Horizontal gene transfer (or lateral gene transfer) is a type of recombination that happens across species boundaries. This leaves a detectable signature in the genome, e.g. a change in nucleotide composition at the 3rd codon position. If the putative donor and recipient genomes are available, you can use quite sophisticated tools to identify such areas and date the timing that such transfer occurred.

Benjamin Ward is a PhD student in my lab who has just released a beta version of the software HybRIDS (Hybridisation, Recombination, Introgression and Dating Software). It is a bioinformatics tool designed to visualize the signal of recombination (and genetic introgression, horizontal gene transfer) in DNA sequence data present in large (multiple kb) contigs and whole genome sequence data of three or more individuals. It reports several summary statistics of these events, including breakpoint positions, number of SNPs, and it estimates the age of the recombination event. HybRIDS can also be applied to analyse smaller amplicons (