Diversity and population pattern of nuclear SNPs
Illumina reads from 13 genomes were successfully mapped on the reference with mean coverage ranging from 20,9x (Ne 125b_SW) to 32,1x (98d_Pro_SW).
None of the assemblies had to be filtered out due to low coverage and/or low Phred scores.
Patterns of population structure obtained using nuclear SNPs differed from genealogies based on maternally inherited genomes (Figure 4). In contrast to mtDNA, the structure derived by PCA from nuclear SNPs did not recognize two compact and mutually distant clusters. Instead, the distances within the geographically broader SW lineage were comparable to the majority of the SW-SE distances. One of the SW mitochondrial samples (98d_Pro_SW) was significantly closer to the SE samples, and in some analyses even positioned within the SE cluster (Figures 4, S4). Within clusters, the distances arranged along the two main axes did not reflect any obvious feature of the samples: for example, the large geographic distance between the NE125b_Kot_SW and other samples was reflected along the main axis, but the distribution of other samples was not strictly correlated with their geography (Figures 4, see map Figure 3.).
ML tree-building method yielded a similar pattern to PCA (Figures 4, S5). All SE samples clustered together with 98d_Pro_SW sample and created a monophyletic lineage with high bootstrap support. The position of Ne125b_Kot_SW remained unclear, probably due to greater genetic and geographic distance, whereas the rest of SW samples (4 specimens) clustered together.