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The two most popular EBMs are parsimony-based tree fitting and dispersalvicariance analysis (Ronquist and Sanmartín 2011). Parsimony-based tree fitting, implemented in the software TreeFitter, was born from methods used in host–parasite tree reconciliation, with which it shares many similarities (Ronquist 2003). In tree fitting, a taxon cladogram is fitted onto the area cladogram by searching for the sequence of events that explain the tip distributions according to the area cladogram and with the minimum cost. The area cladogram may be a hypothesis of relationships based on geological history, in which case we measure how much the observed distributions depart from geologically predicted vicariance (Sanmartín and Ronquist 2004). Alternatively, it may be an unknown parameter, in which case, tree fitting consists of finding the area relationships and the sequence of biogeographic events that explain the tip distributions in the phylogeny with the minimum cost. Searching for the optimal (minimum-cost) area-cladogram implies enumerating and fitting all possible hierarchical combinations of areas. If the number of areas is large, it is possible to use heuristic search tools such as those employed in parsimony phylogenetics (nearest-neighbor interchange, branch and bound, etc.). In Figure 2.2(a), the distribution of species 1– 3 in area A, which is the sister in the area cladogram to the clade BCD (Figure 2.2(b)), is explained by a sequence of events involving duplication of a widespread ancestor in ABCD, extinction of the ancestor of species 1 in part of this range (BCD), successive vicariance events, and dispersal of the ancestor of species 3 and 4 to A, followed by allopatric speciation (Figure 2.2(c)).

From the description above, it can be deduced that the most important problem in EBMs is to find the optimal cost assignments. The most common criterion is to select event costs that maximize the conservation of distribution ranges along the phylogeny (Ronquist 2003). Figure 2.1 shows that dispersal and extinction are not “phylogenetically conserved or constrained” processes because they interrupt the “vertical inheritance” of geographic ranges from ancestor to descendants. In dispersal, the colonized area B is not part of the ancestral range (Figure 2.1(c)); in extinction, part of the ancestral range (A) is lost in the right descendant (Figure 2.1(d)). Conversely, vicariance and duplication are phylogenetically constrained processes because either each descendant inherits the entire ancestral range (duplication) (Figure 2.1(b)) or the union of the two descendants’ ranges equals the ancestral range (vicariance, Figure 2.1(a)). A consequence of this cost assignment is that the frequency of dispersal and extinction events is minimized relative to vicariance and duplication in EBM reconstructions. A similar phylogenetic conservation criterion is used in parsimony-based inference to minimize homoplasies (convergence and parallelism), as evolutionary changes that are not identical by descent, that is, losses and gains of traits in unrelated lineages. In the TreeFitter reconstruction in Figure 2.2(c), extinction (e) receives a cost of 1 and dispersal (i) a cost of 2; vicariance (v) and duplication (d) are given minimum costs (0.01); the lower cost of extinction relative to dispersal is due to extirpation preserving part of the ancestral range (Figure 2.1; Sanmartín and Ronquist 2004).

Figure 2.2. Event-based biogeography. a) An organism phylogeny with six species (1–6) distributed in four areas (A–D). b) Area cladogram depicting relationships among areas of endemism. c) TreeFitter reconstruction: total cost = 3.04. d) DIVA reconstruction, total cost = 2.0. Notice that TreeFitter and DIVA provide a full description of ancestral ranges and explanatory events but differ in the treatment of duplication (see the text). Symbols: vicariance (circle), duplication (rhombus), dispersal (arrow or cross) and extinction (short line). For a color version of this figure, see www.iste.co.uk/guilbert/biogeography.zip