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. 2016 Jun 21;5:e15266. doi: 10.7554/eLife.15266

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© 2016, Busby et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 4. — (A) For each group we show the ancestry region identity of the best matching source for the first and, if applicable, second events. Events involving sources that most closely match FULAI and SEMI-BANTU are highlighted by golden and red colours, respectively. Second events can be either multiway, in which case there is a single date estimate, or two-date in which case 2ND EVENT refers to the earlier event. The point estimate of the admixture date is shown as a black point, with 95% CI shown with lines. MIXTURE MODEL: We infer the ancestry composition of each African group by fitting its copying vector as a mixture of all other population copying vectors. The coefficients of this regression sum to 1 and are coloured by ancestry region. 1ST EVENT SOURCES and 2ND EVENT SOURCES show the ancestry breakdown of the admixture sources inferred by GLOBETROTTER, coloured by ancestry region as in the key top right. (B) and (C) Comparisons of dates inferred by MALDER and GLOBETROTTER. Because the two methods sometimes inferred different numbers of events, in (B) we show the comparison based on the inferred number of events in the MALDER analysis, and in (C) for the number of events inferred by GLOBETROTTER. Point symbols refer to populations and are as in Figure 1 and source data can be found in Figure 4—source data 1.

DOI: http://dx.doi.org/10.7554/eLife.15266.026

Figure 4—source data 1. Results of the main GLOBETROTTER analysis.
$A n a l y s i s$ refers to whether the main or masked analysis was used to produce the final result. Admixture $P$ -values are based on 100 bootstrap replicates of the NULL procedure. Our resulting inference, $r e s$ can be: 1D (two admixing sources at a single date); 1MW (multiple admixing sources at a single date); 2D (admixture at multiple dates); NA (no-admixture); U (uncertain). max( $R_{1}$ ) refers to the $R^{2}$ goodness-of-fit for a single date of admixture, taking the maximum value across all inferred coancestry curves. $F Q_{1}$ is the fit of a single admixture event (i.e. the first principal component, reflecting admixture involving two sources) and $F Q_{2}$ is the fit of the first two principal components capturing the admixture event(s) (the second component might be thought of as capturing a second, less strongly-signalled event. $M$ is the additional $R^{2}$ explained by adding a second date versus assuming only a single date of admixture; we use values above 0.35 to infer multiple dates (although see Supplementary Text for details). As well as the final result, for each event we show the inferred dates, $α$ s and best matching sources for 1D, 1MW, and 2D inferences. Inferred dates are in years(+ 95% CI; B=BCE, otherwise CE); the proportion of admixture from the minority source (source 1) is represented by $α$ . Date confidence intervals are based on 100 bootstrap replicates of the date inference

DOI: http://dx.doi.org/10.7554/eLife.15266.027

elife-15266-fig4-data1.xlsx^{(53.4KB, xlsx)}

DOI: 10.7554/eLife.15266.027

Figure 4—source data 2. Results of the main GLOBETROTTER analysis.
$A n a l y s i s$ refers to whether the main or masked analysis was used to produce the final result. Admixture $P$ -values are based on 100 bootstrap replicates of the NULL procedure. Our resulting inference, $r e s$ can be: 1D (two admixing sources at a single date); 1MW (multiple admixing sources at a single date); 2D (admixture at multiple dates); NA (no-admixture); U (uncertain). max( $R_{1}$ ) refers to the $R^{2}$ goodness-of-fit for a single date of admixture, taking the maximum value across all inferred coancestry curves. $F Q_{1}$ is the fit of a single admixture event (i.e. the first principal component, reflecting admixture involving two sources) and $F Q_{2}$ is the fit of the first two principal components capturing the admixture event(s) (the second component might be thought of as capturing a second, less strongly-signalled event. $M$ is the additional $R^{2}$ explained by adding a second date versus assuming only a single date of admixture; we use values above 0.35 to infer multiple dates (although see Supplementary Text for details). As well as the final result, for each event we show the inferred dates, $α$ s and best matching sources for 1D, 1MW, and 2D inferences. Inferred dates are in years(+ 95% CI; B=BCE, otherwise CE); the proportion of admixture from the minority source (source 1) is represented by $α$ . Date confidence intervals are based on 100 bootstrap replicates of the date inference

DOI: http://dx.doi.org/10.7554/eLife.15266.028

elife-15266-fig4-data2.xlsx^{(65.6KB, xlsx)}

DOI: 10.7554/eLife.15266.028

Figure 4—figure supplement 1. — (A) For each group we show the ancestry region identity of the best matching source for the first and, if applicable, second events. Events involving sources that most closely match FULAI and SEMI-BANTU are highlighted by golden and red colours, respectively. Second events can be either multiway, in which case there is a single date estimate, or two-date in which case 2ND EVENT refers to the earlier event. The point estimate of the admixture date is shown as a black point, with 95% CI shown with lines. MIXTURE MODEL: We infer the ancestry composition of each African group by fitting its copying vector as a mixture of all other population copying vectors. The coefficients of this regression sum to 1 and are coloured by ancestry region. 1ST EVENT SOURCES and 2ND EVENT SOURCES show the ancestry breakdown of the admixture sources inferred by GLOBETROTTER, coloured by ancestry region as in the key top right. (B) and (C) Comparisons of dates inferred by MALDER and GLOBETROTTER. Because the two methods sometimes inferred different numbers of events, in (B) we show the comparison based on the inferred number of events in the MALDER analysis, and in (C) for the number of events inferred by GLOBETROTTER. Point symbols refer to populations and are as in Figure 1 and source data can be found in Figure 4—source data 1.

DOI: http://dx.doi.org/10.7554/eLife.15266.026

Figure 4—source data 1. Results of the main GLOBETROTTER analysis.
$A n a l y s i s$ refers to whether the main or masked analysis was used to produce the final result. Admixture $P$ -values are based on 100 bootstrap replicates of the NULL procedure. Our resulting inference, $r e s$ can be: 1D (two admixing sources at a single date); 1MW (multiple admixing sources at a single date); 2D (admixture at multiple dates); NA (no-admixture); U (uncertain). max( $R_{1}$ ) refers to the $R^{2}$ goodness-of-fit for a single date of admixture, taking the maximum value across all inferred coancestry curves. $F Q_{1}$ is the fit of a single admixture event (i.e. the first principal component, reflecting admixture involving two sources) and $F Q_{2}$ is the fit of the first two principal components capturing the admixture event(s) (the second component might be thought of as capturing a second, less strongly-signalled event. $M$ is the additional $R^{2}$ explained by adding a second date versus assuming only a single date of admixture; we use values above 0.35 to infer multiple dates (although see Supplementary Text for details). As well as the final result, for each event we show the inferred dates, $α$ s and best matching sources for 1D, 1MW, and 2D inferences. Inferred dates are in years(+ 95% CI; B=BCE, otherwise CE); the proportion of admixture from the minority source (source 1) is represented by $α$ . Date confidence intervals are based on 100 bootstrap replicates of the date inference

DOI: http://dx.doi.org/10.7554/eLife.15266.027

elife-15266-fig4-data1.xlsx^{(53.4KB, xlsx)}

DOI: 10.7554/eLife.15266.027

Figure 4—source data 2. Results of the main GLOBETROTTER analysis.
$A n a l y s i s$ refers to whether the main or masked analysis was used to produce the final result. Admixture $P$ -values are based on 100 bootstrap replicates of the NULL procedure. Our resulting inference, $r e s$ can be: 1D (two admixing sources at a single date); 1MW (multiple admixing sources at a single date); 2D (admixture at multiple dates); NA (no-admixture); U (uncertain). max( $R_{1}$ ) refers to the $R^{2}$ goodness-of-fit for a single date of admixture, taking the maximum value across all inferred coancestry curves. $F Q_{1}$ is the fit of a single admixture event (i.e. the first principal component, reflecting admixture involving two sources) and $F Q_{2}$ is the fit of the first two principal components capturing the admixture event(s) (the second component might be thought of as capturing a second, less strongly-signalled event. $M$ is the additional $R^{2}$ explained by adding a second date versus assuming only a single date of admixture; we use values above 0.35 to infer multiple dates (although see Supplementary Text for details). As well as the final result, for each event we show the inferred dates, $α$ s and best matching sources for 1D, 1MW, and 2D inferences. Inferred dates are in years(+ 95% CI; B=BCE, otherwise CE); the proportion of admixture from the minority source (source 1) is represented by $α$ . Date confidence intervals are based on 100 bootstrap replicates of the date inference

DOI: http://dx.doi.org/10.7554/eLife.15266.028

elife-15266-fig4-data2.xlsx^{(65.6KB, xlsx)}

DOI: 10.7554/eLife.15266.028