CoChat
Sign Up
Cited by 41

The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index.

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

Tassi, Francesca, Ghirotto, Silvia, Mezzavilla, Massimo, Vilaça, Sibelle Torres, De Santi, Lisa, Barbujani, Guido·2015·Investigative Genetics
DOI 10.1186/s13323-015-0030-2PMC PMC4636834

Published version of a preprint

Open this paper in CoChat — free account

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 · 10.1186/s13323-015-0030-2

Cites

20 of 20 references verified0 citation errors · 0 not checkable

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?

  • Circuit theory has already been used in paleoanthropological studies to model the migration of early humans from Africa using Circuitscape, taking into account terrain resistance and natural barriers, and to demonstrate that the complex relief of the Caucasus affects human dispersal and gene flow.

    “This theoretical framework has already been used in paleoanthropological studies to model the migration of early humans from Africa, using Circuitscape, taking into account terrain resistance and natural barriers [46] or to demonstrate that the complex relief of the Caucasus affects human dispersal and gene flow [47].”

    From Tracing neanderthal mobility through the romanian carpathians: a GIS-based least-cost connectivity model (2025) · cites this paper as [46]

    Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

    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

Flagged first, then by citations

Research works printed but not linked: 67

  1. Aubert M, Pike AW, Stringer C, Bartsiokas A, Kinsley L, Eggins S, et al. Confirmation of a late middle Pleistocene age for the Omo Kibish 1 cranium by direct uranium-series dating. J Hum Evol. 2012;63(5):704–10. · DOI · Paper page
  2. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, et al. A draft sequence of the Neandertal genome. Science. 2010;328(5979):710–22. · DOI · Paper page
  3. Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet. 2011;89(4):516–28. · DOI · Paper page
  4. Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD. Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci U S A. 2011;108(37):15123–8. · DOI
  5. Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, et al. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell. 2012;150(3):457–69. · DOI
  6. Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, et al. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science. 2011;334(6052):89–94. · DOI · Paper page
  7. Khrameeva EE, Bozek K, He L, Yan Z, Jiang X, Wei Y, et al. Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nat Commun. 2014;5:3584. · DOI
  8. Liu N, Zhao H. A non-parametric approach to population structure inference using multilocus genotypes. Hum Genomics. 2006;2(6):353–64. · DOI
  9. Lahr MM, Foley RA. Multiple dispersals and modern human origins. Evol Anthropol. 1994;3:48–60. · DOI
  10. Reyes-Centeno H, Ghirotto S, Detroit F, Grimaud-Herve D, Barbujani G, Harvati K. Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia. Proc Natl Acad Sci U S A. 2014;111(20):7248–53. · DOI
  11. Field JS, Petraglia MD, Lahr MM. The southern dispersal hypothesis and the South Asian archaeological record: examination of dispersal routes through GIS analysis. J Anthropol Archaeol. 2007;26:88–108. · DOI · Paper page
  12. Di D, Sanchez-Mazas A. Challenging views on the peopling history of East Asia: the story according to HLA markers. Am J Phys Anthropol. 2011;145(1):81–96. · DOI
  13. Ghirotto S, Penso-Dolfin L, Barbujani G. Genomic evidence for an African expansion of anatomically modern humans by a Southern route. Hum Biol. 2011;83(4):477–89. · DOI
  14. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, et al. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science. 2005;308(5724):1034–6. · DOI · Paper page
  15. McEvoy BP, Powell JE, Goddard ME, Visscher PM. Human population dispersal “out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Res. 2011;21(6):821–9. · DOI
  16. Quintana-Murci L, Semino O, Bandelt HJ, Passarino G, McElreavey K, Santachiara-Benerecetti AS. Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat Genet. 1999;23(4):437–41. · DOI
  17. Prugnolle F, Manica A, Balloux F. Geography predicts neutral genetic diversity of human populations. Curr Biol. 2005;15(5):R159–60. · DOI
  18. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, et al. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008;319(5866):1100–4. · DOI
  19. Tishkoff SA, Goldman A, Calafell F, Speed WC, Deinard AS, Bonne-Tamir B, et al. A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations. Am J Hum Genet. 1998;62(6):1389–402. · DOI
  20. Deshpande O, Batzoglou S, Feldman MW, Cavalli-Sforza LL. A serial founder effect model for human settlement out of Africa. Proc Biol Sci. 2009;276(1655):291–300. · DOI
  21. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. 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. · DOI · Paper page
  22. Gonzalez-Ruiz M, Santos C, Jordana X, Simon M, Lalueza-Fox C, Gigli E, et al. Tracing the origin of the east-west population admixture in the Altai region (Central Asia). PLoS One. 2012;7(11):e48904. · DOI
  23. Comas D, Plaza S, Wells RS, Yuldaseva N, Lao O, Calafell F, et al. Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages. Eur J Hum Genet. 2004;12(6):495–504. · DOI
  24. Martinez-Cruz B, Vitalis R, Segurel L, Austerlitz F, Georges M, Thery S, et al. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations. Eur J Hum Genet. 2011;19(2):216–23. · DOI
  25. Nievergelt CM, Maihofer AX, Shekhtman T, Libiger O, Wang X, Kidd KK, et al. Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel. Investig Genet. 2013;4(1):13. · DOI
  26. Mezzavilla M, Vozzi D, Pirastu N, Girotto G, d'Adamo P, Gasparini P, et al. Genetic landscape of populations along the Silk Road: admixture and migration patterns. BMC Genet. 2014;15(1):131. · DOI
  27. Lopez Herraez D, Bauchet M, Tang K, Theunert C, Pugach I, Li J, et al. Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One. 2009;4(11):e7888. · DOI
  28. Pugach I, Delfin F, Gunnarsdottir E, Kayser M, Stoneking M. Genome-wide data substantiate Holocene gene flow from India to Australia. Proc Natl Acad Sci U S A. 2013;110(5):1803–8. · DOI
  29. Xing J, Watkins WS, Witherspoon DJ, Zhang Y, Guthery SL, Thara R, et al. Fine-scaled human genetic structure revealed by SNP microarrays. Genome Res. 2009;19(5):815–25. · DOI
  30. Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, et al. Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping. Genomics. 2010;96(4):199–210. · DOI
  31. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–75. · DOI · Paper page
  32. Relethford JH. Examination of the relationship between inbreeding and population size. J Biosoc Sci. 1985;17(1):97–106. · DOI
  33. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19(9):1655–64. · DOI · Paper page
  34. Jakobsson M, Rosenberg NA. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 2007;23(14):1801–6. · DOI
  35. Rosenberg NA. Distruct: a program for the graphical display of population. Mol Ecol Notes. 2004;4:137–8. · DOI
  36. Jombart T, Devillard S, Balloux F. Discriminant Analysis of Principal Components: a new method for the analysis of genetically structured populations. BMC Genet. 2010;11:94. · DOI
  37. Jombart T, Ahmed I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011;27(21):3070–1. · DOI
  38. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution. 1984;38:1358–70. · DOI
  39. Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, et al. Recent human effective population size estimated from linkage disequilibrium. Genome Res. 2007;17(4):520–6. · DOI · Paper page
  40. Hayes BJ, Visscher PM, McPartlan HC, Goddard ME. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res. 2003;13(4):635–43. · DOI
  41. Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R. Ascertainment bias in studies of human genome-wide polymorphism. Genome Res. 2005;15(11):1496–502. · DOI
  42. Sved JA. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor Popul Biol. 1971;2(2):125–41. · DOI
  43. McVean GA. A genealogical interpretation of linkage disequilibrium. Genetics. 2002;162(2):987–91. · DOI
  44. Holsinger KE, Weir BS. Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet. 2009;10(9):639–50. · DOI
  45. Mezzavilla M, Ghirotto S. Neon: An R package to estimate human effective population size and divergence time from patterns of linkage disequilibrium between SNPS. J Comput Sci Syst Biol. 2015;8:037–044. · DOI
  46. Benazzo A, Panziera A, Bertorelle G. 4P: fast computing of population genetics statistics from large DNA polymorphism panels. Ecol Evol. 2014 (in press). · DOI
  47. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 2002;18(2):337–8. · DOI
  48. Mellars P, Gori KC, Carr M, Soares PA, Richards MB. Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proc Natl Acad Sci U S A. 2013;110(26):10699–704. · DOI · Paper page
  49. Petraglia MD, Haslam M, Fuller DQ, Boivin N, Clarkson C. Out of Africa: new hypotheses and evidence for the dispersal of Homo sapiens along the Indian Ocean rim. Ann Hum Biol. 2010;37(3):288–311. · DOI
  50. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. · DOI
  51. Oppenheimer S. A single southern exit of modern humans from Africa: before or after Toba? Quaternary Int. 2012;258:88–9. · DOI
  52. Beyin A. Upper Pleistocene human dispersals out of Africa: a review of the current state of the debate. Int J Evol Biol. 2011;2011:615094. · DOI
  53. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967;27(2):209–20.
  54. Fisher RA. On the probable error of a coefficient of correlation deduced from a small sample. Metron. 1921;1:3–32.
  55. Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A, Chen Y, et al. Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am J Hum Genet. 2015;96(6):986–91. · DOI · Paper page
  56. 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56–65. · DOI · Paper page
  57. Sved JA. Correlation measures for linkage disequilibrium within and between populations. Genet Res (Camb). 2009;91(3):183–92. · DOI
  58. Harding RM, McVean G. A structured ancestral population for the evolution of modern humans. Curr Opin Genet Dev. 2004;14(6):667–74. · DOI
  59. Eriksson A, Manica A. Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Proc Natl Acad Sci U S A. 2012;109(35):13956–60. · DOI
  60. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature. 2008;451(7181):998–1003. · DOI · Paper page
  61. Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, et al. Classic selective sweeps were rare in recent human evolution. Science. 2011;331(6019):920–4. · DOI
  62. Alves I, Sramkova Hanulova A, Foll M, Excoffier L. Genomic data reveal a complex making of humans. PLoS Genet. 2012;8(7):e1002837. · DOI
  63. Higham T, Douka K, Wood R, Ramsey CB, Brock F, Basell L, et al. The timing and spatiotemporal patterning of Neanderthal disappearance. Nature. 2014;512(7514):306–9. · DOI
  64. Stoneking M, Krause J. Learning about human population history from ancient and modern genomes. Nat Rev Genet. 2011;12(9):603–14. · DOI
  65. Vernot B, Akey JM. Resurrecting surviving Neandertal lineages from modern human genomes. Science. 2014;343(6174):1017–21. · DOI · Paper page
  66. Sanchez-Quinto F, Botigue LR, Civit S, Arenas C, Avila-Arcos MC, Bustamante CD, et al. North African populations carry the signature of admixture with Neandertals. PLoS One. 2012;7(10):e47765. · DOI
  67. Ray N, Currat M, Berthier P, Excoffier L. Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations. Genome Res. 2005;15(8):1161–7. · DOI

Cited by

Sorted by citations

Metadata

Authors
Tassi, F., Ghirotto, S., Mezzavilla, M., Vilaça, S. T., De Santi, L., & Barbujani, G.
ORCID
Barbujani, Guido
Venue
Investigative Genetics
Publisher
Springer Science and Business Media LLC
Published
2015-11-06
Volume
6
Issue
1
ISSN
2041-2223
DOI
10.1186/s13323-015-0030-2
PMC
PMC4636834
Cited by
41
References
20
Language
en
Funders
  • European Research Council (BE) (ERC-2011-AdG_295733)
  • Italian Ministery of Universities and Research (MIUR) (PRIN 2010-2011)

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