Which mechanism can explain different phylogenetic tree topologies when analyzing various genes?

Horizontal gene transfer is a mechanism that can lead to varied phylogenetic tree topologies when analyzing different genes. This process involves the transfer of genetic material between organisms, bypassing the traditional parent-offspring lineage. As a result, genes that are acquired through horizontal gene transfer can exhibit different evolutionary histories compared to the organisms themselves, leading to discrepancies in phylogenetic trees constructed from different genes.

For instance, if a gene is acquired from another species through horizontal gene transfer, its lineage may reflect the evolutionary relationships of the donor species rather than the recipient species. This can produce trees that appear different based on the gene analyzed, as opposed to trees built from other genes that do not undergo the same transfer events.

In contrast, while gene duplication can contribute to divergence and speciation events by creating paralogs, it typically affects the same lineage rather than leading to entirely different topologies. Gene loss can influence the presence of certain genes within a lineage but generally does not create the same variability in tree topology. Gene co-option describes a situation where existing genes or gene products acquire new functions in different contexts but does not typically explain the discrepancies seen across different genes in phylogenetic analyses.