Effect of Ancient Population Structure on the Degree of Polymorphism Shared Between Modern Human Populations and Ancient Hominins

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2012 Aug 16

PMID 22893688

Citations 84

Authors

Anders Eriksson

Andrea Manica

Affiliations

Soon will be listed here.

Abstract

Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.

Citing Articles

High-resolution genomic history of early medieval Europe.

Speidel L, Silva M, Booth T, Raffield B, Anastasiadou K, Barrington C Nature. 2025; 637(8044):118-126.

PMID: 39743601 PMC: 11693606. DOI: 10.1038/s41586-024-08275-2.

Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events.

Tournebize R, Chikhi L Nat Ecol Evol. 2024; 9(2):225-236.

PMID: 39672950 DOI: 10.1038/s41559-024-02591-6.

An explanation for the sister repulsion phenomenon in Patterson's f-statistics.

Atag G, Waldman S, Carmi S, Somel M Genetics. 2024; 228(3).

PMID: 39292210 PMC: 11538414. DOI: 10.1093/genetics/iyae144.

Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation.

Koppetsch T, Malinsky M, Matschiner M Syst Biol. 2024; 73(5):769-788.

PMID: 38912803 PMC: 11639170. DOI: 10.1093/sysbio/syae028.

Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus).

Myers E, Rautsaw R, Borja M, Jones J, Grunwald C, Holding M Syst Biol. 2024; 73(4):722-741.

PMID: 38695290 PMC: 11906154. DOI: 10.1093/sysbio/syae018.

References

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

Stringer C . Modern human origins: progress and prospects. Philos Trans R Soc Lond B Biol Sci. 2002; 357(1420):563-79. PMC: 1692961. DOI: 10.1098/rstb.2001.1057. 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

Rasmussen M, Guo X, Wang Y, Lohmueller K, Rasmussen S, Albrechtsen A . An Aboriginal Australian genome reveals separate human dispersals into Asia. Science. 2011; 334(6052):94-8. PMC: 3991479. DOI: 10.1126/science.1211177. View

Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L . ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics. 2010; 11:116. PMC: 2848233. DOI: 10.1186/1471-2105-11-116. View

Relethford J . Genetic evidence and the modern human origins debate. Heredity (Edinb). 2008; 100(6):555-63. DOI: 10.1038/hdy.2008.14. View

Hawks J, Oh S, Hunley K, Dobson S, Cabana G, Dayalu P . An Australasian test of the recent African origin theory using the WLH-50 calvarium. J Hum Evol. 2000; 39(1):1-22. DOI: 10.1006/jhev.1999.0384. View

Ramachandran S, Deshpande O, Roseman C, Rosenberg N, Feldman M, Cavalli-Sforza L . Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A. 2005; 102(44):15942-7. PMC: 1276087. DOI: 10.1073/pnas.0507611102. View

Reich D, Patterson N, Kircher M, Delfin F, Nandineni M, Pugach I . Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet. 2011; 89(4):516-28. PMC: 3188841. DOI: 10.1016/j.ajhg.2011.09.005. View

10.

Hofreiter M . Drafting human ancestry: what does the Neanderthal genome tell us about hominid evolution? Commentary on Green et al. (2010). Hum Biol. 2011; 83(1):1-11. DOI: 10.3378/027.083.0101. View

11.

Durand E, Patterson N, Reich D, Slatkin M . Testing for ancient admixture between closely related populations. Mol Biol Evol. 2011; 28(8):2239-52. PMC: 3144383. DOI: 10.1093/molbev/msr048. View

12.

Hammer M, Woerner A, Mendez F, Watkins J, Wall J . Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci U S A. 2011; 108(37):15123-8. PMC: 3174671. DOI: 10.1073/pnas.1109300108. View

13.

Manica A, Prugnolle F, Balloux F . Geography is a better determinant of human genetic differentiation than ethnicity. Hum Genet. 2005; 118(3-4):366-71. PMC: 1805472. DOI: 10.1007/s00439-005-0039-3. View

14.

Pamilo P, Nei M . Relationships between gene trees and species trees. Mol Biol Evol. 1988; 5(5):568-83. DOI: 10.1093/oxfordjournals.molbev.a040517. View

15.

DeGiorgio M, Jakobsson M, Rosenberg N . Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proc Natl Acad Sci U S A. 2009; 106(38):16057-62. PMC: 2752555. DOI: 10.1073/pnas.0903341106. View

16.

Trinkaus E, Moldovan O, Milota S, Bilgar A, Sarcina L, Athreya S . An early modern human from the Peştera cu Oase, Romania. Proc Natl Acad Sci U S A. 2003; 100(20):11231-6. PMC: 208740. DOI: 10.1073/pnas.2035108100. View

17.

Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A . A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 1996; 380(6570):152-4. DOI: 10.1038/380152a0. View

18.

Herrera K, Somarelli J, Lowery R, Herrera R . To what extent did Neanderthals and modern humans interact?. Biol Rev Camb Philos Soc. 2009; 84(2):245-57. DOI: 10.1111/j.1469-185x.2008.00071.x. View

19.

Gunz P, Bookstein F, Mitteroecker P, Stadlmayr A, Seidler H, Weber G . Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario. Proc Natl Acad Sci U S A. 2009; 106(15):6094-8. PMC: 2669363. DOI: 10.1073/pnas.0808160106. View

20.

Harding R, McVean G . A structured ancestral population for the evolution of modern humans. Curr Opin Genet Dev. 2004; 14(6):667-74. DOI: 10.1016/j.gde.2004.08.010. View