Additional file 1 of Large-scale genomic analysis reveals the genetic cost of chicken domestication
Creators: name: Wang, Ming-Shan
name: Zhang, Jin-Jin
name: Guo, Xing
name: Li, Ming
name: Meyer, Rachel
name: Ashari, Hidayat
name: Zheng, Zhu-Qing
name: Wang, Sheng
name: Peng, Min-Sheng
name: Jiang, Yu
name: Thakur, Mukesh
name: Suwannapoom, Chatmongkon
name: Esmailizadeh, Ali
name: Hirimuthugoda, Nalini Yasoda
name: Zein, Moch Syamsul Arifin
name: Kusza, Szilvia
name: Kharrati-Koopaee, Hamed
name: Zeng, Lin
name: Wang, Yun-Mei
name: Yin, Ting-Ting
name: Yang, Min-Min
name: Li, Ming-Li
name: Lu, Xue-Mei
name: Lasagna, Emiliano
name: Ceccobelli, Simone
name: Gunwardana, Humpita Gamaralalage Thilini Nisanka
name: Senasig, Thilina Madusanka
name: Feng, Shao-Hong
name: Zhang, Hao
name: Bhuiyan, Abul Kashem Fazlul Haque
name: Khan, Muhammad Sajjad
name: Silva, Gamamada Liyanage Lalanie Pradeepa
name: Thuy, Le Thi
name: Mwai, Okeyo A.
name: Ibrahim, Mohamed Nawaz Mohamed
name: Zhang, Guojie
name: Qu, Kai-Xing
name: Hanotte, Olivier
name: Shapiro, Beth
name: Bosse, Mirte
name: Wu, Dong-Dong
name: Han, Jian-Lin
name: Zhang, Ya-Ping
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Nucleotide diversity for G. g. spadiceus and chicken populations (grouped by samling locations and breeds). Figure S2. Demographic histories for G. g. spadiceus and diverse chicken groups by PSMC. A total of 18 chicken populations were included in this analysis. Figure S3. Four tested demographic models for dadi analysis. Nanc, ancestral population size before the split; T, timepoints; m, migrations; Napop, ancestral population size after split. Ncpop, current population size. Arrows depict migration directions. Figure S4. Comparing observed data and model allele frequency spectrum for the best model (Model 3). Figure S5. Provean-scores for nonsynonymous mutations (for all mutations, left; and for mutations with Provean-scores ≤ –2.5, right) in microchromosomes, macrochromosomes, and intermediate chromosomes. Figure S6. Pipeline for constructing the mouse model with a mutation at the mouse TSHR locus (p. Gly559Arg; c.1675G&gt;A). Figure S7. Photograph showing TSHR-559Arg knock-in homozygous (HO) and wild-type mice at 10 months old. Figure S8. Gly558Arg knock-in mice consumed less food than wild-type. *, P &lt; 0.05. Statistical significance was measured by the Student’s t test. N = 8 for both HO and wild-type male mice were used in each test. Figure S9. Number and ratio of high-impact mutations among chicken populations. GGS, G. g. spadiceus; DC, all domestic chickens; WL, White Leghorn; TC, Tibetan chicken, XJ, Xinjiang local chicken; You; Beijing You chicken. Figure S10. Number and frequency of deleterious mutations in the genomic regions of putatively selective sweeps. Table S1. Information for high-coverage genomes used for PSMC, MSMC, and SMC++ analyses. Table S2. Estimations of likelihoods and AIC scores from four demographic models. Table S3. Summary of population histories calculated from 2D–SFS. Confidence intervals (95%) were obtained by bootstrapping all sites and performing parameter inference on each bootstrap dataset with 100 runs. Table S4. Distribution of variants identified in dog, sheep, goat, cattle, pig, and horse. This data is from our previous publication. Table S5. GO enrichment for genes carrying nonsynonymous mutation with provean-score of &lt;–10. Table S6. Guide RNA sequences for the exon 10 of mouse-TSHR.