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.本数据集应用于丹尼尔·L·杰弗里斯（Daniel L Jeffries）的学位论文《受胁鲫（Carassius carassius (L.)）保护的遗传与基因组学策略：系统地理学、杂交与基因渐渗》，该论文由赫尔大学（University of Hull）的伯恩德·亨弗林博士（Dr. Bernd Haenfling）、洛里·劳森-汉德利博士（Dr. Lori Lawson-Handley）与戈登·科普教授（Prof. Gordon Copp）指导完成。本数据包包含来自鲫属（Carassius）或鲤属（Cyprinus）的三类数据：覆盖1300余尾鱼类的微卫星（microsatellite）分型数据、约240尾鱼类的限制性位点关联测序（RADseq, Restriction-site Associated DNA sequencing）数据，以及约100尾样本的线粒体DNA（mtDNA）细胞色素b（cytb）序列数据。此外还附带了论文中所述分析所需的中间文件与代码脚本，涵盖基于R语言adegenet包开展的基础群体遗传学与判别主成分分析（DAPC, Discriminant Analysis of Principal Components）群体结构分析、DIYABC分析、线粒体DNA系统发育分析，以及使用NewHybrids和Treemix进行的RADseq数据处理与下游分析流程。