Detecting ancient positive selection in humans using extended lineage sorting
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Abstract
Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations, we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes data set, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.
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This approach is similar to the recently described extended lineage sorting (ELS) scan, which prioritized long genomic intervals where modern human and archaic hominin lineages are completely sorted.
“This approach is similar to the recently described extended lineage sorting (ELS) scan (42), which prioritized long genomic intervals where modern human and archaic hominin lineages are completely sorted.”
From An ancestral recombination graph of human, Neanderthal, and Denisovan genomes (2021) · cites this paper as [42]
One of the most comprehensive studies of regions of the modern human genome associated with selective sweep signals compared to archaics specifically included BAZ1B within the detected portions of the WBSCR.
“(iv) the most comprehensive studies focusing on regions of the modern human genome associated with selective sweep signals compared to Neanderthals/Denisovans (hereafter “archaics”) (13, 14), one of which specifically included BAZ1B within the detected portions of the WBSCR;”
COL11A1 lies in a region of the human genome that resisted archaic introgression.
“which lies in a region of the human genome that resisted archaic introgression (13)”
A large proportion of selective sweeps or high-frequency changes on glutamate receptor genes in AMH relative to archaic Homo are found in regulatory regions that control gene expression.
“Similarly, a large proportion of selective sweeps or highfrequency changes on glutamate receptor genes in AMH relative to archaic Homo are found in regulatory regions that control gene expression (Peyrégne et al., 2017;Kuhlwilm and Boeckx, 2019).”
From Glutamate receptors in domestication and modern human evolution (2020) · cites this paper as Peyrégne et al., 2017
Others, like RB1CC1 or PRDM10 and NCOA6, have been found in selective sweep screens, suggesting contributions of individual transcription factors rather than the whole class of proteins.
“Others, like RB1CC120 or PRDM10 and NCOA633 have been found in selective sweep screens, suggesting contributions of individual transcription factors, rather than the whole class of proteins.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [33]
KIF15, an interactor of KIF18A, might have been under positive selection in modern humans and contains two HHMCs.
“an interactor of KIF18A, KIF1597, might have been under positive selection in modern humans33, and contains two HHMCs.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [33]
NOVA1 is an interactor of ELAVL4, a gene that codes for a neuronal-specific RNA-binding protein and might have been under positive selection in humans.
“NOVA1101, which is an interactor of ELAVL4102, a gene that codes for a neuronal-specific RNA-binding protein and might have been under positive selection in humans33,36.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [33]
ADSL has been pointed out before as under positive selection.
“which has been pointed out before as under positive selection31,33,34,122.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [33]
NCOA6 is enriched in HF changes and has been suggested to have been under positive selection on the modern human lineage.
“This putative transcription factor is enriched in HF changes and has been suggested to have been under positive selection on the modern human lineage33,122.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [33]
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Additional file 2 of Modern human changes in regulatory regions implicated in cortical development
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- Authors
- Peyrégne, S., Boyle, M. J., Dannemann, M., & Prüfer, K.
- Affiliations
- Max Planck Institute for Evolutionary Anthropology (DE)
- Corresponding author
- Peyrégne, Stéphane
- Prüfer, Kay
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2017-07-18
- Volume
- 27
- Issue
- 9
- Pages
- 1563-1572
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC5580715
- OpenAlex
- W2952656771
- Cited by
- 93
- References
- 76
- Citations by year
- 2026: 5 · 2025: 10 · 2024: 10 · 2023: 5 · 2022: 11 · 2021: 16 · 2020: 13 · 2019: 9 · 2018: 10 · 2017: 4
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by
- Locations
- Genome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Max Planck Society
- Paul G. Allen Family foundation
- European Research Council (694707)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- selective sweeps, Neanderthals, Denisovans, human evolution, human-specific traits, regulatory evolution, background selection, human genome, 1000 Genomes Project
- MeSH terms
- Animals, Genetics, Population, Humans, Selection, Genetic, Hominidae, Genome, Human, Evolution, Molecular, Neanderthals
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