Geography Reference
In-Depth Information
PAE may be used for panbiogeographic analyses, where the clades ob-
tained are considered generalized tracks (Craw et al. 1999; Luna-Vega et al.
2000; Morrone and Márquez 2001). With the aim that the “1” appears only
once and does not revert to “0” (as in a compatibility analysis), Luna-Vega
et al. (1999) undertook the parsimony analysis with PAUP 4.0.1 (Swofford
1999), setting Goloboff concavity
k
= 0. Luna-Vega et al. (2000) and García-
Barros et al. (2002) proposed that when the most parsimonious cladograms
have been obtained, it is possible to remove or exclude the taxa supporting
the different clades and analyze the reduced matrix to search for alternat-
ive clades supported by other taxa. This procedure has been named parsi-
mony analysis of endemicity with progressive character elimination (PAE-
PCE) (García-Barros 2003; García-Barros et al. 2002).
Equal (nondifferential) weighting is usually used for PAE. However,
Linder (2001) suggested a protocol to weight species inversely to their dis-
tribution areas so that widespread species do not obscure the analyses by
introducing homoplasy into the data. It consists of four steps:
1. Weighteachspeciesineachgridcellbytheinverseofitsdistributionrange
so that a species restricted to a grid cell would be scored as 1, a species
restricted to two grid cells as 0.5, three grid cells as 0.33, and so forth.
2. Transform the values to a scale of 0-20, multiplying each by 20 and round-
ing the product. This results in a matrix with values of 20 (single-grid en-
demics), 10 (two-grid endemics), 7 (three-grid endemics), and so forth.
3. Simplify the matrix by changing the 20s and 10s to 9 (because single-
grid species carry no grouping information in a parsimony analysis) so that
each species will be represented by a single-digit value in each grid cell
score.
4. Input the matrix into a parsimony analysis, treating the characters' states
(0 to 9) as additive.
PAE has received some criticism. Linder and Mann (1998) criticized Mor-
rone's (1994b) approach for identifying areas of endemism with PAE be-
cause grid cells can be used only as presence-absence data, and under-
collecting may result in grid cells being omitted. Some authors suggested
that PAE is not a valid historical method because it does not take into ac-
count the phylogenetic relationships of the taxa analyzed (García-Barros et
al. 2002; Humphries 1989, 2000; Santos 2005). According to Rosen (1988b;
see also Nihei 2006; Trejo-Torres 2003; Trejo-Torres and Ackerman 2002),