Supporting data for "Whole-genome resequencing reveals signatures of selection and timing of duck domestication" ================================================================================================================ Zhang, Z; Jia, Y; Almeida, P; Mank, J, E; Tuinen, M, V; Wang, Q; Jiang, Z; Chen, Y; Zhan, K; Hou, S; Zhou, Z; Li, H; Yang, F; He, Y; Ning, Z; Yang, N; Qu, L (2018) GigaScience Database. http://dx.doi.org/10.5524/100417 Summary ------- The genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic diff erences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new e nvironments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 7 8 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X p er individual. Our population and demographic analyses indicate a complex history of domestication, with earl y selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggest th at genes affecting brain and neuronal development have undergone strong positive selection during domestication. Our FST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis associated transcription factor locus. Our results advance the understanding of animal domestication and selection for complex phenotypic traits. Files ----- #SNP VCF MDN_SNP.vcf.gz - SNP information of 7 mallards form Ningxia province (MDN1-MDN8). MDZ_SNP.vcf.gz - SNP information of 14 mallards form Zhejiang province (MDZ1-MDZ14). PK_SNP.vcf.gz - SNP information of 8 Pekin duck (PK1-PK8).CV_SNP.vcf.gz CV_SNP.vcf.gz - SNP information of 8 Cherry Valley duck (CV1-CV8). ML_SNP.vcf.gz - SNP information of 8 Maple Leaf duck (ML1-ML8). JD_SNP.vcf.gz - SNP information of 8 Jinding duck (JD1-JD8). SM_SNP.vcf.gz - SNP information of 8 Shanma duck (SM1-SM8). SX_SNP.vcf.gz - SNP information of 8 Shaoxing duck (SX1-SX8). GY_SNP.vcf.gz - SNP information of 8 Gaoyou duck (GY1-GY8). #INDEL VCF MDN_INDEL.vcf.gz - INDEL information of 7 mallards form Ningxia province (MDN1-MDN8). MDZ_INDEL.vcf.gz - INDEL information of 14 mallards form Zhejiang province (MDZ1-MDZ14). PK_INDEL.vcf.gz - INDEL information of 8 Pekin duck (PK1-PK8). CV_INDEL.vcf.gz - INDEL information of 8 Cherry Valley duck (CV1-CV8). ML_INDEL.vcf.gz - INDEL information of 8 Maple Leaf duck (ML1-ML8). JD_INDEL.vcf.gz - INDEL information of 8 Jinding duck (JD1-JD8). SM_INDEL.vcf.gz - INDEL information of 8 Shanma duck (SM1-SM8). SX_INDEL.vcf.gz - INDEL information of 8 Shaoxing duck (SX1-SX8). GY_INDEL.vcf.gz - INDEL information of 8 Gaoyou duck (GY1-GY8). #tbi files CV_SNP.vcf.gz.tbi - information of 8 Cherry Valley duck (CV1-CV8) - tabix GY_SNP.vcf.gz.tbi - information of 8 Gaoyou duck (GY1-GY8) - tabix JD_SNP.vcf.gz.tbi - information of 8 Jinding duck (JD1-JD8) - tabix MDN_SNP.vcf.gz.tbi - information of 7 mallards from Ningxia province (MDN1-MDN8) - tabix MDZ_SNP.vcf.gz.tbi - information of 14 mallards from Zhejiang province (MDZ1-MDZ14) - tabix ML_SNP.vcf.gz.tbi - information of 8 Maple Leaf duck (ML1-ML8) - tabix PK_SNP.vcf.gz.tbi - information of 8 Pekin duck (PK1-PK8) - tabix SM_SNP.vcf.gz.tbi - information of 8 Shanma duck (SM1-SM8) - tabix SX_SNP.vcf.gz.tbi - information of 8 Shaoxing duck (SX1-SX8) - tabix CV_INDEL.vcf.gz.tbi - information of 8 Cherry Valley duck (CV1-CV8) - tabix GY_INDEL.vcf.gz.tbi - information of 8 Gaoyou duck (GY1-GY8) - tabix JD_INDEL.vcf.gz.tbi - information of 8 Jinding duck (JD1-JD8) - tabix MDN_INDEL.vcf.gz.tbi - information of 7 mallards from Ningxia province (MDN1-MDN8) - tabix MDZ_INDEL.vcf.gz.tbi - information of 14 mallards from Zhejiang province (MDZ1-MDZ14) - tabix ML_INDEL.vcf.gz.tbi - information of 8 Maple Leaf duck (ML1-ML8) - tabix PK_INDEL.vcf.gz.tbi - information of 8 Pekin duck (PK1-PK8) - tabix SM_INDEL.vcf.gz.tbi - information of 8 Shanma duck (SM1-SM8) - tabix SX_INDEL.vcf.gz.tbi - information of 8 Shaoxing duck (SX1-SX8) - tabix Duck_alignment.fasta - alignments used for generating phylogenetic trees duck_GATK_confidence_snp_intergenic.1p.dadi - dadi input file of 1% intergenic snp sites duck_GATK_confidence_snp_intergenic.dadi - dadi input file of all intergenic snp sites Duck_PCA.eigenvec - Raw output of Duck Principle Component Analysis Duck_phylogeny.ml.tree - Raw output of duck phylogenetic tree file Duck_population_genetic_structure_K=2.txt - Raw output of duck population genetic structure (K=2) Duck_population_genetic_structure_K=3.txt - Raw output of duck population genetic structure (K=3) Duck_population_genetic_structure_K=4.txt - Raw output of duck population genetic structure (K=4) Duck_phylogeny.nex - phylogenetic tree file gene_expression_in_brain.csv - gene expression level of brain in 7 mallards and 7 domestic ducks gene_expression_in_liver.csv - gene expression level of liver in 7 mallards and 7 domestic ducks gene_expression_in_breast_muscle.csv - gene expression level of breast muscle in 7 mallards and 7 domestic ducks wild_domestic_ZFst_log2_theta_pi_10k_top_1.vcf - top 1% sweep regions with Fst, ZFst, pi, log2_theta_pi values wild_domestic_ZFst_log2_theta_pi_10k_top_5.vcf - top 5% sweep regions with Fst, ZFst, pi, log2_theta_pi values wild_domestic_ZFst_log2_theta_pi_10k.vcf - all sweep regions with Fst, ZFst, pi, log2_theta_pi values Combine_wild_domestic_ZFst_log2_theta_pi_10k.pl - perl script of combined ZFst and log2_theta_pi dadi-fit-IM3D_sizeCh-migTo - python script to optimise the different parameters in the model from different starting values. dadi-opt-IM3D_sizeCh-migTo - python script using the best parameters to generate the final estimates (Table 1) and the plots used in figure S4. Differential_Gene_Selection.pl - perl script of gene names located in selected sweep region Fst_to_ZFst_win_10k.pl - perl script to convert Fst to ZFst log2_theta_pi.pl - perl script to convert pi to log2_theta_pi Mallard_Domesticate_Fst_10k_Step_3.pl - perl script of Fst calculation (step 3) Mallard_Domesticate_Fst_Step_1.pl - perl script of Fst calculation (step 1) Mallard_Domesticate_Fst_Step_2.pl - perl script of Fst calculation (step 2) Mallard_Domesticate_Fst.pl - perl script of FST calculation opt-IM3D_noMig-EWM-dadi.py - python script of test Model 4 in duck demographic analysis opt-IM3D_noMig-MWE-dadi.py - python script of test Model 3 in duck demographic analysis opt-IM3D_noMig-WME-dadi.py - python script of test Model 2 in duck demographic analysis opt-SS3D_noMig-dadi.py - python script of test Model 1 in duck demographic analysis VCF_TO_HAPMAP.pl - perl script to convert vcf file to hapmap file. full_command_procotol.sh - full command with procotol of dry-lab MD5sum - MD5sum values for all files.