Thesis data and scripts

This data was used in the Thesis "Genetic and genomic approaches to the conservation of the threatened crucian carp Carassius carassius (L.); phylogeography, hybridisation and introgression" by Daniel L Jeffries, supervised by Dr. Bernd Haenfling, Dr. Lori Lawson-Handley and Prof. Gordon Copp at the university of Hull. The data in this package consits of microsatellite data for over 1300 fish, RADseq data for approx 240 fish and mtDNA (cytb) data for approximately 100 fish from the genus Carassius or Cyprinus. Intermediate files and scripts are also included for the analyses described in the thesis, including basic population genetics and DAPC population structure analyses carried out in R using the adegenet package, DIYABC analyses, mtDNA phylogenetic analyses, and RADseq data processing and and downstream analyses using NewHybrids and Treemix.