Geography Reference
In-Depth Information
Software
DNAMLK of package PHYLIP (Felsenstein 1993), BASEML of
package PAML (Yang 1997), QDATE (Rambaut and Bromham 1998),
PHYBAYES (Aris-Brosou and Yang 2001), RHINO (Rambaut 2001), max-
imum likelihood clock optimization method of PAUP (Swofford 2003), PATH
(Britton et al. 2002), BEAST (Drummond and Rambaut 2003),
MULTIDIVTIME (Thorne and Kishino 2002), TREEEDIT (Rambaut and
Charleston 2002), and R8s (Sanderson 2003).
Empirical Applications
Bossuyt et al. (2006), Caccone et al. (1997), Chen
et al. (2007), Doadrio and Carmona (2003), Fritsch (2001), Hewitt (2004),
Hibbett (2001), Jansa et al. (2006), Krzywinski et al. (2001), Lalueza-Fox et
al. (2005), León-Paniagua et al. (2007), Magallón and Sanderson (2005),
Morell et al. (2000), Olmstead and Palmer (1997), Poux et al. (2005, 2006),
Renner et al. (2001), Ribas et al. (2005), Robalo et al. (2006), Tavares et al.
(2006), Voelker (1999), Waters et al. (2000), Won and Renner (2006), Xiang
et al. (1996, 1998), Yuan et al. (2005), Zakharov et al. (2004), and Zink et
al. (2002).
Primary freshwater fishes, those that are intolerant to marine conditions, have had
an important role in the development of evolutionary biogeographic hypotheses.
Most authors have used them as a model for studying the paleobiogeography of
European rivers, usually from a dispersalist perspective. Banarescu (1992) wrote
that the current distribution of European freshwater fishes resulted from dispersal
through eastern Asia into Siberia toward Central Europe and the Mediterranean,
after the Turgai Strait was closed 35 mya. In contrast with these ideas, Bianco
(1990) suggested that the Mediterranean peninsulas were colonized from the
south, by crossing of the Mediterranean Sea during the Messinian salinity crisis
(5.3mya),whentheMediterraneanbasinwasalmostcompletelydriedupandthen
refilled with freshwater from the Sarmatic Sea. This is known as the Lago Mare
hypothesis. Doadrio and Carmona (2003) analyzed the phylogenetic relationships
of the Cyprinid genera
Chondrostoma
and
Squalius,
both widely distributed in Eur-
asia, on the basis of the mitochondrial cytochrome b gene in order to test the ef-
fect of the Mediterranean Lago Mare hypothesis on their speciation and geograph-
ic distribution. For each genus, complete nucleotide sequences of cytochrome b
were recovered from populations of different species. The Bayesian analysis was
performed with MrBayes version 3.0 (Huelsenbeck and Ronquist 2001). In order
to examine whether lineages evolved according to a molecular clock, the Likeli-
