Marine Area Relationships from Twenty Sponge Phylogenies. A Comparison of Methods and Coding Strategies

Abstract

Published phylogenies of 20 marine sponge groups are used to build general area cladograms of marine areas of endemism under three different methods for which algorithms adapted for personal computers are available, viz. COMPONENT, BPA and TAS, and two different coding strategies, Assumption 0 (A0) and "no assumption" (NA). The latter is a recently proposed procedure for handling the distributions of widespread taxa by treating these as separate areas of endemism, rather than as suites of smaller constituent areas. The 20 phylogenies contained large numbers of problem data which prevented an exhaustive search for all possible equally "best" general area cladograms. The Nelson consensus trees and their equivalents in parsimony analysis for all six attempts (viz. three different methodologies under two different coding strategies) were compared using their fit with the 20 sponge phylogenies as a measure of quality. Fit was determined using the number of "cospeciations" between a general area cladogram and a taxon area cladogram computed with TreeMap 1.0. No single method or coding strategy yielded a clearly better fit, each cladogram fitting variously better or worse with various phylogenies. In general, fit with NA coding was higher than with A0 coding, but random tree tests failed to generate statistically significant support for the conclusion that NA coding improves fit. Assuming that available sponge phylogenies are representative of marine benthic groups, software and hardware limitations are serious obstacles to a successful development of marine general area cladograms under any method or coding strategy.

Biological geography of the European seas: results from the MacroBen database

“…For example, the provinces of Briggs (1995) were primarily defined using fish species distributions, those of Pierrot-Bults & Nair (1991) using chaetognaths, whereas Van Soest & Hajdu (1997) used sponges, Glasby (2005) used polychaetes, and Deprez (2006) used hyperbenthic mysids. However, even in the studies using multi-taxon distributions, rigorous hypothesis testing to validate findings has rarely been attempted.…”

Hovenkamp's ostracized vicariance analysis: testing new methods of historical biogeography

“…Particularly problematic is the choice among different assumptions in CA. This problem has been strongly debated recently (Van Soest and Hajdu, 1997; Enghoff, 1998; Ebach, 1999; Van Veller et al., 1999, 2000, 2001a,b; Van Veller and Brooks, 2001), and Ebach (2001) and Ebach and Humphries (2002) pointed out that if the cause of ambiguity is not allopatry, using A0 or BPA adds spurious information, leading researchers to extrapolate beyond reason. To better manage with reticulate processes, Brooks and colleagues have proposed a modified version of BPA (e.g., Brooks, 1990; Brooks et al., 2001; Brooks and McLennan, 2002).…”

When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography

“…For all a posteriori methods, that conceptual framework is one of complexity, i.e. that nature may have regularities but also has exceptions (perhaps many exceptions) to those regularities, including the possibility that areas can have reticulated biological histories (see also Cracraft, 1988, 1994; Brooks, 1990; Axelius, 1991; Brooks & McLennan, 1991; Crother & Guyer, 1996; Hovenkamp, 1997; Van Soest & Hajdu, 1997; De Jong, 1998; Marshall & Liebherr, 2000; Green et al ., unpublished data). BPA compensates for flaws in the null hypothesis by falsifying the null hypothesis; each area duplication in a secondary BPA represents an empirical falsification of the null hypothesis that the data can be explained by listing each area once.…”

“…Because areas may be duplicated in both Component 2.0 (by lineage duplication) and secondary BPA (by area duplication), comparison of the area cladograms obtained with Component 2.0 and secondary BPA is more appropriate than comparison of the results obtained with Component 2.0 and primary BPA, as has been carried out previously (e.g. Page, 1990b; Crisci et al ., 1991; Nelson & Ladiges, 1991b; Morrone & Carpenter, 1994; Morrone & Crisci, 1995; Van Soest & Hajdu, 1997; Page & Charleston, 1998). This exemplar shows that Component 1.5, Component 2.0, primary BPA and secondary BPA all derive the same general area cladogram.…”

“…Despite these two different ways of deriving resolved area cladograms ( sensu Morrone & Carpenter, 1994; Enghoff, 1996), the methods in both categories share the same null hypothesis, vicariant speciation, and make the assumption that phylogenetic and distribution data of taxa are informative for the reconstruction of the historical relationships among their areas of distribution (Brooks & McLennan, 1991; Ronquist, 1997a,b). As a result, researchers comparing the methods have generally assumed that they are designed to implement the same research programme and share a common conceptual framework (Crisci et al ., 1991; Morrone & Carpenter, 1994; Morrone & Crisci, 1995; Van Soest & Hajdu, 1997).…”