11 INDEX

  • AI Report 10

  • AMOVA (Analysis of MOlecular VAriance) 7.4

  • API key 10

  • Bayesian Information Criterion (BIC) 6.2

  • Chromosome Info. 4.3

  • Circos Plot 7.2

  • Core Sample Set 9.1

  • Core SNP Set 9.2

  • DAPC (Discriminant Analysis of Principal Components) 6.2

  • data.frame 3.1

  • Demo Data 3.1

  • Diversity Parameter 7.1

  • Genetic Distance 7.3

  • genind 5

  • genlight 5

  • Group Info. 6.6

  • Hardy-Weinberg equilibrium (HWE) 4.2

  • Heterozygosity rate 4.1

  • IBS (Identity By State) 8.3

  • Kinship Analysis 6.5

  • Manhattan Plot 8.4

  • Minor allele frequency (MAF) 4.2

  • Missing rate 4.1

  • NJ (Neighbor-Joining) Tree 6.4

  • OutFLANK 8.2

  • PCA (Principal Component Analysis) 6.1

  • pcadapt 8.1

  • Permutation Test 7.4

  • Sample QC 4.1

  • Scatter Plot 6.6

  • ShiNyP 2

  • Site Info. 3.1

  • SNP Density 4.3

  • SNP QC 4.2

  • Tree Plot 6.7

  • UPGMA (Unweighted Pair Group Method with Arithmetic mean) Tree 6.3

  • VCF 3.1

Bibliography

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Kang, Hyun Min, Jae Hoon Sul, Susan K Service, Noah A Zaitlen, Sit-yee Kong, Nelson B Freimer, Chiara Sabatti, and Eleazar Eskin. 2010. “Variance Component Model to Account for Sample Structure in Genome-Wide Association Studies.” Nature Genetics 42 (4): 348–54. https://doi.org/10.1038/ng.548.
Luu, Keurcien, Eric Bazin, and Michael G. B. Blum. 2016. “Pcadapt: An R Package to Perform Genome Scans for Selection Based on Principal Component Analysis.” Molecular Ecology Resources 17 (1): 67–77. https://doi.org/10.1111/1755-0998.12592.
Paradis, Emmanuel, and Klaus Schliep. 2018. “Ape 5.0: An Environment for Modern Phylogenetics and Evolutionary Analyses in R.” Edited by Russell Schwartz. Bioinformatics 35 (3): 526–28. https://doi.org/10.1093/bioinformatics/bty633.
Whitlock, Michael C., and Katie E. Lotterhos. 2015. “Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model Through Trimming the Distribution ofFST.” The American Naturalist 186 (S1): S24–36. https://doi.org/10.1086/682949.
Yu, Guangchuang, David K. Smith, Huachen Zhu, Yi Guan, and Tommy Tsan-Yuk Lam. 2016. “Ggtree: An r Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data.” Edited by Greg McInerny. Methods in Ecology and Evolution 8 (1): 28–36. https://doi.org/10.1111/2041-210x.12628.