... combining genes withdifferent histories into a single data set will almost certainlyresult in a phylogeny that represents neither the history of any individual gene, nor the history of the ... supporting an organismaltree. For example, because of such highways of gene sharingthese types of analyses group members of the orderThermotogales with the Firmicutes, and the members of the 54.2Journal ... 88::272.http://jbiol.com/content/8/6/54Journal of Biology2009, Volume 8, Article 54 Swithers et al.54.3Journal of Biology 2009, 88::54transfer, and then using the remaining genes to reconstruct the presumed vertical lines of descent...