Incongruence between phylogenetic trees constructed from different gene sequences has bothered practitioners for decades. Paraphyletic or polyphyletic clustering has been traditionally treated as noise that distorts its genealogical bases. Nevertheless, recent genomic data have provided a first indication that horizontal gene transfer (HGT) in microbes and interspecific hybridization (or polyploidization) in eukaryotes challenge the doctrine of common descent. Due to promiscuous recombination, the initial stages of life would have not had a genealogical history but a common physical one whose graphic representation is known as evolutionary reticulation. Reticulate evolution in plants has long been recognized, and recent genomic evidence from animals also indicates its widespread occurrence. Taking into consideration that mounting evidence for hybridization and polyploidy in eukaryotic taxa accumulates, it is essential to have methods to infer reticulate evolutionary histories. Considering the different forms of transpecific genetic transference and introgression across the tree of life, the origin of a given species may not coincide with the origin of its genes. Accordingly, molecular mutation rates might be erroneous if based on strict genealogical thinking. Given abundant new data, it is time to move forward because a major shift in our understanding of species, speciation and phylogenetics is taking place.
Part of the book: Phylogenetics