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8 Coventry, A., Bull-Otterson, L.M., Liu, X., Clark, A.G., Maxwell, T.J., Crosby, J., Hixson, J.E., Rea, T.J., Muzny, D.M., Lewis, L.R., et al. Deep resequencing reveals excess rare recent variants consistent with explosive population growth. Nat Commun, 1, 2010, 131.
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This study, along with the parallel study by Nelson et al. [9] that appeared in the same issue, provides the first significant empirical evidence — based on large-scale data (whole exome in this case) — for recent explosive growth in the history of Europeans and West Africans, with growth rate far exceeding those reported in studies with smaller sample size, which is along the predictions made in the same issue by Keinan and Clark [13].
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10•• Tennessen, J.A., Bigham, A.W., O'Connor, T.D., Fu, W., Kenny, E.E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337 (2012), 64–69 This study, along with the parallel study by Nelson et al. [9] that appeared in the same issue, provides the first significant empirical evidence — based on large-scale data (whole exome in this case) — for recent explosive growth in the history of Europeans and West Africans, with growth rate far exceeding those reported in studies with smaller sample size, which is along the predictions made in the same issue by Keinan and Clark [13].
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Tennessen, J.A.1
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11 Fu, W., O'Connor, T.D., Jun, G., Kang, H.M., Abecasis, G., Leal, S.M., Gabriel, S., Rieder, M.J., Altshuler, D., Shendure, J., et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493 (2013), 216–220.
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This study inferred recent growth in a homogenous European population based on targeted sequencing of regions in which variants are putatively neutral, thereby reducing confounding by purifying and background selection.
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12•• Gazave, E., Ma, L., Chang, D., Coventry, A., Gao, F., Muzny, D., Boerwinkle, E., Gibbs, R.A., Sing, C.F., Clark, A.G., et al. Neutral genomic regions refine models of recent rapid human population growth. Proc Natl Acad Sci U S A 111 (2014), 757–762 This study inferred recent growth in a homogenous European population based on targeted sequencing of regions in which variants are putatively neutral, thereby reducing confounding by purifying and background selection.
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13 Keinan, A., Clark, A.G., Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 336 (2012), 740–743.
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This paper introduced analytical computation of the SFS and a fast optimization technique, packaged as an efficient method (fastNeutrino) for inference of population history in a single population. Its application confirms the results of recent European population growth in several studies.
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18•• Bhaskar, A., Wang, Y.X., Song, Y.S., Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data. Genome Res 25 (2015), 268–279 This paper introduced analytical computation of the SFS and a fast optimization technique, packaged as an efficient method (fastNeutrino) for inference of population history in a single population. Its application confirms the results of recent European population growth in several studies.
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This study presented a method tailored for the inference of recent history for a single population based on the total number of segregating sites as a function of sample size. On the basis of the method, they showed evidence of recent explosive growth in European and West African history.
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19•• Chen, H., Hey, J., Chen, K., Inferring very recent population growth rate from population-scale sequencing data: using a large-sample coalescent estimator. Mol Biol Evol, 2015 This study presented a method tailored for the inference of recent history for a single population based on the total number of segregating sites as a function of sample size. On the basis of the method, they showed evidence of recent explosive growth in European and West African history.
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Chen, H.1
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Exploring population size changes using SNP frequency spectra
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20•• Liu, X., Fu, Y.X., Exploring population size changes using SNP frequency spectra. Nat Genet 47 (2015), 555–559 This study is unique in presenting a non-parametric method, stairway plot, for population size history inference of a single population based on many epochs of constant population size that are iteratively added.
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This paper presented momi, an efficient and analytical method for computing multi-population SFS based on coalescent theory and Moran models.
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21•• Kamm, J.A., Terhorst, J., Song, Y.S., Efficient computation of the joint sample frequency spectra for multiple populations. J Comput Graph Stat, 2016, 1–37 This paper presented momi, an efficient and analytical method for computing multi-population SFS based on coalescent theory and Moran models.
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This study presented EGGS, an efficient method for analytically calculating the SFS and additional summary statistics for a single population under models according to which each epoch throughout history captures a more generalized form than previously possible, which includes the form of sub-exponential or super-exponential growth. Application of the method provided evidence for super-exponential (faster than exponential) growth in the recent history of Europeans.
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27 Steinrucken, M., Paul, J.S., Song, Y.S., A sequentially Markov conditional sampling distribution for structured populations with migration and recombination. Theor Popul Biol 87 (2013), 51–61.
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28
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This study developed a popular inference method, MSMC, which infers the history of a single population in a non-parametric fashion. It extends a previous method from the same group, PSMC, by considering haplotypes from multiple individuals.
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28•• Schiffels, S., Durbin, R., Inferring human population size and separation history from multiple genome sequences. Nat Genet 46 (2014), 919–925 This study developed a popular inference method, MSMC, which infers the history of a single population in a non-parametric fashion. It extends a previous method from the same group, PSMC, by considering haplotypes from multiple individuals.
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33 Ni, X., Guo, W., Yuan, K., Yang, X., Ma, Z., Xu, S., Zhang, S., A probabilistic method for estimating the sharing of identity by descent for populations with migration. IEEE/ACM Trans Comput Biol Bioinform 13 (2016), 281–290.
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