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Additional file 2: Figure S1.Venndiagrams summarize unique and common variants among groups. Fig. S2. Theheat map of ChromoPainter���s coancestry matrix. Each row corresponds to therecipient genomes and columns represent the donor individuals. Fig. S3. Cross validationerror (CV) plot from ADMIXTURE. Fig. S4. Box plots of nucleotide diversity, calculated in 50kb sliding window with 20 kb increments across the genome. Fig. S5. Genomic regions with selection signals in nativechickens by �� method. (A) Indigenousgroup versus Arian chickens. (B) Indigenous group versus White Leghornchickens. Fig. S6. Haplotype network based on pairwise differenceswithin the selective sweep region (Chr1: 176.34-176.36) inHSPH1.

The list of selected hypoxia- associated genes for gene network analysis. Table S2: Principle component analysis of phenotypic traits for discriminate analysis and clustering the highland and lowland populations. Table S3: The classification of highland and lowland chickens based on the discriminate analysis.

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

Additional file 10: Figure S1. Results of the overlap analysis between the regions of signatures of selection (set A) and known QTL regions in chicken (set B). The y-axis shows the number of overlaps between the two datasets. AinB refers to the region in A encompassed by a region in B; BinA refers to the region in B encompassed by a region in A; AleftB and ArightB refer to the end and the start of the region of signatures of selection that overlap with the beginning and the end of a region of QTL, respectively.

Supplementary material

Additional file 2: Figure S1. Horse breeds used in this study. The figure was designed by the first author. Figure S2. Genome sequence depth for each horse in this study. Figure S3. Cross validation error (CV) plot from ADMIXTURE. Figure S4. Genomic landscape of positive selection signatures using the FST (A) and XP-CLR (B) values, between DBPs and all other horses.

Additional file 1: Tables S1-S15 and Figs. S1-S19.

Table S1. Allele and genotype frequencies of three LP variants in Iranian ethnic groups. Table S2. Allele and genotype frequencies of the neighboring countries of Iran. Table S3. Comparison of the levels of nucleotide diversity in lactase persistent, lactase intermediate persistent and lactase nonpersistent measured across the three sequence regions from 400 Iranian Individuals. Table S4. The phased 400 sequences into 38 haplotypes based on the 18 SNPs of the regulatory region and the flanking control regions. Figure S1. Map of Iran showing approximate locations of the ethnic groups included in the present study. Figure S2. Phased Haplotypes for the LCT enhancer. Control region 1 and Control region 2, in Intron 9 and 13 of MCM6 and 1 kb Upstream of LCT from 7 ethnic groups in 400 Iranian Individuals. Method S1. Whole-Genome Resequencing and Detection of Selective Signals. (DOCX 804 kb)

Figure S1-S20.. Supplementary figures supporting the manuscript. (DOCX 5084 kb)