Data from: Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes

During the last years, simple sequence repeats (SSRs, also known as
microsatellites) and single-nucleotide polymorphisms (SNPs) have become
the most popular molecular markers for describing neutral genetic
variation in populations of a wide range of organisms. However, only a
limited number of studies has focused on comparing the performance of
these two types of markers for describing the underlying genetic structure
of wild populations. Moreover, none of these studies targeted fungi, the
group of organisms with one of the most complex reproductive strategies.
We evaluated the utility of SSRs and SNPs for inferring the neutral
genetic structure of Armillaria cepistipes (basidiomycetes) at different
spatial scales. For that, 407 samples were collected across a small
(150 km2) area in the Ukrainian Carpathians and a large (41 000 km2) area
in the Swiss Alps. All isolates were analyzed at 17 SSR loci distributed
throughout the whole genome and at 24 SNP loci located in different
single-copy conserved genes. The two markers showed different patterns of
structure within the two spatial scales studied. The multi-allelic SSR
markers seemed to be best suited for detecting genetic structure in
indigenous fungal populations at a rather small spatial scale (radius of
~50-100 km). The pattern observed at SNP markers rather reflected ancient
divergence of distant (~1000 km) populations that in addition are
separated by mountain ranges. Despite these differences, both marker types
were suitable for detecting the weak genetic structure of the two A.
cepistipes populations investigated.