التفاصيل البيبلوغرافية
| العنوان: |
Additional file 1 of Large-scale genomic analysis reveals the genetic cost of chicken domestication |
| المؤلفون: |
Ming-Shan Wang (10976517), Jin-Jin Zhang (8059304), Xing Guo (103312), Ming Li (91180), Rachel Meyer (6850295), Hidayat Ashari (10976520), Zhu-Qing Zheng (10119665), Sheng Wang (339979), Min-Sheng Peng (166207), Yu Jiang (234328), Mukesh Thakur (5848142), Chatmongkon Suwannapoom (800543), Ali Esmailizadeh (3106152), Nalini Yasoda Hirimuthugoda (10976523), Moch Syamsul Arifin Zein (10976526), Szilvia Kusza (534338), Hamed Kharrati-Koopaee (10976529), Lin Zeng (161089), Yun-Mei Wang (4358425), Ting-Ting Yin (654260), Min-Min Yang (10976532), Ming-Li Li (395686), Xue-Mei Lu (10976535), Emiliano Lasagna (456418), Simone Ceccobelli (456414), Humpita Gamaralalage Thilini Nisanka Gunwardana (10976538), Thilina Madusanka Senasig (10976541), Shao-Hong Feng (10976544), Hao Zhang (15339), Abul Kashem Fazlul Haque Bhuiyan (10976547), Muhammad Sajjad Khan (10976550), Gamamada Liyanage Lalanie Pradeepa Silva (10976553), Le Thi Thuy (10976556), Okeyo A. Mwai (7070306), Mohamed Nawaz Mohamed Ibrahim (10976559), Guojie Zhang (146963), Kai-Xing Qu (10976562), Olivier Hanotte (89422), Beth Shapiro (30433), Mirte Bosse (116283), Dong-Dong Wu (53954), Jian-Lin Han (425226), Ya-Ping Zhang (53956) |
| سنة النشر: |
2021 |
| المجموعة: |
Smithsonian Institution: Digital Repository |
| مصطلحات موضوعية: |
Genetics, Domestication, Bottleneck, Genetic load, Deleterious mutation, Domestic chicken |
| الوصف: |
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>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 < 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 ... |
| نوع الوثيقة: |
article in journal/newspaper |
| اللغة: |
unknown |
| Relation: |
https://figshare.com/articles/journal_contribution/Additional_file_1_of_Large-scale_genomic_analysis_reveals_the_genetic_cost_of_chicken_domestication/14788353 |
| DOI: |
10.6084/m9.figshare.14788353.v1 |
| الاتاحة: |
https://doi.org/10.6084/m9.figshare.14788353.v1 |
| Rights: |
CC BY + CC0 |
| رقم الانضمام: |
edsbas.56A6EE65 |
| قاعدة البيانات: |
BASE |