Surprising effects of differential loss in genome evolution: the last-one-out

Gene loss is an important process in genome evolution, though its power is often underestimated. If a gene is present at the root of a phylogenetic tree and can be lost in one lineage across the tree, it can potentially be lost in all, leading to gene extinction. Just before gene extinction, there will be one lineage that still retains the gene, generating a "last-one-out" distribution. Such an isolated gene presence will emulate the result of recent lateral gene acquisition, even though its distribution was generated by loss. How probable is it to observe "last-one-out" distributions in real data? Here, we mathematically derive this probability and find that it is surprisingly high, depending upon the tree and the gene loss rate. Examples from real data show that loss can readily account for observed frequencies of last-one-out gene distributions that might otherwise be attributed to lateral gene transfer.