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of more than 1/100 of being incorrectly called) were excluded from the analysis or re-
sequenced. Sequences with Phred scores values between 20 and 40 (a probability between
1/100 and 1/10,000 of being incorrectly called) were checked by eye. All sequences were
manually edited and aligned using Sequencher 4.1 software (Gene Codes Corporation). CR
haplotypes were defined using MacClade (Maddison & Maddison, 2000). Haplotype
sequences were submitted to GenBank as accession numbers EF027006 to EF027092.
The model of substitution for the CR was tested in Modeltest v3.06 (Posada & Crandall,
1998) and the settings for this model were used in the phylogenetic reconstructions performed
in PAUP version 4.0b1 (Swofford, 2002). In order to investigate genealogical relationships
among Sotalia fluviatilis CR haplotypes, Union of Maximum Parsimonious Trees (UPM)
(Cassens et al . , 2005) was used to calculate and construct a network of control region
haplotypes. This method requires two consecutive steps. First, a Maximum Parsimony
analysis was performed for the CR haplotype data set and the most parsimonious trees were
saved with their respective branch lengths. We used the TBR branch-swapping (1000
replicates with random sequence addition) heuristic search option in P AUP * v.4b10
(Swofford, 2002). Second, all the saved MP trees were combined into a single reticulated
graph, merging branches (sampled or missing) that were identical among different trees (see
Cassens et al. 2005 for additional details on this analysis). The haplotype frequency was
combined with the CR haplotype network, and the final network was drawn by hand.
Analyses of diversity and population structure were performed in the program Arlequin
(Schneider et al., 2000) and restricted to the CR (577 bp) because of the larger sample size for
this locus. To evaluate genetic boundaries between the populations studied, we performed a
spatial analysis of molecular variance (SAMOVA) (Dupanloup et al . , 2002). In this analysis,
the sample localities (entered as geographic coordinates) are connected using an algorithm
and a graphical method in order to define the genetic composition of groups or population
units and to maximize the F CT index, which is the proportion of total genetic variance due to
differences between groups or populations (Dupanloup et al., 2002). Genetic differences
among the estimated populations detected in the SAMOVA analysis were then quantified by
an analysis of molecular variance (AMOVA) as implemented in Arlequin (Excoffier et al . ,
1992) based on conventional F ST and  ST statistics. The significance of the observed  ST and
F ST statistics were tested using 10,000 random permutations. The control region haplotype
and nucleotide diversity were estimated using the program Arlequin (Schneider et al . , 2000).
The number of female migrants per generation ( N mf ), as a measure of gene flow among
localities, was estimated based on the F ST value, using the equation N mf = 1/2(1/ F ST -1)
(Takahata & Palumbi, 1985) assuming Wright's island model.
R ESULTS
Phylogeography
A total of 577 bp of the CR and 425 bp of the Cyt- b gene were analyzed. For CR,
fourteen haplotypes were defined by eleven variable sites (Table 2) (For haplotype
nomenclature please refer to Caballero et al. 2007). Two haplotypes were defined for Cyt- b ,
differing by one site (for further information refer to Caballero et al., 2007). Overall, high
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