reconciliation

sity Reviewferences, their evolutionary fates might differ and result in novel gene functions [2]. In asexual species, HGT shapes the genomic repertoire and imports new genes, sometimes of beneficial conse-quences, into the host genome [3,4]. HGT occurs mainly through one of three mechanisms: (i) transformation, which is the uptake of naked DNA from the environment; (ii) transduction, which is the transfer of genetic material through a plasmid or bacteriophage; and (iii) conjugation, which is the direct transfer of DNA between two cells. In eukaryotes, the evolutionary histories of various groups of plants and animals have been shown to involve es that shaped the gene trees and their phenotypic conse-quences. Multilocus analyses provide power, in terms of phylogenetic signal, to solve both tasks with high accuracy, yet pose new modeling and computational challenges for phylogenetic inference that mostly stem from a phenome-non known as gene tree incongruence. Phylogenetic incongruence: a signal, rather than a problem As illustrated in Figure 1, each of the evolutionary pro-cesses operating on a gene leaves its signature on the gene tree. These processes alone do not necessarily result in signatures in the form of incongruence between gene trees and the species phylogeny. It is often the evolutionary fates of gene copies that result in such signatures. These evolu-tionary fates are determined by forces such as mutation, drift, and selection. For example, in Figure 1A, if the gene copies b1, c1, and a2 are lost, the resulting gene tree differs from the species tree. In Figure 1B, if the HGT event 0169-5347/ $ – see front matte