The process of cladogenesis mostly takes place by gradual branching apart of the individual lines of organisms. If a speciation event occurs, two daughter species are formed in a certain moment from a single parent species. One of these species can be basically identical in its phenotype with the parent species for a long time. Nonetheless, in the first phase of reconstruction of cladogenesis, it is preferable to consider both daughter species to be new species. The evolutionary fates of the parent and daughter species differ substantially. All the genetic changes relating to the parent species can be passed on to both the daughter species and subsequently to both phylogenetic lines that can be formed from them by repeated speciation. In contrast, the genetic changes that occur after splitting off of the daughter species can affect only the progeny of one of the two daughter species and cannot be transferred to the sister phylogenetic line.
Speciation can occur in rapid succession in a certain phylogenetic line. In fact, in some cases, a certain species can decompose into a whole series of daughter species at a single moment. For example, such a situation can occur on a decrease in the water level in a lake and subsequent division of the original continuous population of a certain aquatic species into a number of isolated populations (Fig. XXIII.1). In this case, it is also useful, although not always technically feasible, to express the entire process of cladogenesis as a sequence of binary branchings of the particular phylogenetic line. In actual fact, the physical division of the population occurred at a single moment on a decrease in the water level in the lake; however, branching of the population probably occurred gradually, as the individual parts of the population occupied the individual parts of the original lake. Simultaneously, it is highly improbable that two populations that will, in the future, occupy two different parts of the lake and that led to the formation of the two new species would split off from the parent population at the same instant. Consequently, in reconstruction of cladogenesis we primarily attempt to express this process as a sequence of binary branchings of the particular phylogenetic line and, only if the available data do not make this possible, can we create a scheme of cladogenesis including multifurcation.
In rare cases, two originally independent lines can merge to form a single line, which can then branch apart. Fundamentally, there are two basic mechanisms of syngenesis, i.e. the formation of a new phylogenetic line by the merging of two older lines: symbiogenesis and interspecies hybridization (Fig. XXIII.2). Symbiogenesis refers to the formation of a new species of organism by the integration of two unrelated organisms that live for some time in some form of symbiosis, most probably parasitism or mutualism, into a single organism. If both symbionts begin to reproduce together in a coordinated manner, i.e. so that each daughter organism of symbiotic origin begins to inherit from its parents only the genetic material of both symbionts, the evolutionary fates of the two original species become so interconnected that they sooner or later merge into a single species. Evolutionary dissolution of one species in another species, for example a microscopic parasite or mutualist in its macroscopic host, is sometimes term the Cheshire cat effect (unfortunutly, this term is also used for at least two unrelated phenomena). The relevant literary sources state that, under suitable conditions, a Cheshire cat can gradually disappear and, in the last stage, only its smile remains and, after a certain time, this also disappears. If both symbionts that form a common symbiotic organism produce independent progeny and a new symbiotic organism is formed each time (or at least frequently) through new integration of both symbionts that grew from embryos produced by two unrelated and independent individuals, both species will most probably preserve their species identity (Fig. XXIII.3). This is the frequent case of the symbiosis of fungi and vascular plants. The best known opposite case is the formation eukaryotes, occurring through gradual integration of the members of several unrelated lines of prokaryotic organisms. Completely unrelated phylogenetic lines of organisms can merge through symbiogenesis.
Two lines can also merge through interspecies hybridization, i.e. accidental crossing of the members of two different species. However, in contrast to symbiogenesis, this mechanism can occur only in closely related species with sexual reproduction. The effect of symbiogenesis and hybridization on the topology of the phylogenetic tree is the same; in both cases, the cladogenesis scheme can have a recticular structure instead of a tree structure at some places.