Additional file 2: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

Figure S1. Phylogenetic tree of mtDNA macrohaplogroup L complete African sequences produced in this study. (XLSX 71 kb

Additional file 1: of Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

Table S1. Complete mtDNA macrohaplogroup L sequences. Table S2. Frequencies of mtDNA haplogroups L2 and L3 and Y-chromosome haplogroup E lineages across Africa. Table S3. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for the main mitochondrial DNA African haplogroups. Table S4. Coalescence ages in thousand years (kya) with 95% coefficient intervals (CI), or standard deviations, for Y-chromosome most recent common ancestor (MRCA), the out-of-Africa event, and the splits of haplogroup DE and E. Table S5. Population clustering into five classes. Table S6. k-means cluster results using African populations characterized by mtDNA L3 and Y-chromosome E haplogroup frequencies. Table S7. k-means cluster results using African populations characterized by mtDNA L2 and L3 and Y-chromosome E haplogroup frequencies. (XLSX 403 kb

Additional file 2: Table S1. of Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Haplogroup M in Saudi Arabia. In bold haplotypes from this study. Table S2. Super-haplogroup Ages and Geographic links. Table S3. Haplogroup M geographic ranges and ages in kiloyears (kya). Table S4. Populations used in the AMOVA and k-means clustering analyses. Table S5. Mitochondrial DNA M haplogroup ages and coordinates for their respective geographic centers used in the correlation analysis. Table S6. Modern human oldest fossil dating in different regions of Asia and oldest archaeological dating at the eastern side of the Wallace Line. (XLSX 91 kb

Additional file 1: Figure S1. of Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Phylogenetic tree of M complete sequences from this study. (XLSX 66 kb

Additional file 1: Table S1. of Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area

Worldwide mtDNA haplogroup U3 sequences. Table S2. MtDNA haplogroup U3 haplotypic frequencies (%) in Eurasian and northern Africa main regions. Table S3. MtDNA complete U and P sequences obtained in this study. Table S4. Mitochondrial DNA haplogroup P frequencies (%) in the West Pacific Islands. Table S5. Mitochondrial DNA haplogroup frequencies (%) in Australia. Table S6. Frequency (%) of major mtDNA macrohaplogroup R branches in different regions of Eurasia and Australasia. Table S7. MtDNA macrohaplogroup M, N and R frequencies (%) in Eurasia and Australasia. Table S8. Mantel tests based on correlations between geographic distances (a), genetic distances (b), and genetic identities (c). Table S9. Coalescence ages for the main branches of mtDNA haplogroup R in different geographic areas. (XLSX 266 kb

Additional file 2: of Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area

Figure S1. MtDNA haplogroup U phylogeny with emphasis on the U3 branch. Figure S2. MtDNA haplogroup P phylogeny. (XLSX 175 kb

Association analysis between <i>ABCC5</i> rs1401999 and primary angle closure glaucoma in all chip-typed sample collections (top panel), de-novo genotyped sample collections (middle panel), and PACG cases and clinically certified controls with open angles (bottom panel).

<p>MAF case: Minor allele frequency in PACG cases.</p><p>MAF control: Minor allele frequency in controls.</p><p>OR: Odds ratio.</p><p><i>P</i>: <i>P</i>-value for association with PACG.</p><p>I²: I-squared index for between-collection heterogeneity.</p><p>* Results here are presented based on raw minor allele frequency counts without further adjustment.</p>†<p>PACG patients were recruited from the Beijing Tongren Hospital and controls were recruited from the Handan Eye Study (HES), a population-based study of eye disease in rural Chinese aged 30 years and over.</p

Association analysis between <i>ABCC5</i> rs1401999 and susceptibility to primary angle closure glaucoma (PACG).

<p>The PACG sample collections have been described elsewhere <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004089#pgen.1004089-Vithana1" target="_blank">[6]</a>. The vertical line represents a per-allele odds ratio of 1.00. The oblongs represent point estimates (referring to the per-allele odds ratio), with the height of the oblongs inversely proportional to the standard error of the point estimates. Horizontal lines indicate the 95% confidence interval for each point estimate. Meta-analyses of samples are reflected by blue diamonds. The width of the diamonds indicates their 95% confidence intervals. All point estimates in Stage 1 have been adjusted for the top axes of genetic stratification using logistic regression.</p

Quantitative trait analysis between <i>ABCC5</i> rs1401999 and anterior chamber depth in SIMES, SINDI, and BES.

<p>SIMES: Singapore Malay Eye Study (typed with Illumina 610K GWAS chip).</p><p>SINDI: Singapore Indian Eye Study (typed with Illumina 610K GWAS chip).</p><p>BES1: Beijing Eye Study typed with Illumina 610K GWAS chip.</p><p>BES2: Beijing Eye Study typed with direct sequencing.</p><p>β: Per-allele effect size of <i>ABCC5</i> rs1401999 on anterior chamber depth.</p><p>SE: Standard error for β.</p><p><i>P</i>gc: Genomic control corrected <i>P</i>-value.</p><p>MAF: Minor allele frequency.</p><p>*: I²-index for heterogeneity = 0%.</p