Data from: Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer

Introgressive hybridization offers a unique platform for studying the
molecular basis of natural selection acting on mitogenomes. Most of the
mtDNA protein-coding genes are extremely conserved; however, some of the
observed variations have potentially adaptive significance. Here, we
evaluated whether the evolution of mtDNA in closely related roe deer
species affected by widespread mtDNA introgression is neutral or adaptive.
We characterized and compared 16 complete mitogenomes of European
(Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four
of Siberian origin introgressed into European species. The average
sequence divergence of species-specific lineages was estimated at 2.8% and
varied across gene classes. Only 21 of 315 fixed differences identified in
protein-coding genes represented nonsynonymous changes. Only three of them
were determined to have arisen in the C. pygargus lineage since the time
to the most recent common ancestor (TMRCA) of both Capreolus species,
reflecting a decelerated evolutionary ratio. The almost four-fold higher
dN/dS ratio described for the European roe deer lineage is constrained by
overall purifying selection, especially pronounced in the ND4 and ND5
genes. We suggest that the highly divergent C. capreolus lineage could
have maintained a capability for genomic incorporation of the
well-preserved and almost ancestral type of mtDNA present in C. pygargus.
Our analyses did not indicate any signs of positive selection for Siberian
roe deer mtDNA, suggesting that the present widespread introgression is
evolutionarily neutral.