An improved node mapping algorithm for the cophylogeny reconstruction problem

References

• Bender MA, Farach-Colton M. 2004. The level ancestor problem simplified. Theor Comput Sci. 321:5–12.
   Google Scholar
• Charleston MA. 2003. Recent results in cophylogeny mapping. Adv Parasitol. 54:303–330.
   Google Scholar
• Charleston MA, Perkins SL. 2006. Traversing the tangle: algorithms and applications for cophylogenetic studies. J Biomed Inform. 39:62–71.
   PubMed Web of Science ®Google Scholar
• Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R. 2010. Jane: a new tool for the cophylogeny reconstruction problem. Algorithm Mol Biol. 5:16.
   PubMed Web of Science ®Google Scholar
• Cruaud A, Cook J, Da-Rong Y, Genson G, Jabbour-Zahab R, Kjellberg F, Pereira RAS, Rnsted N, Santos-Mattos O, Savolainen V, et al. 2011. Fig-fig wasp mutualism: the fall of the strict cospeciation paradigm? In: Evolution of plant-pollinator relationships. Cambridge: Cambridge University Press; p. 68–102.
   Google Scholar
• Doyon J-P, Ranwez V, Daubin V, Berry V. 2011. Models, algorithms and programs for phylogeny reconciliation. Briefings Bioinf. 12:392–400.
   Google Scholar
• Doyon J-P, Scornavacca C, Yu Gorbunov K, Szöllősi GJ, Ranwez V, Berry V. 2011. An efficient algorithm for gene/species trees parsimonious reconciliation with losses duplications and transfers. In: Proceedings from the 14th International Conference on Research in Computational Molecular Biology (RECOMB-CG). Springer; p. 93–108.
   Google Scholar
• Hafner MS, Nadler SA. 1988. Phylogenetic trees support the coevolution of parasites and their hosts. Nature. 332:258–259.
   PubMed Web of Science ®Google Scholar
• Harel D, Tarjan RE. 1984. Fast algorithms for finding nearest common ancestors. SIAM J Comput. 13:338–355.
   Google Scholar
• Hoyal Cuthill J, Charleston M. 2012. Phylogenetic codivergence supports coevolution of mimetic heliconius butterflies. PloS One. 7:e36464.
   Google Scholar
• Jackson AP. 2004. Cophylogeny of the ficus microcosm. Biol Rev. 79:751–768.
   Google Scholar
• Libeskind-Hadas R. 2010. Who is Jane? Available from: http://www.cs.hmc.edu/~hadas/jane/Jane1/index.html
   Google Scholar
• Libeskind-Hadas R. 2013. Jane 4. Available from: http://www.cs.hmc.edu/~hadas/jane
   Google Scholar
• Libeskind-Hadas R, Charleston MA. 2009. On the computational complexity of the reticulate cophylogeny reconstruction problem. J Comput Biol. 16:105–117.
   Google Scholar
• Merkle D, Middendorf M. 2005. Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. Theor Biosci. 123:277–299.
   Google Scholar
• Merkle D, Middendorf M, Wieseke N. 2010. A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinf. 11:S60.
   Google Scholar
• Ovadia Y, Fielder D, Conow C, Libeskind-Hadas R. 2011. The cophylogeny reconstruction problem is np-complete. J Comput Biol. 18:59–65.
   Google Scholar
• Page RDM. 1994a. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst Biol. 43:58–77.
   Google Scholar
• Page RDM. 1994b. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics. 10:155–173.
   Google Scholar
• Page RDM. 2002. Tangled trees: phylogeny, cospeciation, and coevolution. Chicago: University of Chicago Press.
   Google Scholar
• Paterson AM, Wallis GP, Wallis LJ, Gray RD. 2000. Seabird and louse coevolution: complex histories revealed by 12s rrna sequences and reconciliation analyses. Syst Biol. 49:383–399.
   Google Scholar
• Paterson AM, Palma RL, Gray RD. 2002. Drowning on arrival, missing the boat, and x-events: how likely are sorting events. In: Page RDM, editor. Tangled trees: phylogeny, cospeciation, and coevolution. Chicago: University of Chicago Press; p. 287–309.
   Google Scholar
• Percy DM, Page RDM, Cronk QCB. 2004. Plant–insect interactions: double-dating associated insect and plant lineages reveals asynchronous radiations. Syst Biol. 53:120–127.
   PubMed Web of Science ®Google Scholar
• Refrégier G, Le Gac M, Jabbour F, Widmer A, Shykoff JA, Yockteng R, Hood ME, Giraud T. 2008. Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation. BMC Evol Biol. 8:100.
   Google Scholar
• Ronquist F. 1997. Phylogenetic approaches in coevolution and biogeography. Zool Scr. 26:313–322.
   Google Scholar
• Ronquist F. 1998. Three-dimensional cost-matrix optimization and maximum cospeciation. Cladistics. 14:167–172.
   PubMed Web of Science ®Google Scholar
• Ronquist F. 2002. Parsimony analysis of coevolving species associations. In: Page RDMTangled trees: phylogeny, cospeciation and coevolution. Chicago: Chicago University Press; p. 22–64.
   Google Scholar
• Sorenson MD, Balakrishnan CN, Payne RB. 2004. Clade-limited colonization in brood parasitic finches (vidua spp.). Syst Biol. 53:140–153.
   PubMed Web of Science ®Google Scholar
• Yodpinyanee A, Cousins B, Peebles J, Schramm T, Libeskind-Hadas R. 2011. Faster dynamic programming algorithms for the cophylogeny reconstruction problem. HMC CS Technical Report. Claremont: Harvey Mudd College.
   Google Scholar