PACT: an efficient and powerful algorithm for generating area cladograms

Abstract

Aim To introduce and describe the functioning of a new algorithm, phylogenetic analysis for comparing trees (PACT), for generating area cladograms that provide accurate representation of information contained in taxon–area cladograms. Methods PACT operates in the following steps. Convert all phylogenies to taxon–area cladograms. Convert all taxon–area cladograms to Venn diagrams. Choose any taxon–area cladogram from the set of taxon–area cladograms to be analysed and determine its elements. This will be the template area cladogram. Select a second taxon–area cladogram. Determine its elements. Document which elements in the second tree occur in the template tree (denoted by ‘Y’) and which do not (denoted by ‘N’). Each ‘Y’ indicates a match with previous pattern and these are combined. Each ‘N’ is a new element and is attached to the template area cladogram at the node where it is linked with a Y. This requires two rules: (1) ‘Y + Y = Y’ (combine common elements) as long as they are connected at the same node; and (2) ‘Y + N = YN’ (add novel elements to the template area cladogram at the node where they first appear). Once the novel elements in the second taxon–area cladogram have been added to the template area cladogram, see if any of them can be further combined. This requires three additional rules: (1) ‘Y(Y− = Y(Y−’ (do not combine Y's if they are attached at different nodes on the template area cladogram); (2) ‘Y + YN = YN’ (Y is part of group YN); and (3) ‘YN + YN = YNN’ (Y is the same for each, but each N is different). Repeat for all available taxon–area cladograms. Results Three exemplars demonstrate that PACT provides the most accurate area cladograms for vicariance‐driven biotic diversification, dispersal‐driven biotic diversification and taxon pulse‐driven biotic diversification. PACT can also be used as an a priori method of biogeographical analysis. Main conclusions PACT embodies all the strong points and none of the weaknesses of previously proposed methods of historical biogeography. It is most useful as an a posteriori method, but it is also superior to all previous a priori methods because it does not specify costs, or weights or probabilities, or likelihoods of particular biogeographical processes a priori and is thus sensitive to clade‐specific historical contingencies.

A biophysical perspective on dispersal and the geography of evolution in marine and terrestrial systems

“…Analytical approaches in, for example, biogeography are equally applicable to data from marine and terrestrial systems (e.g. Marshall & Liebherr 2000;Santini & Winterbottom 2002;Wojcicki & Brooks 2005; but see Siddall 2005), and the coupled biophysical models increasingly employed to study dispersal of marine larvae (e.g. Cowen et al 2000Cowen et al , 2006Galindo et al 2006) can be expected to promote similar approaches to studying aerial dispersal (e.g.…”

Historical Biogeography: Evolution in Time and Space

“…Cladistic biogeographers use different methods that differ in the way they treat these ambiguous data to derive a "resolved" area cladogram in which each area is represented only once (Fig 1c, right). These include Component Analysis (Nelson and Platnick 1981;Page 1990), Brooks Parsimony Analysis (BPA, Brooks 1990;Wiley 1988), Tree Reconciliation (Page 1994), and Paralogy-free subtrees (Nelson and Ladiges 1996) and more recently, Phylogenetic Analysis for Comparing Trees (PACT, Wojciki and Brooks 2005) and Threearea-cladistics (Ebach et al 2003); see Crisci et al 2003 andMorrone 2009 for a more detailed explanation on these methods. An area cladogram is a hierarchical, branching pattern of relationships that groups areas based on their shared endemic taxa and which presumably reflects the history of biotic connections between the areas of endemism for the group of organisms analyzed.…”

“…These unique events that affect single lineages can include extinction, postspeciation range expansion, jump dispersal, or failure to speciate in response to a vicariant event (Wojciki and Brooks 2005;Lieberman 2000Lieberman , 2003Stigall and Lieberman 2005). Still, these methods share the goal with standard cladistic approaches of producing "area cladograms," hierarchical patterns of biotic relationships between areas of endemism that are interpreted in terms of processes (e.g., Maguire and Stigall 2008), but which are inferred without explicit reference to an underlying statistical process model (see below).…”

The historical biogeography of Mammalia

“…Another recent approach that builds on earlier cladistic biogeography methods is phylogenetic analysis of comparing trees (PACT) [45][46][47]. Unlike earlier cladistic biogeography methods, PACT explicitly incorporates molecular dates into general area cladograms.…”