Fig. 1
From: Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation
Concept that was used for the identification of Phytophthora hybrids using genotyping-by-sequencing (GBS) and flow cytometry. a) simplified representation of the evolution of four species and the consequences it has on one of the GBS loci concerning presence/absence of the locus and the SNPs it harbours. For the sake of clarity it does not take other biological processes into account that are important in speciation such as polyploidisation, gene duplication or other genomic rearrangements; b) simplified representation of the effect of speciation and hybridization on the genome size, the number of GBS loci and the number of alleles of each locus. The diploid non-hybrid species A-D have a similar number of GBS loci (six in this case). Genetically closely related species are expected to share more loci, while distant species are expected to present more unique loci. The proportion of shared alleles of loci common to two species will also depend on the phylogenetic distance between species (illustrated for loci 9–14). The sexual reproduction system (homo- or heterothallic) will also influence the number of alleles at a given locus. For example, the heterothallic species C will display a larger proportion of biallelic loci than the homothallic species A, B and D. The barplot is based on real numbers (see Table S4); c) colour-coded matrix that is the result of the pairwise comparison of the GBS loci as presented in Fig. 1b. The number of loci per species is determined (by adding them up horizontally in Fig. 1b) and is placed in the diagonal of the matrix. Next, the loci that are shared among each pair of species are scored vertically in Fig. 1b and the resulting number is placed in the corresponding cell in the lower triangle of the matrix. Finally, the allele similarity is determined for the shared loci and is placed in the upper triangle of the matrix; d) example of the colour-coded matrix that is the result of the pairwise comparison of the loci of P. cactorum, P. hedraiandra, P. nicotianae, P. ×serendipita and P. ×pelgrandis. Below the matrix the calculations are shown for P. cactorum, P. hedraiandra, and their hybrid P. ×serendipita (see also Table 2)