Abstract: Historical biogeography is the science that deals with relationships between biogeographic areas, understood as set of taxa distributions. The complex geological history of South East Asia and the Indo‐West Pacific region makes it a very interesting area for biogeography studies. We propose a new approach, cladistic, for the study of this area around the famous “Wallace’s line”, placing our study in the paradigm of vicariance where speciation appears following the implementation of a geographic barrier (as opposed to the dispersal model from a center of origin, classically admitted). Indeed, here we use the existing analogy between Systematics and Biogeography to apply cladistics methods for Systematics to Biogeography. This is to answer the question : "Why is there such distributions of taxa in this region of the world ?” The expected results are a better understanding of the evolutionary history of the region and the life history traits of taxa that inhabit it. Provided that the joint distribution of several unrelated taxa cannot be obtained by "chance", thus it is necessarily due to a common event (ie a vicariant event) which affected equally these taxa. The cladistics approach we propose has been made possible by the completion of a software that implements the so‐called 3‐element analysis (3ia) method : LisBeth is now freely available for download from our website and offers new perspectives of analysis to its users, whether systematicians and biogeographers. We show that the representation of characters offered by LisBeth allows new inferences about the existing relationship between areas of endemism studied. We have highlighted the emergence of a general "pattern" from a joint analysis of 35 unrelated taxa (plants and animals). In a second step we are interested in a major theoretical problem of contemporary biogeography : "What about the time dimension in historical biogeography?". How to account unambiguously different time scales during diachronic analyzes ? We propose a model based on the 3ia which ...
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