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Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation.

Li S, Jakobsson M - BMC Genet. (2012)

Bottom Line: We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data.Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC.We conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from these data, suggesting that the ABC approach will be a useful tool for analyzing large genome-wide datasets.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Evolutionary Biology, EBC, Uppsala University, Norbyvägen 18D, Uppsala SE-75236, Sweden.

ABSTRACT

Background: The Approximate Bayesian Computation (ABC) approach has been used to infer demographic parameters for numerous species, including humans. However, most applications of ABC still use limited amounts of data, from a small number of loci, compared to the large amount of genome-wide population-genetic data which have become available in the last few years.

Results: We evaluated the performance of the ABC approach for three 'population divergence' models - similar to the 'isolation with migration' model - when the data consists of several hundred thousand SNPs typed for multiple individuals by simulating data from known demographic models. The ABC approach was used to infer demographic parameters of interest and we compared the inferred values to the true parameter values that was used to generate hypothetical "observed" data. For all three case models, the ABC approach inferred most demographic parameters quite well with narrow credible intervals, for example, population divergence times and past population sizes, but some parameters were more difficult to infer, such as population sizes at present and migration rates. We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data. Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC. Finally, increasing the amount of data beyond some hundred loci will substantially improve the accuracy of many parameter estimates using ABC.

Conclusions: We conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from these data, suggesting that the ABC approach will be a useful tool for analyzing large genome-wide datasets.

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The mean difference between the true and the estimated parameter value and the width of the 95% credible interval as functions of the number of loci for A) the divergence time T and B) the migration rate m12.
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Figure 8: The mean difference between the true and the estimated parameter value and the width of the 95% credible interval as functions of the number of loci for A) the divergence time T and B) the migration rate m12.

Mentions: We used a simulation approach to investigate the impact of the number of loci on accuracy of the ABC estimation, in particular the accuracy of the divergence time estimate and the migration rate estimates. We simulated 147 "observed" dataset from model 1 (each true parameter was varied for 49 values, T = 0.01, 0.02, ..., 0.49; m12 = 0.1, 0.2, ..., 4.9; and m21 = 0.1, 0.2, ..., 4.9, and the other true parameters were set as in Table 1) for increasing numbers of loci (100; 500; 1,000; 2,000; 3,000; 4,000; 5,000; 6,000; 7,000; 8,000; 9,000 and 10,000 genome-regions) and used the ABC approach to infer the divergence time T and migration rates. For increasing numbers of loci, Figure 8 shows the mean difference (across 49 choices of true parameter values for each parameter) of the true value and the mean of the posterior sample and the width of the 95% credible interval for the divergence time T and the migration rate m21 (the results for m12 were very similar to m21). The mean values of the posterior samples rapidly approach the true parameter value when the number of loci increases from 100 to 1,000 and the width of the 95% credible intervals rapidly decrease until about 2,000 loci, and continue to decrease at a low rate for increasing numbers of loci.


Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation.

Li S, Jakobsson M - BMC Genet. (2012)

The mean difference between the true and the estimated parameter value and the width of the 95% credible interval as functions of the number of loci for A) the divergence time T and B) the migration rate m12.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368717&req=5

Figure 8: The mean difference between the true and the estimated parameter value and the width of the 95% credible interval as functions of the number of loci for A) the divergence time T and B) the migration rate m12.
Mentions: We used a simulation approach to investigate the impact of the number of loci on accuracy of the ABC estimation, in particular the accuracy of the divergence time estimate and the migration rate estimates. We simulated 147 "observed" dataset from model 1 (each true parameter was varied for 49 values, T = 0.01, 0.02, ..., 0.49; m12 = 0.1, 0.2, ..., 4.9; and m21 = 0.1, 0.2, ..., 4.9, and the other true parameters were set as in Table 1) for increasing numbers of loci (100; 500; 1,000; 2,000; 3,000; 4,000; 5,000; 6,000; 7,000; 8,000; 9,000 and 10,000 genome-regions) and used the ABC approach to infer the divergence time T and migration rates. For increasing numbers of loci, Figure 8 shows the mean difference (across 49 choices of true parameter values for each parameter) of the true value and the mean of the posterior sample and the width of the 95% credible interval for the divergence time T and the migration rate m21 (the results for m12 were very similar to m21). The mean values of the posterior samples rapidly approach the true parameter value when the number of loci increases from 100 to 1,000 and the width of the 95% credible intervals rapidly decrease until about 2,000 loci, and continue to decrease at a low rate for increasing numbers of loci.

Bottom Line: We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data.Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC.We conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from these data, suggesting that the ABC approach will be a useful tool for analyzing large genome-wide datasets.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Evolutionary Biology, EBC, Uppsala University, Norbyvägen 18D, Uppsala SE-75236, Sweden.

ABSTRACT

Background: The Approximate Bayesian Computation (ABC) approach has been used to infer demographic parameters for numerous species, including humans. However, most applications of ABC still use limited amounts of data, from a small number of loci, compared to the large amount of genome-wide population-genetic data which have become available in the last few years.

Results: We evaluated the performance of the ABC approach for three 'population divergence' models - similar to the 'isolation with migration' model - when the data consists of several hundred thousand SNPs typed for multiple individuals by simulating data from known demographic models. The ABC approach was used to infer demographic parameters of interest and we compared the inferred values to the true parameter values that was used to generate hypothetical "observed" data. For all three case models, the ABC approach inferred most demographic parameters quite well with narrow credible intervals, for example, population divergence times and past population sizes, but some parameters were more difficult to infer, such as population sizes at present and migration rates. We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data. Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC. Finally, increasing the amount of data beyond some hundred loci will substantially improve the accuracy of many parameter estimates using ABC.

Conclusions: We conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from these data, suggesting that the ABC approach will be a useful tool for analyzing large genome-wide datasets.

Show MeSH