However, speciation can often be a gradual process. A good example is the recent evolutionary history of species related to wheat. Each genome is inferred to have arisen from the same common ancestor, but diverged into separate species. However, subsequent hybridization events have produced cereal species with all combinations of genomes, or which wheat is only one example. Horizontal gene flow is even more critical when considering prokaryotic genomes.
Prokaryotes appear to have fewer fundamental barriers to horizontal gene transfer.
Among prokaryotes, horizontal DNA transfer is relatively easy. At the other extreme, higher eukaryotes have germlines that are physically sequestered from contact with foreign species. Homology A second factor that is critical to phylogenetic analysis is that homologous characters be compared across species. For DNA and proteins, this means that gaps must be correctly in multiple alignments to ensure that the same position is being compared for each species. Consequently, if a multiple alignment is poor, phylogeny construction will also be poor.