Subject: tree-of-life | Phylogenetic tree | Quantitative Biology - Populations and Evolution | Computer Science - Data Structures and Algorithms | phylogenetic network | evolution | tree-based
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking ... View more
 D. H. Huson, R. Rupp, and C. Scornavacca, Phylogenetic networks: concepts, algorithms and applications. Cambridge University Press, 2010.
 E. Bapteste, L. van Iersel, A. Janke, S. Kelchner, S. Kelk, J. O. McInerney, D. A. Morrison, L. Nakhleh, M. Steel, L. Stougie, and J. Whitfield, “Networks: expanding evolutionary thinking,” Trends in Genetics, vol. 29, no. 8, pp. 439 - 441, 2013.
 T. Dagan and W. Martin, “The tree of one percent,” Genome Biol, vol. 7, no. 10, p. 118, 2006.
 W. F. Martin, “Early evolution without a tree of life,” Biol Direct, vol. 6, p. 36, 2011.
 W. F. Doolittle and E. Bapteste, “Pattern pluralism and the tree of life hypothesis,” Proceedings of the National Academy of Sciences, vol. 104, no. 7, pp. 2043-2049, 2007.
 E. Corel, P. Lopez, R. Mheust, and E. Bapteste, “Network-thinking: Graphs to analyze microbial complexity and evolution,” Trends in Microbiology, 2016, http://dx.doi.org/10.1016/j.tim.2015.12.003.
 A. R. Francis and M. Steel, “Which phylogenetic networks are merely trees with additional arcs?” Systematic Biology, vol. 64, no. 5, pp. 768-777, 2015.
 L. van Iersel, “Different topological restrictions of rooted phylogenetic networks. Which make biological sense?” 2013, http://phylonetworks.blogspot.nl/2013/03/different-topological-restrictions-of.html.
 L. Zhang, “On tree based phylogenetic networks,” arXiv:1509.01663 [q-bio.PE], 2015.
 T. Marcussen, K. S. Jakobsen, J. Danihelka, H. E. Ballard, K. Blaxland, A. K. Brysting, and B. Oxelman, “Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae),” Systematic Biology, vol. 61, no. 1, pp. 107-126, 2012.