title: Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L.
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.
authors.affiliation: Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK.|Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Jeffries
authors.affiliation: Salmon & Freshwater Team, Cefas, Pakefield Road, Lowestoft, Suffolk, NR33 0HT, UK.|Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK.
authors.forename: Gordon H
authors.initials: GH
authors.lastname: Copp
authors.affiliation: Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK.
authors.forename: Lori
authors.initials: L
authors.lastname: Lawson Handley
authors.affiliation: School of Natural Science, Technology and Environmental Studies, Södertörn University, Alfred Nobels allé 7, Flemingsberg, Huddinge, 141 89, Sweden.
authors.forename: K Håkan
authors.initials: KH
authors.lastname: Olsén
authors.affiliation: Environmental Change Research Centre, Department of Geography, University College London, Pearson Building, Gower Street, London, WC1E 6BT, UK.
authors.forename: Carl D
authors.initials: CD
authors.lastname: Sayer
authors.affiliation: Evolutionary Biology Group, School of Biological, Biomedical and Environmental Sciences, University of Hull, Hardy Building, Hull, HU6 7RX, UK.
authors.forename: Bernd
authors.initials: B
authors.lastname: Hänfling
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002347:Carps / Q000235:genetics*; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D005060:Europe; D056426:Genetic Loci; D005828:Genetics, Population; D060005:Genotyping Techniques / Q000379:methods*; D018895:Microsatellite Repeats; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: approximate Bayesian computation; conservation biology; landscape genetics; population structure; postglacial recolonization; study design