”. TJ’s research is supported in part by NIH grant LM008991 and NSF grant IIS-0711129. LW is supported by a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project No. CityU 121207).
- Bonizzoni P, Della Vedova G, Dondi R, Mauri G (2008) The comparison of phylogenetic networks: algorithms and complexity. In: Mandoiu I, Zelikovsky A (eds) Bioinformatics algorithms: techniques and applications. Wiley-Interscience Publisher, Hoboken, NJ, pp 143–173Google Scholar
- Burleigh JG, Bansal MS, Wehe A, Eulenstein O (2008) Locating multiple gene duplications through reconciled trees. In: Proceedings of the 12th conference on research in computational molecular biology, (RECOMB), pp 273–284Google Scholar
- Chan BM-Y, Chan JW-T, Chin FYL, Fung SPY, Kao M-Y (2006) Linear-time haplotype inference on pedigrees without recombinations. In: Proceedings of the 6th workshop on algorithms in bioinformatics (WABI), pp 56–67Google Scholar
- Chang W-C, Eulenstein O (2006) Reconciling gene trees with apparent polytomies. In: Proceedings of the 12th conference on computing and combinatorics (COCOON), pp 235–244Google Scholar
- Doi K, Li J, Jiang T (2003) Minimum recombinant haplotype configuration on tree pedigrees. In: Proceedings of the 3rd workshop on algorithms in bioinformatics (WABI). Springer, pp 339–353Google Scholar
- Gòrecki P (2004) Reconciliation problems for duplication, loss and horizontal gene transfer. In: Proceedings of 8th conference on research in computational molecular biology, (RECOMB), pp 316–325Google Scholar
- Hallett M, Lagergren J (2001) Efficient algorithms for lateral gene transfer problems. In: Proceedings of 5th annual international conference on research in computational molecular biology, (RECOMB), pp 149–156Google Scholar
- Hallett M, Lagergren J, Tofigh A (2004) Simultaneous identification of duplications and lateral transfers. In: Proceedings of 8th annual international conference on research in computational molecular biology, (RECOMB), pp 347–356Google Scholar
- Nakhleh L, Ruths DA, Wang L-S (2005a) RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer. In: Proceedings of the 11th conference on computing and combinatorics (COCOON), pp 84–93Google Scholar
- Page R (1994) Maps between trees and cladistic analysis of historical associations among genes. Syst Biol 43:58–77Google Scholar
- Than C, Nakhleh L (2008) SPR-based tree reconciliation: non-binary trees and multiple solutions. In: Proceedings of the 6th Asia-Pacific bioinformatics conference (APBC), pp 251–260Google Scholar
- van Iersel L, Keijsper J, Kelk S, Stougie L, Hagen F, Boekhout T (2008) Constructing level-2 phylogenetic networks from triplets. In: Proceedings of 5th annual international conference on computational molecular biology, (RECOMB), pp 450–462Google Scholar
- Xiao J, Liu L, Xia L, Jiang T (2007) Fast elimination of redundant linear equations and reconstruction of recombination-free mendelian inheritance on a pedigree. In: Proceedings of the 18th symposium on discrete algorithms (SODA), pp 655–664Google Scholar