Answer
Horizontal gene transfer means that there are one or more genes in a genome which are both out-of-place and out-of-species. These could cause an organism to be placed in a very incorrect position in a phylogenetic tree or at least confuse analysis since they would not place on the tree in the same location as all of the rest of the genes in that organism.
Work Step by Step
Horizontal gene transfer puts "foreign" DNA into a genome which, as a character in phylogenetics, greatly disagrees with other characters in that organism, confusing and complicating analysis.
