DOI: 10.5061/dryad.qrfj6q5m0
title: SAMBA: Super Area-cladogram after resolving Multiple Biogeographical Ambiguities

description: Aim: Cladistic biogeography is all about congruence: when individual area
 cladograms coincide, they result in a general area cladogram that reveals
 shared history. However, the complexities of the natural world hamper the
 reconstruction of fully solved biogeographical patterns. Herein, we
 present SAMBA (Super Area-cladogram after resolving Multiple
 Biogeographical Ambiguities), a pattern-based method combining supertrees
 and area cladograms to depict the relationships among areas. We also
 present a prototypical implementation of SAMBA as a web-based framework
 named iSAMBA. Location: Global Taxon: Any taxon can be analyzed with SAMBA
 Methods: SAMBA is based on phylogenetic supertrees, a technique that
 combines previously calculated phylogenetic trees to produce a general
 area cladogram representing conciliatory and non-ambiguous patterns of
 relationships. In our method, the input topologies are individual area
 cladograms. SAMBA is implemented through a web-based framework named
 iSAMBA. We analyzed a theoretical and a real scenario to compare SAMBA
 with Primary BPA, Component Analysis, TAS and Transparent Method. Results:
 SAMBA produces area cladograms that converge with the actual history of
 fragmentations of both hypothetical and real scenarios used as examples of
 implementation of the method. Primary BPA, Component Analysis, TAS and the
 Transparent Method are much more affected by the "biogeographical
 noise" (e.g., multiple areas in a single terminal, paralogies and
 missing areas) than SAMBA. Main conclusions: SAMBA results in more
 informative general area cladograms than other pattern-based
 biogeographical methods. SAMBA reveals shared patterns of biotic
 distribution without generating multiple unreliable area cladograms. The
 main advantage of SAMBA is the simplicity of using a single technique to
 extract biogeographical information from individual area cladograms and
 combine them to depict a non-ambiguous general pattern of relationships
 among areas.
description: Please see the README document
 ("README_dm") and the accompanying paper: Santos, D., Sampronha,
 S., Hammoud, H., Gois, J.P. & Santos, C.M.D. 2023. SAMBA: Super
 Area-cladogram after resolving Multiple Biogeographical Ambiguities.
 Journal of Biogeography. Accepted. <br><br>We implemented
 SAMBA as a web-based framework named iSAMBA. It is freely available at
 http://nuvem.ufabc.edu.br/isamba. The input for iSAMBA is a set of individual area cladograms in parenthetical format. After uploading a text file with the input area cladograms, iSAMBA generates the MRP-combined matrix, making it available to download in “.nex” and “.ss” files format. The MRP-combined matrix can be analyzed in any software that performs parsimony analysis. The result is the super area-cladogram.
description: This dataset contains the iSAMBA tool's code, the
 instructions to run it locally, the input tree files used in the scenarios
 described in the paper, and the resulting matrices for each scenario after
 SAMBA (formats .ss and .nex). The iSAMBA tool is freely
 available online (http://nuvem.ufabc.edu.br/isamba)