Geography Reference
In-Depth Information
Algorithm
The algorithm of primary BPA consists of the following steps
(Dowling 2002; Wiley 1987, 1988a, 1988b):
1. Obtain the taxonomic cladograms of the taxa distributed in the areas ana-
lyzed.
2. Replace the terminal species in the taxonomic cladograms with the areas
inhabited by them to obtain taxon-area cladograms.
3. Label the components and the widespread terminal species (assumption
0) in the taxon-area cladograms.
4. Construct a data matrix in which areas are the rows and components and
widespread terminal species are the columns, coding “1” if the area is
present and “0” if it is absent. Use “?” for missing areas. Add a row with all
“0” to root the cladogram.
5. Analyze the data matrix with a parsimony algorithm in order to obtain the
general area cladogram.
6. Optimize the components in the general area cladogram to identify vicari-
ance events (synapomorphies), dispersal events (parallelisms), and ex-
tinctions (reversals).
Software
Hennig86 (Farris 1988), PHYLIP (Felsenstein 1993), NONA (Go-
loboff 1998), PAUP (Swofford 2003), Pee-Wee (Goloboff, retrieved May
25, 2008, from
http://www.zmuc.dk/public/phylogeny/Nona-PeeWee/
)
, and
TNT (Goloboff et al., retrieved May 25, 2008, from
http://www.zmuc.dk/
public/phylogeny/TNT/
). For reading and editing data files and cladograms:
Winclada (Nixon 1999), compatible with NONA, Pee-Wee, and Hennig86;
and MacClade (Maddison and Maddison, retrieved May 25, 2008, from
ht-
tp://macclade.org/macclade.html
)
, compatible with PAUP.
Empirical Applications
Biondi (1998), Brooks (1990), Brooks and McLen-
nan (2001), Brooks et al. (2003), Contreras-Medina et al. (2007b), Cracraft
(1988),Craw(1989b),Criscietal.(1991b),CrotherandGuyer(1996),Dowl-
ing(2002),EspinosaOrganistaetal.(2006),GesundheitandMacíasGarcía
(2005), Glasby (2005), Griswold (1991), Halas et al. (2005), Kluge (1988),
Ladiges et al. (1992), Lieberman (2000), Liebherr (1991), Lovejoy (1997),
Marshall and Liebherr (2000), Mayden (1988), McLennan and Brooks
(2002), Morafka et al. (1992), Morrone and Carpenter (1994), Morrone
and Urtubey (1997), Morrone et al. (1997), Nihei and de Carvalho (2007),
Pinto-da-Rocha and da Silva (2005), Posadas and Morrone (2003), Retana-
