Population genetics, demographic and evolutionary history of the Dudley’s lousewort, a rare redwood forest specialist (Pedicularis dudleyi)
Misiewicz, Tracy (2021), Population genetics, demographic and evolutionary history of the Dudley’s lousewort, a rare redwood forest specialist (Pedicularis dudleyi), Dryad, Dataset, https://doi.org/10.6078/D1S415
ddRADseq libraries were constructed following a modified version of the protocol described in Peterson et al.(2012)where amplification was performed prior to size selection. 500150 ng of genomic DNA were digested using the restriction enzymes EcoRI and SphI-HF.P1 and P2 flex adapters were ligated to the digested DNA. Ligation products with similar concentrations were combined into a total of eight pools with each pool containing 1024 samples. Each pool was then divided, and PCR amplified in eight separate 25ul reactions using dual indexed PCR primers as described in Meyer and Kircher(2010). After amplification, indexed libraries were then re-pooled, quantified using qPCR and combined in equimolar ratios. The final library was size-selected for 750bp and the final Illumina library was sequenced by Novogene at the UC Davis Sequencing Center on a single lane of Illumina HiSeq X Ten(150bp, paired-end). The files included here include the final SNP data set formatted for STRUCTURE, GENPOP, and DIYABC and VCF.a
Phylogenetic data includes aligned gene sequences for the concatenated ITS and the matK-5trnK intron dataset.
Save the Redwoods League, Award: 144
National Science Foundation, Award: 1810989