Fig. 1

Overview of the analysis. Step 1 of the workflow illustrates DNA extraction and target capture sequencing. Step 2 includes standard NGS data clean - up steps such as read trimming, mapping to reference, and variant calling performed as described in the “Sequence and haplotype assembly” subsection of the methods. Haplotypes were phased using assembly with the HapCompass program, which utilizes the fact that alleles of different markers will co-occur in NGS reads if they are present within same the haplotypes. Step 3 of the workflow includes a procedure for identifying regions of contiguous haplotype assembly across individuals represented by haplotypes within the alignments. Then standard steps in phylogeny reconstructions are included to obtain gene phylogenies. However, since some alignments were short with few informative sites, we used the SH test to evaluate if alignments do contain detectable phylogenetic signal. Step 4 of this workflow illustrates inference of a species tree from a set of gene trees. Step 5 depicts the summarizing of gene trees into consensus network. Step 6 shows the testing of candidate hybridizations in an ILS-aware framework