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For molecular clock analysis the concatenated Gblock-dataset was analysed in five partitions as for the phylogenetic analyses.
For comparison and to evaluate the impact of removing ambiguous parts of the alignment on molecular clock analyses, we repeated the analysis with the raw (i.e. uncut) alignment of our data (again using the concatenated four-marker dataset in five partitions).
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The background, development and test databases were allocated evenly in three partitions, with each having 20 speakers.
Consequently, we examined cox1 in two partitions, one with first and second codon positions and one with third positions (1+2, 3).
This resulted in six partitions for myzostomids and nine partitions for hosts.
Data were simulated independently in two partitions and then concatenated to obtain a composite dataset.
The concatenated dataset was analyzed 1) without partitioning, 2) in two partitions (nuclear 28S rRNA and mitochondrial 16S rRNA + COI) and 3) in three partitions (corresponding to each marker) and topologies are compared.
A total of 584 variables were entered into a forward selection method and analyzed in two partitions.
This test examines the congruence of phylogenetic information in two partitions of data using a likelihood ratio test.
As further explained in Table 6, codon partitions with similar models and model parameters were merged, resulting in nine partitions for the Bayesian analyses.
The topology of the maximum-likelihood analyses of the concatenated three-marker dataset analyzed in three partitions is shown in Figure 1A.
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