Summary of dataset structure types found in our comparative analyses.

1Consensus support was arbitrarily considered moderate for datasets with 30–60% of branches supported by at least two fragments and High for datasets with more than 60%.
2Bootstrap support was arbitrarily considered moderate for datasets with 40%–60% of branches supported by bootstrap higher than 80% and High for datasets with more than 60% with bootrstrap value higher than 80%.
3Topological incongruence was considered moderate for datasets with 20–40% of branches with n-1 fragments topologically incompatible with the validity of the near-clade in the concatenated tree and high incongruence was considered for datasets with more than 40% of branches with n-1 fragments topologically incompatible.
4Significant NJ-LILD after Bonferroni correction.
*Thresholds are only used to define limits to different genetic structure types, which clearly emerge from a visual comparison of Figures 1, 2 and 3, S2, S3 and S4. It is important to note that the used thresholds are applicable to define structure types when only datasets around 24 STs are used.