Data from: Comparing the performance of microsatellites and RADseq in population genetic studies: analysis of data for pike (Esox lucius) and a synthesis of previous studies

Population genetic studies reveal biodiversity patterns and inform about
drivers of evolutionary differentiation and adaptation, including gene
flow, drift and selection. This can advance our understanding and aid
decision making regarding management and conservation efforts.
Microsatellites have long been used in population genetic studies.Thanks
to the development of newer techniques, sequencing approaches such as
restriction site associated DNA sequencing (RADseq) are on their way to
replace microsatellites for some applications. However, the performance of
these two marker types in population genetics have rarely been
systematically compared. We utilized three neutrally and
adaptively differentiated populations of anadromous pike (Esox lucius)
to assess the relative performance of microsatellites
and RADseq with respect to resolution and conclusiveness of estimates of
population differentiation and genetic structure. To this end, the same
set of individuals (N = 64) were genotyped with both RADseq and
microsatellite markers. To assess effects of sample size, the same subset
of 10 randomly chosen individuals from each population (N = 30 in
total) were also genotyped with both methods. Comparisons of estimated
genetic diversity and structure showed that both markers
were able to uncover genetic structuring. The full RADseq dataset
provided the clearest detection of the finer scaled genetic structuring,
and the other three datasets (full and subset microsatellite, and subset
RADseq) provided comparable results. A search for outlier loci
performed on the full SNP dataset poninted to signs of selection
potentially associated with salinity and
temperature, exemplifying the utility of RADseq to inform about
the importance of different environmental factors. To evaluate
whether performance differences between the markers are general or context
specific, the results of previous studies that have investigated
population structure using both marker types were synthesized. The
synthesis revealed that RADseq performed as well as, or better than
microsatellites in detecting genetic structuring in the included studies.
The differences in the ability to detect population structure, both in the
present and the previous studies, are likely explained by the
higher number of loci typically utilized in RADseq compared to
microsatellite analysis, as increasing the number
of markers will (regardless of the marker type) increase power
and allow for clearer detection and higher resolution of genetic
structure.