Bayesian Inference of Ancient Human Demography from Individual Genome Sequences

Overview

Journal Nat Genet

Specialty Genetics

Date 2011 Sep 20

PMID 21926973

Citations 258

Authors

Ilan Gronau

Melissa J Hubisz

Brad Gulko

Charles G Danko

Adam Siepel

Affiliations

Soon will be listed here.

Abstract

Whole-genome sequences provide a rich source of information about human evolution. Here we describe an effort to estimate key evolutionary parameters based on the whole-genome sequences of six individuals from diverse human populations. We used a Bayesian, coalescent-based approach to obtain information about ancestral population sizes, divergence times and migration rates from inferred genealogies at many neutrally evolving loci across the genome. We introduce new methods for accommodating gene flow between populations and integrating over possible phasings of diploid genotypes. We also describe a custom pipeline for genotype inference to mitigate biases from heterogeneous sequencing technologies and coverage levels. Our analysis indicates that the San population of southern Africa diverged from other human populations approximately 108-157 thousand years ago, that Eurasians diverged from an ancestral African population 38-64 thousand years ago, and that the effective population size of the ancestors of all modern humans was ∼9,000.

Citing Articles

Phylogenetic analysis of microbial CP-lyase cluster genes for bioremediation of phosphonate.

Richard P, Baltosser W, Williams P, He Q AMB Express. 2025; 15(1):42.

PMID: 40064825 PMC: 11893972. DOI: 10.1186/s13568-025-01856-y.

A humanized NOVA1 splicing factor alters mouse vocal communications.

Tajima Y, Vargas C, Ito K, Wang W, Luo J, Xing J Nat Commun. 2025; 16(1):1542.

PMID: 39966351 PMC: 11836289. DOI: 10.1038/s41467-025-56579-2.

Genomes of Galápagos Mockingbirds Reveal the Impact of Island Size and Past Demography on Inbreeding and Genetic Load in Contemporary Populations.

Vlcek J, Espinoza-Ulloa S, Cowles S, Ortiz-Catedral L, Coutu C, Chaves J Mol Ecol. 2025; 34(5):e17665.

PMID: 39912126 PMC: 11842953. DOI: 10.1111/mec.17665.

A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact.

Deng Y, Nielsen R, Song Y Genetics. 2024; 229(1):1-3.

PMID: 39679949 PMC: 11708913. DOI: 10.1093/genetics/iyae192.

Evolutionary genomics of Leishmania braziliensis across the neotropical realm.

Heeren S, Sanders M, Shaw J, Pinto Brandao-Filho S, Cortes Boite M, Motta Cantanhede L Commun Biol. 2024; 7(1):1587.

PMID: 39609617 PMC: 11605123. DOI: 10.1038/s42003-024-07278-z.

References

Zhivotovsky L, Rosenberg N, Feldman M . Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet. 2003; 72(5):1171-86. PMC: 1180270. DOI: 10.1086/375120. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Paul J, Steinrucken M, Song Y . An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics. 2011; 187(4):1115-28. PMC: 3070520. DOI: 10.1534/genetics.110.125534. View

Tishkoff S, Reed F, Friedlaender F, Ehret C, Ranciaro A, Froment A . The genetic structure and history of Africans and African Americans. Science. 2009; 324(5930):1035-44. PMC: 2947357. DOI: 10.1126/science.1172257. View

Kondrashov A . Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Hum Mutat. 2002; 21(1):12-27. DOI: 10.1002/humu.10147. View

Liu H, Prugnolle F, Manica A, Balloux F . A geographically explicit genetic model of worldwide human-settlement history. Am J Hum Genet. 2006; 79(2):230-7. PMC: 1559480. DOI: 10.1086/505436. View

Gonder M, Mortensen H, Reed F, De Sousa A, Tishkoff S . Whole-mtDNA genome sequence analysis of ancient African lineages. Mol Biol Evol. 2006; 24(3):757-68. DOI: 10.1093/molbev/msl209. View

Bentley D, Balasubramanian S, Swerdlow H, Smith G, Milton J, Brown C . Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008; 456(7218):53-9. PMC: 2581791. DOI: 10.1038/nature07517. View

Fagundes N, Ray N, Beaumont M, Neuenschwander S, Salzano F, Bonatto S . Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci U S A. 2007; 104(45):17614-9. PMC: 2077041. DOI: 10.1073/pnas.0708280104. View

10.

Cavalli-Sforza L, Feldman M . The application of molecular genetic approaches to the study of human evolution. Nat Genet. 2003; 33 Suppl:266-75. DOI: 10.1038/ng1113. View

11.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

12.

Wall J, Lohmueller K, Plagnol V . Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol. 2009; 26(8):1823-7. PMC: 2734152. DOI: 10.1093/molbev/msp096. View

13.

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

14.

Patterson N, Richter D, Gnerre S, Lander E, Reich D . Genetic evidence for complex speciation of humans and chimpanzees. Nature. 2006; 441(7097):1103-8. DOI: 10.1038/nature04789. View

15.

Keinan A, Mullikin J, Patterson N, Reich D . Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet. 2007; 39(10):1251-5. PMC: 3586588. DOI: 10.1038/ng2116. View

16.

Hobolth A, Christensen O, Mailund T, Schierup M . Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 2007; 3(2):e7. PMC: 1802818. DOI: 10.1371/journal.pgen.0030007. View

17.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

18.

Cann R, Stoneking M, Wilson A . Mitochondrial DNA and human evolution. Nature. 1987; 325(6099):31-6. DOI: 10.1038/325031a0. View

19.

Nielsen R, Wakeley J . Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics. 2001; 158(2):885-96. PMC: 1461674. DOI: 10.1093/genetics/158.2.885. View

20.

Gutenkunst R, Hernandez R, Williamson S, Bustamante C . Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009; 5(10):e1000695. PMC: 2760211. DOI: 10.1371/journal.pgen.1000695. View