such as "Introduction", "Conclusion"..etc
The Recent, Ancient and Free event-based options have been implemented in the computer program TreeFitter 1.0 (RONQUIST, 2001). TreeFitter is a program for finding the optimal biogeographic reconstruction/s (GACs), given one or more TACs. TreeFitter is available as free software on the website: http://www.ebc.uu.se/systzoo/research/ treefitter/treefitter.html.
An empirical example: Xiphophorus and Heterandria (Rosen, 1978)
ROSEN (1978)’s study on the poeciliid fishes Heterandria and Xiphophorus is probably the most widely used benchmark data set in the development of biogeographic methods. Because the solutions under Assumptions 0, 1, and 2 for this data set are well known, it provides a useful comparison with the results of the event–based options.
Figure 8 shows the taxon-area cladograms for Heterandria (fig. 8a) and Xiphophorus (fig. 8b). They include widespread taxa (e.g., X. alvarezi in areas 4, 5, 6), redundant distributions (e.g., area 2 in Xiphophorus), and missing areas (e.g., area 3 in Heterandria or area 7 in Xiphophorus). Using TreeFitter 1.0 (RONQUIST, 2001), we searched for the optimal GAC for the two genera treating widespread taxa under the different event–based options.
The recent option (fig. 8c) finds an optimal GAC that basically follows the pattern of area relationships in Heterandria. The areas included in widespread (4–5, 6, 9 and 10) or redundant (2) distributions in Xiphophorus are positioned in the optimal GAC according to the TAC of Heterandria; only area 3, missing in Heterandria, is placed according to its position in Xiphophorus (basal to areas 4–5). The optimal GAC under the recent option is one of the three GACs found under A2 (fig. 8f) by PAGE (1989) and VAN VELLER et al. (2000) but is different from the single GAC obtained under either A0 (fig. 8g) or A1 (fig. 8h). The optimal GAC under the ancient option (fig. 8d) agrees mainly with the relationships among areas in Xiphophorus. Areas 1 and 3 are placed basally in the cladogram, whereas areas 4– 5 and 6, and areas 9 and 10, are grouped together as sister–areas. This is the same GAC found by VAN VELLER et al. (2000) using COMPONENT 2.0 (PAGE, 1993) under A0 (fig. 8g), which is not surprising considering that both the ancient option and A0 group areas based on widespread distributions. It is also similar to the GAC obtained under A1 (fig. 8h) except that the areas forming part of the widespread distribution are not monophyletic in A1. This assumption, like the ancient option, considers the widespread distribution to be ancestral and only allows extinction and vicariance events as possible explanations. In this case, treating the widespread taxa as fully informative about area relationships conflicts with the evidence from endemic taxa because for each pair of areas in a widespread terminal in the Xiphophorus TAC (e.g., 9 and 10), the corresponding endemic taxa in the Heterandria TAC are not closely related (species B and species D). Nevertheless, the grouping information provided by the widespread taxa is strong enough to override the signal from the endemic taxa. The free option finds the same optimal GAC as the recent option. Thus, the widespread terminal distributions in Xiphophorus are best explained as due to recent dispersal when all processes are allowed and the cost of all implied events, ancestral as well as terminal, is considered (see fig. 9). As mentioned above, this GAC is one of the three solutions found under A2 by PAGE (1989: his fig. 10) and VAN VELLER et al. (2000: their fig. 13c). The other two solutions place area 3 basal to area 9 or areas 3 and 9 in a monophyletic clade, in both cases requiring an extra extinction event in the event–based framework. For these data, A2 is clearly associated with a loss in resolving power compared to A0 and A1 because it allows three instead of one solution. This information loss does not occur for the free option in the event– based analyses.
Our analyses of the Rosen data show some of the similarities and differences between the traditional pattern–based assumptions and the event–based options. Clearly, there is no one– to–one correspondence between the options and assumptions. Both the recent and free options share properties with A2, whereas the ancient option is more similar to A0 and A1. For Rosen’s data, the results obtained with the free option support those obtained with the recent option. This suggests that the ancient option may force unrealistic constraints onto the analysis and that the optimal GAC under the free and recent options may be preferable. This is also the GAC that is better supported by the phylogenetically determined (as opposed to the within–terminal) area relationships in the two TACs.
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