CoChat
Sign Up
PreprintCited by 4Forensic and Genetic ResearchGenetic diversity and population structurePleistocene-Era Hominins and Archaeology

The DOI matches its Crossref record.

Temporal variation in introgressed segments’ length statistics sheds light on past admixture pulses

Open access
Di Santo, Lionel N., Quilodran, Claudio S., Currat, Mathias·2023·Molecular Biology and Evolution
DOI 10.1101/2023.05.03.539203PMC PMC10715198

Preprint — published as 10.1093/molbev/msad252

Open this paper in CoChat — free accountOpen PDF

Abstract

Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remains a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomics data for a two-population system and described temporal neutral introgression patterns under a single- and two-pulse admixture model. We computed three summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within-genomes, as well as genome-wide introgression proportions. The first two statistics can confidently be used to infer inter-lineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions provided more limited insights. We then computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse with Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of genomes.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2023.05.03.539203

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The paper's results are consistent with a continuous series of hybridization events distributed in time and space during the out-of-Africa expansion, which could be considered as one major admixture pulse.

    “Our results are consistent with a continuous series of hybridization events distributed in time and space during the OOA expansion, which could be considered as one major admixture pulse (30).”

    From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [30]

    The Introduction (p. 4) says a continuous model of hybridization through space and time is compatible with human Neanderthal introgression, and the results section (p. 10) identifies a clear admixture pulse. But the Introduction explicitly says it is difficult to relate a continuous model to a number of pulses; the paper does not establish that a distributed series of events could be counted as one major pulse. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 65

  1. 10.1016/j.tree.2005.02.010 · DOI · Paper page
  2. 2008, Introduction. Extent, processes and evolutionary impact of interspecific hybridization in animals, Philos. Trans. R. Soc. B Biol. Sci, 363, 2805, 10.1098/rstb.2008.0055 · DOI
  3. 2016, A genomic perspective on hybridization and speciation, Mol. Ecol, 25, 2337, 10.1111/mec.13557 · DOI
  4. 10.1534/g3.120.401616 · DOI
  5. Gower, G. , Picazo, P. I. , Fumagalli, M. & Racimo, F . Detecting adaptive introgression in human evolution using convolutional neural networks. eLife 10, e64669 (2021). · DOI · Paper page
  6. 2021, An Extended admixture pulse model reveals the limitations to Human–Neandertal introgression dating, Mol. Biol. Evol, 38, 5156, 10.1093/molbev/msab210 · DOI
  7. Hibbins, M. S. & Hahn, M. W . Phylogenomic approaches to detecting and characterizing introgression. Genetics 220, iyab173 (2022). · DOI
  8. Corbett-Detig, R. & Nielsen, R . A Hidden Markov Model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. PLOS Genet. 13, e1006529 (2017). · DOI
  9. Medina, P. , Nielsen, R. , Thronlow, B. & Corbett-Detig, R . Estimating the timing of multiple admixture pulses during local ancestry inference. Genetics 210, 1089–1107 · DOI
  10. 10.1126/science.1188021 · DOI · Paper page
  11. 10.1093/molbev/msr048 · DOI · Paper page
  12. 10.1093/sysbio/syt032 · DOI
  13. 10.1111/mec.12814 · DOI
  14. 10.1111/evo.12712 · DOI
  15. 10.1111/evo.13643 · DOI
  16. 2002, Approximate Bayesian Computation in population genetics, Genetics, 162, 2025, 10.1093/genetics/162.4.2025 · DOI · Paper page
  17. 10.1007/s11222-009-9116-0 · DOI
  18. 10.1111/evo.13486 · DOI
  19. 10.1038/s41467-018-08089-7 · DOI · Paper page
  20. 2022, Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana parry) with implications for rare species conservation, Mol. Ecol, 31, 4622, 10.1111/mec.16615 · DOI
  21. 10.1534/genetics.112.139808 · DOI · Paper page
  22. 10.1371/journal.pgen.1007641 · DOI · Paper page
  23. 10.1038/nature25738 · DOI · Paper page
  24. 10.1126/science.aat7487 · DOI
  25. 2021, Genomic insights into the formation of human populations in East Asia, Nature, 591, 413, 10.1038/s41586-021-03336-2 · DOI
  26. 10.1126/science.abi8208 · DOI
  27. 2021, Inferring archaic introgression from hominin genetic data, Evol. Anthropol. Issues News Rev, 30, 199, 10.1002/evan.21895 · DOI
  28. 10.1038/nature09710 · DOI · Paper page
  29. 10.1126/science.aao1887 · DOI · Paper page
  30. 10.1534/genetics.112.148213 · DOI · Paper page
  31. 10.1038/nature12961 · DOI · Paper page
  32. 10.1126/science.1245938 · DOI · Paper page
  33. 2020, Identifying and interpreting apparent Neanderthal ancestry in African individuals, Cell, 180, 677, 10.1016/j.cell.2020.01.012 · DOI · Paper page
  34. 2019, Multiple episodes of interbreeding between Neanderthal and modern humans. Nat, Ecol. Evol, 3, 39
  35. 10.1534/genetics.120.303167 · DOI · Paper page
  36. 10.1073/pnas.1107450108 · DOI · Paper page
  37. 2020, The spatial signature of introgression after a biological invasion with hybridization, Front. Ecol. Evol, 8, 569620, 10.3389/fevo.2020.569620 · DOI · Paper page
  38. 2020, Assessing biological factors affecting postspeciation introgression, Evol. Lett, 4, 137, 10.1002/evl3.159 · DOI
  39. 10.1101/2022.12.22.521596 · DOI
  40. 10.1038/nature12886 · DOI · Paper page
  41. 2021, Ancient DNA analysis, Nat. Rev. Methods Primer, 1, 14, 10.1038/s43586-020-00011-0 · DOI · Paper page
  42. 2021, Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir, Sci. Data, 8, 31, 10.1038/s41597-021-00816-y · DOI
  43. 10.1038/s41586-021-03236-5 · DOI · Paper page
  44. 10.1016/j.cell.2018.02.031 · DOI · Paper page
  45. 10.1073/pnas.1514696113 · DOI · Paper page
  46. 10.1371/journal.pgen.1002947 · DOI · Paper page
  47. 10.1146/annurev-genom-083117-021749 · DOI · Paper page
  48. 10.1038/nature14558 · DOI · Paper page
  49. 10.1038/nature10617 · DOI
  50. 10.1038/nature10484 · DOI
  51. 2021, Quantifying the contribution of Neanderthal introgression to the heritability of complex traits, Nat. Commun, 12, 4481, 10.1038/s41467-021-24582-y · DOI · Paper page
  52. 10.1371/journal.pgen.1006340 · DOI · Paper page
  53. 10.1534/genetics.116.186890 · DOI · Paper page
  54. 10.1016/j.ajhg.2015.01.006 · DOI · Paper page
  55. 10.1111/j.1558-5646.2008.00413.x · DOI · Paper page
  56. 2019, The spatial scale of dispersal revealed by admixture tracts, Evol. Appl, 12, 1743, 10.1111/eva.12829 · DOI
  57. 2020, The multiple population genetic and demographic routes to islands of genomic divergence, Methods Ecol. Evol, 11, 6, 10.1111/2041-210X.13324 · DOI
  58. 2020, Reconstructing prehistoric demography: what role for extant hunter[gatherers?, Evol. Anthropol. Issues News Rev, 29, 332, 10.1002/evan.21869 · DOI
  59. 10.1038/ng0302-241 · DOI
  60. 10.1093/bioinformatics/btz030 · DOI
  61. 10.1534/genetics.112.145037 · DOI · Paper page
  62. 10.1101/gr.186684.114 · DOI
  63. 10.1038/ng.3559 · DOI
  64. 2002, Diagnostic Checking in Regression Relationships, R News, 2, 7
  65. Wood, S. N . Generalized additive models: an introduction with R. (CRC press, 2017). · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Di Santo, L. N., Quilodran, C. S., & Currat, M.
Affiliations
University of Geneva (CH)
Corresponding author
Currat, Mathias
ORCID
Venue
Molecular Biology and Evolution
Publisher
openRxiv
Published
2023-05-03
Volume
40
Issue
12
ISSN
0737-4038 (ISSN-L)
DOI
10.1101/2023.05.03.539203
PMC
PMC10715198
OpenAlex
W4388892621
Cited by
4
References
0
Citations by year
2026: 2 · 2025: 1 · 2023: 1
FWCI
0.66
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Molecular Biology and Evolution (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Archive ouverte UNIGE (University of Geneva) (submittedVersion, other-oa)
Funders
  • National Science Foundation
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (182577, 203169)
  • Université de Genève
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
Keywords
introgression, hybridization, ancient genomes, Neanderthal admixture, human, paleogenomics, temporal variation, simulation study
MeSH terms
Animals, Biological Evolution, Paleontology, Genome, Genomics, Neanderthals

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review