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Title
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Comparative biogeography of Southeast Asia and the West Pacific region
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Visotheary UNG 1*, 2, René ZARAGUETA-BAGILS 1, 2, 3 and David M. WILLIAMS 4
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1
CNRS UMR 7205 (CNRS-UPMC-MNHN), 57 rue Cuvier CP43 75005 Paris, France.
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CNRS UMR 7207 (CNRS-UPMC-MNHN), 57 rue Cuvier CP43 75005 Paris, France.
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3
UPMC Univ Paris 06
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4
Department of Life Sciences, the Natural History Museum, Cromwell Road, London, SW7
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5BD, United Kingdom.
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* Corresponding author: [email protected]
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Short running title: Comparative biogeography of Southeast Asia
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Abstract (1630 words)
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The relationship between areas located in Southeast Asia and the West Pacific region,
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is still debated because of its complex historical geology and the enormous diversity of taxa
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occupying the region. Cladistic methods have previously been used to reconstruct the
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relationships between areas in the region but never with such a high number of unrelated taxa
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(35). We use a compilation of phylogenies to investigate area relationships among Southeast
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Asia and the West Pacific region, run the comparative analysis with LisBeth (based on the
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three-item analyses approach, i.e. 3ia) and compare the results with recently published
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geological reconstructions of the region and discuss the relevance of such an approach to the
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interpretation of general pattern. The main questions addressed are: how to explain actual
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distributions of taxa in Southeast Asia and the West Pacific region? Is there an emerging
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common pattern? Three-item analysis found 27 most optimal trees. An intersection tree, i.e.
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an area cladogram, reconstructed from the taxon-area statements (common to all 27) had an
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overall retention index 84.8% and retrieved 13 nodes with two major branches congruent with
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a separation between Southeast Asia and the West Pacific region. Congruent patterns revealed
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by the combination of unrelated taxa should reflect a common cause. The extraction of
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information on area relationships contained in phylogenetic analyses of taxa consists of
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testing for area homologs. We obtained an area cladogram from this region based on an
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empirical dataset which give account for new insights regarding area classification in the
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region.
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Key-words: Areas of endemism, Cladistics, Comparative biogeography, Southeast Asia, West
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Pacific, Three-item analysis (3ia), Pattern, Process.
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Introduction
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Comparative biogeography is the analysis of taxon distributions with respect to
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understanding Earth history (Parenti and Ebach 2009). It involves diverse taxon cladogram
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related together via their distributions. The ichthyologist Donn Eric Rosen (1929—1986;
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Nelson et al. 1987) first proposed the idea, stating “…that biological and geological patterns
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can shed light on one another (by the process of “reciprocal illumination”) but cannot test, and
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therefore cannot reject, one another” (Rosen 1978; see also Parenti 2006).
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Cladistics, as applied to area relationships, makes no a priori assumptions about the
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process (or processes) responsible for patterns of distribution. However, vicariance – the
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diversification of biotas following the creation of a barrier (most commonly a geological
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fragmentation) – may more parsimoniously explain the congruence of distributional patterns
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found among unrelated taxa rather than any other processes. For example, De Boer has
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written that “when several monophyletic groups of species comply with one and the same
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generalized area cladogram, we can safely assume that these groups did not acquire their
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distribution patterns independently by chance dispersals, but that they responded similarly to
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the same geological events. Area cladistic analysis should therefore always be based on two
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or more, preferably unrelated, groups” (de Boer 1995d).
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Although historical biogeography is sometimes considered to be the same as
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vicariance biogeography, it is not designed to provide explanations about processes involved
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in taxon diversification and current distributions of taxa. Nonetheless, finding congruence
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amongst a large number of non-related taxa may indeed imply a common cause. Of course,
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dispersal as a cause of taxon distribution may be an explanation it remains a problem
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interpreting congruent patterns of non-related taxa which have different dispersal capabilities.
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The Southeast Asia and the West Pacific region (SEA-WP) have long been noted as a
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centre of biodiversity for both marine and terrestrial taxa (Michaux 2010; Woodruff 2010).
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The complex geological history of the SEA-WP region makes it a compelling area for
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biogeographical studies (Hall 1998, 2002, 2011). To this end, a large dataset was compiled
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composed of 35 non-related taxa and a general area cladogram of the region was constructed
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as one is currently lacking (Ung 2013).
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The complexity of the geo-tectonic activity makes SEA-WP a challenging area for
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historical biogeographical studies, since many of the changes that occurred in the relative
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positions of the various islands and their parts suggest that a great amount of vicariant
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speciation has taken place. Therefore, as in systematics, where characters are discussed
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according to their discovered status (synapomorphy versus homoplasy), the obtained
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areagram will be interpreted in terms of the combination of taxa used to reconstruct it.
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The purpose of this study is to perform a comparative biogeographical analysis of a
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compiled dataset composed of cladograms of taxa (plants and animals). The comparison with
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recently published geological reconstructions will give new clues concerning relationships
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between areas of endemism in the region. Finally we will discuss the relevance of such an
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approach to the interpretation of the general pattern retrieved.
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Material and Methods
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Data
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Areas of endemism
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As SEA-WP biogeography is a highly debated topic, we begin by focusing on the earlier
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study of Turner et al. (2001). These authors collected (for the first time) a large number of
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cladograms for both plants and animals. Their dataset consists of the phylogenies and
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distribution patterns for 29 monophyletic groups. These were selected according to the
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following criteria:
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1. Availability of a cladistic hypothesis at species level, constructed using Wagner
parsimony (Kluge & Farris 1969);
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2. Availability of detailed information for the distribution patterns of all terminal species;
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3. Species exclusively – or at least predominantly – occurring in the region of interest;
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4. The degree of confidence in the accuracy of the cladogram.
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From this collection of 29 cladograms of taxa, 22 were retained according to the number
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of informative characters generated (i.e. once analysed some cladograms don’t produce any
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informative TAC, thus are excluded, see explanation bellow). Thirteen recently published
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cladograms of taxa distributed over SEA-WP have been selected to increase the dataset
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following the same criteria as described above.
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The areas of endemism used are illustrated in Fig. 1. They have been delimited by the
presence of a unique combination of taxa (Axelius, 1991).
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Following the recommendations made in Turner et al., all taxa occurring outside the
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regions of interest were discarded. That is, terminal taxa were merely deleted and the branch
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pruned from the cladogram. In total, 18 areas of endemism were defined (Table 1).
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Taxon cladograms
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Tables 2 presents the list of taxa used by Turner et al. (2001) (all details are available
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here:
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http://www.blackwellpublishing.com/products/journals/suppmat/jbi/jbi526/jbi526sm.htm).
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Table 3 presents the additional dataset. The new dataset consists of 35 cladograms with a total
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of 839 species (see Appendix S1 for all distributions).
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Three-item analysis
The taxon cladograms were constructed using three-item analysis (3ia), a method
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designed to represent taxon relationships directly, rather than as binary variables. Thus, for an
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area cladogram AB(CD)), there are two three-item statements (3is), A(CD) and B(CD), for
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the area cladogram A(B(CD)), there are four three-item statements, A(BC), A(BD), A(CD),
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B(CD) and so on. For each area cladogram, the suite of three-item statements obtained are
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fitted to an optimal tree, that which accommodates the greatest number of statements.
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A new computer program, LisBeth v.1.3 (Zaragüeta-Bagils et al. 2012)
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(http://infosyslab.fr/downloadlisbeth/LisBeth.exe), has been developed in order to analysis
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three-item statements for biogeographical characters using a new method of implementation
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of three-item analysis (3ia) (Nelson & Ladiges 1991a, b, 1992; Nelson & Platnick 1991).
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LisBeth finds optimal trees by applying a compatibility analysis (Estabrook et al., 1976) to the
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suites of three-item statements (Cao 2008; Zaragüeta-Bagils et al. 2012). In biogeography,
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there are two well-known problems: redundant areas due to taxic paralogy (i.e. taxon
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diversification prior to area duplication) and widespread taxa (or Multiple Areas in Single
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Terminals [MASTs] according to Ebach et al. 2005) are respectively resolved using Paralogy-
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free Subtree analysis (Nelson and Ladiges 1996) and the ‘transparent method’ (Ebach et al.
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2005), the latter implements a version of Assumption 2 (Nelson and Platnick 1981).
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LisBeth builds a summary tree, called an intersection tree (Cao et al. 2009), by
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combining the three-item statements present in all optimal trees; the intersection tree can be
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viewed as the minimal tree (for more details, see Zaragüeta-Bagils et al. 2012) and is rooted
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since it is reconstructed from 3is. LisBeth uses taxon-area cladograms (TAC) as ‘characters’
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rather than the usual binary characters displayed in a tabular matrix. Thus, LisBeth utilises the
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paralogy-, MAST-free TACs (Cao et al. 2007).
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It is not the intention of this paper to described all the features of LisBeth . Here we
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simply draw attention to one new tool which traces the distribution of taxa that ‘support’ each
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node (see Fig. 5, Table 5 and Appendix 2 for full algorithm); this ‘support’ is analogous to the
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concept of synapomorphy in systematics.
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The large number of areas analysed (18) was accommodated by exporting three-area
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statements into a NEXUS matrix for analysis in PAUP* 4b10 (Swofford, 2003; Zaragüeta-
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Bagils et al., 2012), which was used to find optimal taxon-area cladograms. These were then
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imported into LisBeth to reconstruct an intersection tree (Zaragüeta-Bagils et al., 2012). We
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offer one word of caution. The result from the intersection tree method implemented in
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LisBeth 1.3 cannot be interpreted as a cladogram whenever polytomies are present. We are
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currently working on an implementation for a new tree calculation that will fix this
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inconsistency (in version 1.4, in prep., Zaragüeta-Bagils et al. in prep.). However, this
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problem is not relevant in this case as there are only two polytomies, one which is perfectly
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explained as artifact (see Results) due to sampling and the other concerns clade C, which is a
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terminal clade. The full procedure to run a biogeographical analysis with LisBeth 1.3 is
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described in Appendix S2 of Hoagstrom et al. (2014).
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Results
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Fig. 2 shows the optimal intersection tree derived from the analysis of the 35 taxa
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cladograms selected: 1016 characters were extracted and 27 compatible trees were found.
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For the intersection tree (Fig. 2), the overall retention index (RI) = 0.848 and the
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Completeness Index (Compl) = 56,6% (see Zaragüeta-Bagils et al. 2012 for an explanation of
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the completeness index). The 3ia analysis yields a reasonably quite resolved cladogram of the
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areas in SEA-WP: thirteen nodes (clades) are identified (Table 4).
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A general pattern emerges from the 3ia analysis (Fig. 3): The tree is clearly divided in
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two parts separating the Pacific islands (Fig. 3, ‘Pacific’ clade and Table 4) from the rest of
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Southeast Asia (Fig. 3, ‘Southeast’ Asian clade—‘Australian’ clade). The first part is named
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the ‘Pacific’ clade in reference to its location. The second part is named the “Australian”
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clade. That is, the clade separate from the rest of the Archipelago. Apart from the unresolved
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basal position of the Lesser Sunda Islands (due to the few number of taxa distributed there),
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Weber’s (1902) line is clearly identified, which is said to trace ‘the boundary of the North
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Moluccas, separating first Timor and Australia and then, between the islands of the Babar and
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Tanimbar groups, west around Buru and Halmahera and to the Pacific’ (van Oosterzee, 1997:
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00) (Fig. 4). In all, five clades are distinguishable: ‘Pacific’ (clade K), ‘Australian’ (clade I),
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‘Indonesian’ (clade H), ‘Southeast Asian’ (clade C) and ‘Wallacean’ (clade G). The latter is
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closer to the ‘Indonesian’ clade than to the ‘Southeast Asian’. Both are included in the clade
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D which in turn is sister clade to the ‘Southeast Asian’ clade. The ‘Australian’ clade (clade I)
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is closer to clade B than to the ‘Pacific’ clade despite its geographical proximity.
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DISCUSSION
The aim of this study is to find the general pattern for the area SEA-WP and illustrated
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it by areagram. The analyses were conducted as a way of testing biogeographical hypotheses.
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Van Welzen et al. (2003) reassessed the Turner et al. dataset in a unrooted analysis and they
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gained a result similar to our. They concluded that the pattern retrieved was related more to
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proximity than to cladistics relatedness. Although their result is similar to our general pattern,
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we cannot interpret them similarly. With an unrooted tree, nothing can be said regarding
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relationships between the areas as there is no root. Nonetheless, their result is still relevant for
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our purpose since it gives the same results.
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The clades found are due to specific combinations of taxa. For example, clade G
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(grouping the Moluccas islands with Sulawesi, ‘Wallacean’ clade in Fig. 3) is supported by
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the combined presence of species from the following 3 plants and 3 insects: Megarthrus,
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Rhysotoechia, Xenobates (the three insect groups), Rhododendron, Chlorocystini, and Parkia
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the three plant groups (Table 5, Fig. 5). The best-supported nodes are those with the highest
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number of taxa, those which are can be termed ‘synapomorphic taxa’. Hence, clade D is the
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best supported with 15 taxa; clade I, the ‘Australian’ clade, and clade E are supported by 13
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taxa each; 12 taxa support clade F; clades B and J are supported by 11 taxa each; clade A is
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supported by 9 taxa; clade L is supported by 7 taxa; clade G supported by 6 taxa and clades C
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(the ‘Southeast asian’ clade), K (the ‘Pacific’ clade) and M are supported by just 4
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‘synapomorphic’ taxa.
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Clade K is interesting because despite the number of taxa distributed over those areas
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(13), it gains support from only five (Cosmopsaltriina, Cyrtandra, Cupianopsis, Gehyra and
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Halobates princeps).
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In Table 5, we have indicated in bold taxa that support only one node: Erismanthus,
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Dundubia jacoona assemblage, Fordia, whose distributions are unambiguous
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‘synapomorphies’ of clades B, D, E. Calicmeniinae, Cycas and Haloveloides support clade I.
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Table 6 shows distributions of taxa and nodes supported.
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Fig. 6 illustrates their distributions to which we add the Varanus distribution because
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it supports clades J and I (J being included in I). It is noteworthy that although these taxa are
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broadly distributed over the region, each distribution supports only one area, Erismanthus
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appears as a ‘synapomorphy’ of area B, the Dundubia jaccona assemblage of area D, Fordia
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distribution supports area E, and I has the distributions of Chlorocyphidae, Cycas and
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Halobates as unambiguous ‘synapomorphies’. These results highlight the fact that, in spite of
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what seems complex biogeographical relationships, the distributions of these taxa may be
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assigned to a single area. The identification of distribution of taxa as ‘synapomorphies’ of
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biogeographical areas allows focusing the discussion on the pattern of relationships.
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Comparison with the geology
Exploring cladistics relationships between areas of endemism leads to a consideration
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of the geological history of a region of interest. In our case, regarding SEA-WP, different
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interpretations regarding its evolution because of its complex geology were discovered (e.g.
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Hamilton 1979; Holloway 1979; Duffels 1986; Hall 1998, 2002, 2011 among others). Some
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of the complexity is captured by Hall:
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“…it is clear from the geology of the region that the snapshot we see today is no less complicated than
in the past. The region has developed by the interaction of major lithospheric plates, principally those of
the Pacific, India-Australia and Eurasia, but at the present day a description only in terms of these three
plates is a very great oversimplification.” (Hall 1998: 99)
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“ The abrupt division between faunas and floras in Indonesia first recognized by Wallace in the
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According to Hall, therefore, much of the evidence that must be used in a regional
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tectonic model of SE Asia is based on the interpretation of geological data from the small
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ocean basins, their margins, and from the geologically more complicated land areas around
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them. He goes on to note:
nineteenth century, has its origin in the rapid plate movements and reorganisation of land-masses in SE
Asia” (Hall 1998: 100)
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“The reader should be aware that, as in other areas of science, geologists differ in their interpretations of
these data, and much of the information does not lend itself to unambiguous reconstruction.
Nonetheless, a complete tectonic history can only be deduced from the geology on land combined with
data from the oceans.” (Hall 1998: 105)
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In another paper from the same book, Holloway and Hall (1998) claim that to a
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geologist the dismissal of the role of dispersal is odd. Judging from the geological history of
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SE Asia it seems highly unlikely that any understanding of the biogeographic patterns can be
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achieved without considering both vicariance and dispersal. Certainly, the Cenozoic
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development of the region is characterised more by amalgamation than fragmentation.
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Nevertheless, this reasoning misses that the source of relationships of areas is based on
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relationships of distribution of taxa. These are tree-like independently of the geological
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history of the region. Moreover, a tree of areas derived from biological evidence could
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reasonably be interpreted as: the fragmentation of a previously continuous land area such as
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Gondwanaland, or Pleistocene division of Sundaland through marine transgression (Ruedi
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1995); the approach and accretion of terranes (and thus dispersal to) onto a larger land mass;
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or the slow dispersal of organisms, with speciation, through an archipelago with stable
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geography.
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The Gondwana origins of all component continental blocks of SE Asia, i.e. the core of
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Sundaland, is now widely accepted (Hall 2009, 2011, 2012; Hall et al. 2011; Metcalfe 2011).
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Sundaland was assembled from continental blocks that separated from Gondwana in the
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Paleozoic and amalgamated with Asian blocks in the Triassic (Hall 2011; Hall et al. 2011;
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Metcalfe 2011). The first event that shaped the region (about 180 Ma ago) is the break-up of
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the Gondwana which led to the separation of India and Australia-Antarctica from Africa. The
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Indian subcontinent moved northward towards Asia and collided later (at about 50 Ma ago)
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(de Boer and Duffels 1996 and references herein). Australia, which had become separated
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from Antarctica by the opening of the Tasman Sea (95 Ma ago), changed its course
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northwards (de Boer and Duffels 1996). The floor of the Thethys sea was forced to subducted
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under the Pacific plate which gave rise to a volcanic island arc (the West Pacific island arc,
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also named the Outer Melanesian arc by Duffels (1986) and Holloway (1979) although not
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entirely recognized as the same (Michaux 1994; de Boer & Duffels 1996) and simply the
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Melanesian arc system by Hall (2002)). Remnants of this West Pacific island arc have been
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recognized and are as follows: the central Philippines, northern, central, and southeastern
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New Guinea, and the Bismarck Archipelago. The collision between the Pacific plate and the
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Asian continent must have occurred about 40-42 Ma ago and caused the fracture of the West
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Pacific island with its northern western part rotating clockwise which made the central
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Philippines collide with the continental western Philippines (Rangin et al. 1990a, b; Daly et
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al. 1991; Honza 1991).
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To the east, the continuous South-West Pacific island arc (also known as the East
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Melanesian arc) is composed of current Vanuatu linked to Solomon and Fiji (de Boer 1995d
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and references therein). At about 9-12 Ma ago, it collided with the Australian continent in the
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Solomon area and simultaneously in the New Guinea area, which makes it broken up giving
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rise to Vanuatu, Fiji and the Tonga-Kermode (de Boer 1995d). By 3 Ma ago Fiji was totally
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isolated. The palaeogeographic reconstruction presented here can be summarized in the
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“cladogram-like” graph for the West Pacific island arc (Fig. 7).
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Some geological events can be drawn from examination of the geological area
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cladogram (Fig.7) and the intersection tree (Fig. 2). The main one is the vicariant event that
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separated the areas emerged from the East Melanesian Arc (sensu de Boer, 1995d).
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That scheme is consistent with our areagram. Node 11 of Fig. 2 shows that after the first
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vicariant event that has separated Samoa, successive events may be reconstructed: Vanuatu
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and New Caledonia, then Fiji and Tonga. Furthermore, this clade is revealed by the presence
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of only four taxa: Cosmopsaltriina, Cyrtandra, Gehyra, Cupaniopsis and Halobates princeps
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whose dispersal abilities varied a lot from one to another. Hence, we could hypothesize that
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those taxa were present on the Melanesian arc and that its fracture led to this distribution.
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Nonetheless, the rest of the general areagram suggest relationships emerging from
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geographical proximity (clade I, clade C, clade H and clade G). Thus, dispersal events would
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be a more probable explanation despite the different dispersal capabilities of the taxa under
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study. However, one has to keep in mind that the areagram shows relationships between areas
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of endemism that are biogeographic areas and not geographic areas even if they are given
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names from geography. Many islands in that region should be considered as separate
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fragments because they are geologically composite. For instance Sulawesi should be
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separated in three distinct areas: north, west and south (Hall 1996; Michaux 2010; Hall 2011),
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New Guinea in at least two areas, north and south (Hall 2002). The main impediment remains
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the availability of precise distributional data since most published cladograms of taxa do not
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present accurate distributions.
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Cladistic biogeography
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Biogeography and geology are often opposed, although these two disciplines are
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definitively complementary (Holloway & Hall 1998; Hall 2002, 2011; Michaux 2009). If
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there is a contradiction between them, then one discipline should not prevail. Congruence
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between geological reconstructing/modelling history and biogeographical reconstruction of
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relationships between areas of endemism emphasize the fact that both can indeed be true.
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From 35 different taxa, including both animals and plants, we have shown that a
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pattern does emerge from the analysis and, to a certain extent, fits with the most common
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geological reconstructions of SEA-WP evolution (Hall 2002, 2011, Hall et al. 2011; Metcalfe
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2011). This result emphasizes the accuracy of the 3ia method in revealing a biogeographical
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pattern that does not only consider dispersal as the main process of organism distribution.
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CONCLUSIONS
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Caledonia and Samoa from the rest, which corroborates the results of de Boer and Duffels
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who examined the historical biogeography of the cicadas of Wallacea, New Guinea and the
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West pacific (de Boer & Duffels, 1996). They compared each cicada area-cladogram with the
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geological cladogram (Fig. 7) and concluded that:
Our analysis indicates that a vicariant event separated Fiji, Tonga, Vanuatu, New
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“from the high degree of congruence between the geological cladogram and the two taxon-area
cladograms we conclude it is highly probable that vicariance caused by the fragmentation of a West and
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a South-West Pacific island arc is responsible for most of the present-day generic diversification” (de
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They intended at first to use the cladistic method of Platnick and Nelson (1978) and
Boer & Duffels 1996:174).
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Humphries & Parenti (1986), i.e. combining taxon-area cladograms based on several
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unrelated groups into a general area cladogram. Nevertheless, they considered that the area
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cladograms for the two groups of cicadas provided an insufficient basis for the construction of
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such a general cladogram. We agree: congruence among two cladograms may provide the
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weakest support. Indeed, their general argument strengthens our case, as we combined 35
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different taxon cladograms from both plants and animals and obtained the general areagram
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shown in Fig. 2 where relationships between the areas of endemism can be discussed in term
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of combination of taxa that supported the nodes of the tree. Our analysis has recovered five
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‘monophyletic’ clades : ‘Pacific’ (clade K), ‘Australian’ (clade I), ‘Indonesian’ (clade H),
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‘Southeast asian’ (clade C) and ‘Wallacean’ (clade G) supported by a certain assemblage of
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taxa. Furthermore, Weber’s Line is revealed which confirms that drawing lines is informative.
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Systematic biogeography is similar to phylogenetic systematics in that proposal of area
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relationships to be tested and accepted or rejected in an effort to form relevant area
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classifications (Parenti & Ebach, 2009). 3ia is a straightforward method that serves historical
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biogeographic purposes. The hierarchical representation of knowledge available in LisBeth
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authorise new discussions in term of relationships between areas towards a natural
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classification.
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ACKNOWLEDGEMENTS
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Visotheary UNG is grateful to Peter van Welzen for reviewing a draft of the manuscript and
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for fruitful discussions about the biogeography of the region.
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The authors would like to thank several anonymous referees for constructive critiques of
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previous version of the manuscript.
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This research is supported by a grant (I3iaSEAB, AAP-IN-2009-033) from the Fundation for
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Research on Biodiversity (FRB).
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SUPPORTING INFORMATION
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Appendix S1: Distributions of all taxa in the corresponding areas.
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Appendix S2: Algorithm for traceability of characters.
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