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Most analyses of polymorphism and divergence were performed using the DnaSP program [39].
Basic analyses of polymorphism and divergence were performed using the computer program DNAsp [30].
Molecular clock estimates of divergence were performed to corroborate the geologic timing of hypothesized isolating barriers (Table 1).
Estimates of genetic divergence were performed in Mega 5.0 [ 51].
All analyzes of sequence divergence were performed using scripts written in BioPython (Cock et al. 2009).
Basic analyses of genetic polymorphisms and divergence were performed using DnaSP v5 [ 60].
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The analysis of functional divergence was performed using DIVERGE v2.0 [ 61].
An analysis of genetic divergence was performed using DNAsp vs 5.00.07 [ 79] using the 31 selected housekeeping genes.
In order to present a clearer view of trends at different levels of divergence, analyses were performed on high and low divergence read pools separately rather than considering divergence level directly as an independent variable.
G+C content and sequence divergence calculations were performed using shareware programs respectively: GCUA (General Codon Usage Analysis) [43] and SNAP (Synonymous Non-synonymous Analysis Program; www.hiv.lanl.gov) [22].
Nucleotide diversities and species divergence calculations were performed using MEGA 4.1 [ 25] and DnaSP v5 [ 31].
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