Results
SNPs were considered species-diagnostic for 55 out of 64 markers, with
missing data amounting to 2.7% (Table S.2). Significant deviations from
Hardy-Weinberg equilibrium (heterozygote deficit) were found four times
in four populations, involving the loci BF, mrpl41 and sostdc1. Per
population deviations were significant three times in populations 10, 13
and 21. No significant pairwise linkage disequilibrium was detected per
locus pair or population. Admixture linkage disequilibrium was
significant for population 13. The water bodies involved in significant
instances of heterozygote deficit and admixture linkage disequilibrium
were highly isolated and had small dimensions (< 3
m2).
Protein functions were described for the 47 markers that could be
annotated (Table S.3). Interactions were uncovered among nine marker
pairs; however, these markers do not appear to be co-expressed or
involved in significant deviations from Hardy-Weinberg equilibrium. All
markers were included in downstream analyses, as they appear to be
physically and functionally unlinked.
Structure classified 20 individuals from two populations (nos. 1 and 2)
as admixed and 334 individuals from 30 populations (nos. 3 - 32) asT. pygmaeus (Table S.4). For mtDNA, the SNP allele representing
the T. marmoratus haplotype was found in populations 1 and 2, and
the T. pygmaeus allele was found in all other populations.
Allelic profiles consistent with enclave formation or genomic footprints
were not observed (Table S.4). Accordingly, the genetic signature ofT. marmoratus was restricted to the previously documented enclave
and displayed notable levels of introgression with T. pygmaeus(Figure 1).
The selected two-species distribution model is represented by the
logistic equation Pm=(1/(1+exp(-0.156*Bio17+7.767), in
which Pm is the probability for the presence of T.
marmoratus at the locality investigated, on a zero to unity scale and
bio17 is ‘precipitation of driest quarter’. Model fit is
AUC=0.931±0.025. The model describes more arid summer conditions forT. pygmaeus (mean precipitation over 60 localities = 36.4 mm)
than for Triturus marmoratus (mean precipitation over 48
localities = 67.4 mm). The spatial interpretation of the model is shown
in Figure 2A. Temporal extrapolations of the model (or ‘hindcasts’) are
in Figure 2B for climate conditions of the Mid Holocene and in Figure 2C
for the Last Glacial Maximum.