To assemble data sets suitable for demographic analysis (see below), reference strains from epidemiologically unlinked individuals were chosen according to the following criteria: 1. known country were the infection was acquired; 2. known year of sampling, and 3. sequences from therapy naïve subjects and/or without known mutations associated with drug-resistance.
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SNPs are characterized by low mutation rate and low probabilities of back and parallel mutation, making SNP analysis suitable for tracing early demographic events in human history.
Species-wide sampling is appropriate for testing for deviations from neutral equilibrium if metapopulation dynamics apply [6], and may also be suitable for inferring major demographic changes in a species' history [7] [10].
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The Iberian Peninsula provides a suitable region for examination of the demographic impact of such recent events, because its complex recent history has involved the long-term residence of two very different populations with distinct geographical origins and their own particular cultural and religious characteristics North African Muslims and Sephardic Jews.
The mutation rate of STRs is much higher than that of SNPs and, therefore, the former are suitable for investigating details of demographic events occurring on a more recent time-scale.
Although mismatch distributions for these two populations did not perfectly fit the expected pattern under the sudden expansion model, they did not differ significantly (P > 0.05) from this model and therefore were suitable for the analysis of demographic patterns.
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Actiheart data were non-valid (i.e. < 2 days of accelerometer recordings for at least 360 minutes between 6.00 am-11.00 pm) in 136 children, and imputation of independent mobility and socio-demographic data was not suitable for 35 children because responses such as 'Other' and 'Don't go there' could not be classified into available response categories.
However, species-wide samples are not suitable for investigating population processes of divergence, demographic change, and local adaptation.
