Data from: Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander

Ecological models predict that, in the face of climate change, taxa
occupying steep altitudinal gradients will shift their distributions,
leading to the contraction or extinction of the high-elevation
(cold-adapted) taxa. However, hybridization between eco-morphologically
divergent taxa commonly occurs in nature and may lead to alternative
evolutionary outcomes, such as genetic merger or gene flow at specific
genes. We evaluate this hypothesis by studying patterns of divergence and
gene flow across three replicate contact zones between high- and
low-elevation ecomorphs of the fire salamander (Salamandra salamandra)
that have experienced altitudinal range shifts over the current
postglacial period. Strong population structure with high genetic
divergence in mitochondrial DNA suggests that vicariant evolution has
occurred over several glacial-interglacial cycles, and that it has led to
cryptic differentiation within ecomorphs. In current parapatric boundaries
we do not find evidence for local extinction and replacement upon
postglacial expansion. Instead parapatric taxa recurrently show
discordance between mitochondrial and nuclear markers, suggesting nuclear
mediated gene flow across contact zones. Isolation with migration models
support this hypothesis by showing significant gene flow across all five
parapatric boundaries. Together, our results suggest that, while some
genomic regions, such as the mitochondria, may follow morphologic species
traits and retreat to isolated mountain tops, other genomic regions, such
as nuclear markers, may flow across parapatric boundaries, sometimes
leading to a complete genetic merger. We show that despite high ecologic
and morphologic divergence over prolonged periods of time, hybridization
allows for evolutionary outcomes alternative to extinction and replacement
of taxa in response to climate change.