Genome-wide SNP Generation from ddRAD and quaddRAD
Genome‐wide single nucleotide polymorphisms (SNPs) were generated from sequencing double digested restriction‐associated (ddRAD, Peterson et al., 2012 (link)) and quadruple barcode ddRAD (quaddRAD) libraries (Franchini et al., 2017 (link)). Common minke whale and southern right whale libraries were generated from ddRAD libraries following Peterson et al. (2012 (link)). Fin whale libraries were generated from using the quaddRAD protocol as outlined by Franchini et al. (2017 (link)), which enables the removal of PCR clones. All libraries were prepared from genomic DNA digested with HindIII and MspI and insert sizes between 300 and 400 bp. Libraries were sequenced on an Illumina HiSeq™ 2500 (ver. 4) as paired‐end sequencing at 100 (ddRAD) or 125 (quaddRAD) cycles, with 10% PhiX spike‐in.
Cabrera A.A., Schall E., Bérubé M., Anderwald P., Bachmann L., Berrow S., Best P.B., Clapham P.J., Cunha H.A., Dalla Rosa L., Dias C., Findlay K.P., Haug T., Heide‐Jørgensen M.P., Hoelzel A.R., Kovacs K.M., Landry S., Larsen F., Lopes X.M., Lydersen C., Mattila D.K., Oosting T., Pace RM I.I.I., Papetti C., Paspati A., Pastene L.A., Prieto R., Ramp C., Robbins J., Sears R., Secchi E.R., Silva M.A., Simon M., Víkingsson G., Wiig Ø., Øien N, & Palsbøll P.J. (2022). Strong and lasting impacts of past global warming on baleen whales and their prey. Global Change Biology, 28(8), 2657-2677.
Clones Fin whale Genomic Minke whale Single nucleotide polymorphisms Southern right whale
Corresponding Organization : Center for Coastal Studies
Other organizations :
Swiss National Park, University of Oslo, Galway-Mayo Institute of Technology, University of Pretoria, Universidade do Estado do Rio de Janeiro, Universidade Federal do Rio Grande, Cape Peninsula University of Technology, Norwegian Institute of Marine Research, Durham University, Norwegian Polar Institute, Technical University of Denmark, Victoria University of Wellington, NOAA National Marine Fisheries Service Northeast Fisheries Science Center, NOAA National Marine Fisheries Service, University of Padua, Hellenic Mediterranean University, Institute of Marine Research, Universidade dos Açores, University of St Andrews, Marine and Freshwater Research Institute
Genome-wide single nucleotide polymorphisms (SNPs)
Sequencing protocols (ddRAD and quaddRAD)
dependent variables
Genome-wide SNP data
control variables
Genomic DNA digested with HindIII and MspI
Insert sizes between 300 and 400 bp
Illumina HiSeq™ 2500 (ver. 4) sequencing platform
10% PhiX spike-in
controls
Positive control: Not specified
Negative control: Not specified
Annotations
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