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Limits of Long-Term Selection Against Neandertal Introgression

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Limits of Long-Term Selection Against Neandertal Introgression Limits of long-term selection against Neandertal introgression Martin Petra, Svante Pääboa, Janet Kelsoa,1,2, and Benjamin Vernota,1,2 aDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany Edited by Sarah A. Tishkoff, University of Pennsylvania, Philadelphia, PA, and approved December 12, 2018 (received for review August 22, 2018) Several studies have suggested that introgressed Neandertal DNA studies. Our analysis shows that the Neandertal ancestry pro- was subjected to negative selection in modern humans. A striking portion in Europeans has not decreased significantly over the observation in support of this is an apparent monotonic decline in last 45,000 y. Using simulations of selection and introgression, Neandertal ancestry observed in modern humans in Europe over the we show that a model of weak selection against deleterious past 45,000 years. Here, we show that this decline is an artifact likely Neandertal variation also does not predict significant changes in caused by gene flow between modern human populations, which is Neandertal ancestry during the time period covered by existing not taken into account by statistics previously used to estimate ancient modern human samples. In contrast, these simulations Neandertal ancestry. When we apply a statistic that avoids assump- do predict a depletion of Neandertal ancestry around functional tions about modern human demography by taking advantage of genomic regions. We then use our updated Neandertal ancestry two high-coverage Neandertal genomes, we find no evidence for a estimates to examine the genomic distribution of introgressed change in Neandertal ancestry in Europe over the past 45,000 years. Neandertal DNA and find that selection against introgression We use whole-genome simulations of selection and introgression to was strongest in regulatory and conserved noncoding regions investigate a wide range of model parameters and find that negative compared with protein-coding sequence (CDS), suggesting that selection is not expected to cause a significant long-term decline in regulatory differences between Neandertals and modern humans genome-wide Neandertal ancestry. Nevertheless, these models re- may have been more extreme than protein-coding differences. capitulate previously observed signals of selection against Neander- tal alleles, in particular the depletion of Neandertal ancestry in Results EVOLUTION conserved genomic regions. Surprisingly, we find that this depletion Previous Neandertal Ancestry Estimate. A number of methods have is strongest in regulatory and conserved noncoding regions and in been developed to quantify Neandertal ancestry in modern hu- the most conserved portion of protein-coding sequences. man genomes (14). Among the most widely used is the f4-ratio statistic, which measures the fraction of drift shared with one of Neandertal | selection | introgression | modern human | demography two parental lineages to determine the proportion of ancestry, α, contributed by that lineage (Fig. 1 and SI Appendix, Fig. S1) (15, nterbreeding between Neandertals and modern humans 16). Although they have been used to draw inferences about I∼55,000 y ago has resulted in all present-day non-Africans gene flow between archaic and modern human populations, – inheriting at least 1 2% of their genomes from Neandertal an- f4-ratio statistics are known to be sensitive to violations of the cestors (1, 2). There is significant heterogeneity in the distribution underlying population model (15). Estimating α, the proportion of this Neandertal DNA across the genomes of present-day people (3, 4), including a reduction in Neandertal alleles in conserved Significance genomic regions (3). This has been interpreted as evidence that some Neandertal alleles were deleterious for modern humans and Since the discovery that all non-Africans inherit 2% of their were subject to negative selection following introgression (3, 5). genomes from Neandertal ancestors, there has been a great Several studies have suggested that low effective population sizes N interest in understanding the fate and effects of introgressed ( e) in Neandertals led to decreased efficacy of purifying selection Neandertal DNA in modern humans. A number of recent and the accumulation of weakly deleterious variants. Following studies have claimed that there has been continuous selec- introgression, these deleterious alleles, along with linked neutral tion against introgressed Neandertal DNA over the last 55,000 Neandertal alleles, would have been subjected to more efficient years. Here, we show that there has been no long-term purifying selection in the larger modern human population (6, 7). genome-wide removal of Neandertal DNA, and that the pre- In apparent agreement with this hypothesis, a study of Ne- vious result was due to incorrect assumptions about gene flow andertal ancestry in a set of anatomically modern humans from between African and non-African populations. Nevertheless, Upper-Paleolithic Europe used two independent statistics to selection did occur following introgression, and its effect was conclude that the amount of Neandertal DNA in modern human A strongest in regulatory regions, suggesting that Neandertals genomes decreased monotonically over the last 45,000 y (Fig. 1 , may have differed from humans more in their regulatory than dashed line) (8). This decline was interpreted as direct evidence in their protein-coding sequences. for continuous negative selection against Neandertal alleles in – modern humans (8 11). However, it was not formally shown that Author contributions: M.P., S.P., J.K., and B.V. designed research; M.P., J.K., and B.V. selection on deleterious introgressed variants could produce a performed research; M.P. and B.V. contributed new reagents/analytic tools; M.P., J.K., decline in Neandertal ancestry of the observed magnitude. and B.V. analyzed data; and M.P., S.P., J.K., and B.V. wrote the paper. Nevertheless, this decrease in Neandertal ancestry—together The authors declare no conflict of interest. with the suggestion of a higher burden of deleterious alleles in This article is a PNAS Direct Submission. Neandertals—are now commonly invoked to explain the fate of This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY). Neandertal ancestry in modern humans (9–12). 1J.K. and B.V. contributed equally to this work. Here, we reexamine estimates of Neandertal ancestry in an- 2To whom correspondence may be addressed. Email: [email protected] or cient and present-day modern humans, taking advantage of a [email protected]. second high-coverage Neandertal genome that recently became This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. available (13). This allows us to avoid some key assumptions 1073/pnas.1814338116/-/DCSupplemental. about modern human demography that were made in previous Published online January 15, 2019. www.pnas.org/cgi/doi/10.1073/pnas.1814338116 PNAS | January 29, 2019 | vol. 116 | no. 5 | 1639–1644 Downloaded by guest on September 25, 2021 f A or Mbuti in the third position of the 4 statistic), demonstrating x Statistic that this trend is not shared by all non-Africans. 0.04 x x f x Direct f4 To evaluate the sensitivity of the indirect 4-ratio to migration x x Indirect f4 events, we performed neutral simulations of Neandertal, West x x 0.03 Eurasian, and African demographic histories (Fig. 2). All simulations x x x x included introgression from Neandertals into West Eurasians, and xx SNP Count varying levels of migration between Africans and West Eurasians, 0.02 x x (million) x xxx and between African populations. We find that gene flow from West x 0.5 x x x 1.0 Eurasians into Africans leads to misestimates of Neandertal ancestry 0.01 x x when using the indirect f4-ratio statistic, and results in the incorrect x 1.5 inference of a continuous decline in Neandertal ancestry. This de- Neandertal ancestry proportion 2.0 0.00 cline is not observed in the true simulated Neandertal ancestry (Fig. 40000 30000 20000 10000 0 2A). The magnitude of this bias depends on the total amount of y ears before present West Eurasian gene flow into Africa, with larger amounts leading to apparent steeper declines (Fig. 2A). Additionally, gene flow between B C the two African populations used in the indirect f4-ratio calculation leads to overestimation of the true level of Neandertal ancestry (Fig. 2C). Overall, we find that a combination of West Eurasian migration to Africa and gene flow between African populations can produce patterns that are very similar to those observed in the empirical data 1- (Fig. 2D and SI Appendix,Fig.S3A). However, we caution that ef- fective population sizes and the timing of migration also affect C.&W. Afr. E. Afr. X Archaics Chimp Altai Vindija X Dinka Chimp SI Appendix BA BA these estimates ( ,Fig.S3), and that there are likely many additional models that match the empirical data. = f4(C. and W. Afr., Chimp; X, Archaics) = f4(Altai, Chimp; X, Dinka) f4(C. and W. Afr., Chimp; E. Afr., Archaics) f4(Altai, Chimp; Vindija, Dinka) We note that an independent statistic, using a different set of genomic sites in the same ancient individuals, had been used as a Fig. 1. Direct and indirect f -ratio estimates of Neandertal ancestry. (A) Best 4 second line of evidence for an ongoing decrease in Neandertal linear fits for indirect and direct f4-ratio estimates of Neandertal ancestry in “ ancient and modern West Eurasians (solid points for direct f -ratio, “x” for ancestry (8). This statistic, which we refer to as the admixture 4 ” indirect f4-ratio). Shaded areas are 95% CIs (SI Appendix, section S1). (B) Tree array statistic, measures the proportion of Neandertal-like al- model and formula used for the indirect f4-ratio. (C) Tree model and formula leles in a given sample at sites where present-day Yoruba indi- used for the direct f4-ratio. Present-day individuals are West Eurasians from viduals carry a nearly fixed allele that differs from homozygous the SGDP panel, excluding individuals from the Near East (Neandertal an- sites in the Altai Neandertal (22).
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