These records where assigned the quality label G. Subsequently, in step 3, the workflow performs an environmental congruence analysis: it checks that occurrence records are not located in the sea or lakes.
Moreover, some spoligotype signatures could also be used as an independent reference for congruence analysis, especially when LSP analysis was not informative.
14 We also performed congruence analysis to calculate a congruence coefficient using the free software, Orthosim 2.1.
Future efforts will aim to develop programs that speed up the construction of haplowebs from FASTA sequence alignments and help perform the congruence analysis outlined in this article.
F1 hybrids present a more difficult problem since they cannot be detected by a congruence analysis such as our bipartition scoring approach.
We computed GFA using all three combinations, and used the factors for common components shared by each data set in the congruence analysis.
We also performed Mantel's randomization test using 'ade4' R package (Dray and Dufour, 2007) and obtained similar results to those of Kendall-based congruence analysis.
The results of the congruence analysis presented in Table 4 show that 25 (60%) of 42 of the pairwise comparisons of the 7 MLST loci were incongruent.
To determine how strong the phylogenetic signal is present in the signature topology, a congruence analysis of phylogenetic trees [ 40] can be performed.
As with any taxonomic congruence analysis, the resulting trees are often then either inspected to identify discordant relationships implied by the different trees or tested statistically to evaluate whether they are more similar than expected by chance.
Congruence analysis, on the other hand, reveals the variety of evolutionary signals in the underlying collection of genes, and thus provides a more conservative interpretation of the phylogenomic signals, thereby informing data collation strategies.
