The best way to detect whether lateral gene transfer has occurred would be by

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Looking for genes whose phylogenies differ from those of most other genes is the best way to detect lateral gene transfer. This is because genes that have been horizontally transferred will have a different evolutionary history than the rest of the organism's genome, leading to a different phylogenetic tree. Other methods, such as comparing the ratios of synonymous and nonsynonymous substitutions, can also provide evidence of lateral gene transfer, but they may not be as reliable or specific as looking at the gene's phylogeny.

The Best Way to Detect Whether Lateral Gene Transfer Has