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

Jeffries, Daniel L.; Copp, Gordon H.; Lawson Handley, Lori; Olsén, K. Håkan; Sayer, Carl D.; Hänfling, Bernd

Abstract

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

Citation

Jeffries, D. L., Copp, G. H., Lawson Handley, L., Olsén, K. H., Sayer, C. D., & Hänfling, B. (2016). Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L. Molecular ecology, 25(13), 2997-3018. https://doi.org/10.1111/mec.13613

• Journal Article Type: Article
• Acceptance Date: Feb 29, 2016
• Online Publication Date: Mar 12, 2016
• Publication Date: 2016-07
• Deposit Date: Jun 27, 2016
• Publicly Available Date: Jun 27, 2016
• Journal: Molecular ecology
• Print ISSN: 0962-1083
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 25
• Issue: 13
• Pages: 2997-3018
• DOI: https://doi.org/10.1111/mec.13613
• Keywords: Approximate Bayesian computation, Postglacial recolonisation, Landscape genetics, Conservation biology, Study design, Population structure
• Public URL: https://hull-repository.worktribe.com/output/474274
• Publisher URL: http://onlinelibrary.wiley.com/doi/10.1111/mec.13613/abstract
• Additional Information: Authors' accepted manuscript of article published in: Molecular ecology, 2016, v.25, issue 13.
• Contract Date: Jun 27, 2016