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.