Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L.

• DOI: 10.1111/mec.13613
• Publication Date: 2016-03-14T06:34:29Z
• Authors: Daniel L. Jeffries; Gordon H. Copp; Lori Lawson Handley; K. Håkan Olsén; Carl D. Sayer; Bernd Hänfling
• Keywords: Carassius; Crucian carp

The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomized the freshwater fish Carassius carassius, which in decline across much its European range. Restriction site-associated DNA sequencing (RADseq) increasingly used for such applications; however, RADseq expensive, and limitations on sample number weighed against benefit large numbers markers. trade-off has previously been examined using simulation studies; empirical comparisons between these markers, especially a context, are lacking. Here, we compare results from microsatellites phylogeography C. carassius to test whether it more advantageous genotype fewer markers (microsatellites) many samples, or (SNPs) samples. These data sets, along with mitochondrial cytochrome b gene, agree broad patterns, showing existence two unidentified lineages Europe: one found throughout northern central-eastern drainages second almost exclusively confined Danubian catchment. have isolated approximately 2.15 m years should considered separate units. recovered finer population structure stronger patterns IBD than microsatellites, despite including only 17.6% samples (38% populations 52% per population). was also approximate Bayesian computation show that postglacial colonization routes differ general Europe, likely as result their distinctive ecology.