We also developed a likelihood ratio test, generalizing the Hotelling T -test, to evaluate the statistical evidence for larger values of N , allowing us to estimate the minimum number of exchanges between Asia and America that are needed to explain the genetic data. We used the Admixture Graph AG framework 24 to fit models of population separation followed by mixture to the data.
An AG makes predictions about the correlations in allele frequency differentiation statistics f -statistics that will be observed among all pairs, triples, and quadruples of populations 24 , and these can be compared to the observed values along with a standard error from a Block Jackknife to test hypotheses about population relationships Note S7.
We do not have a formal goodness-of-fit test for whether a given AG fits the data correcting for the number of hypotheses tested and number of degrees of freedom, but use two approximations. This results in a nominal P-value, but it is unclear to us at present whether the empirical covariance matrix that we obtain can be equated with the theoretical covariance matrix that is needed to compute a formal P-value. We are grateful to the volunteers who provided the samples that made this study possible.
We thank E. Ruiz for assistance in the collection involving the Mixtec, Zapotec and Mixe; A. Carnevale, M. Crawford, M. Metspalu, F. Nielsen, X. Soberon, R. Villems and E. Willerslev for facilitating sharing of data from Mexican, Siberian and Arctic populations; and C.
Stevens and A. Crenshaw for assistance with genotyping. We thank P. Bellwood, D. Bolnick, K. Bryc, J. Diamond, T. Dillehay, R. Hammer, J.
Hill, B. Kemp, S. LeBlanc, D. Meltzer, P. Moorjani, A. Moreno-Estrada, B. Pakendorf, J. Pickrell, M. Ruhlen, D. Smith, M. Stoneking, N. Tuross and A. Williams for thoughtful critiques and valuable discussions. Author contributions. All other authors contributed to collection of samples and data. Data access. The data analyzed here are available for non-profit research on population history under an inter-institutional data access agreement with the Universidad de Antioquia, Colombia.
Queries regarding data access should be sent jointly to G. National Center for Biotechnology Information , U. Author manuscript; available in PMC Apr 3. Dib , 8 Claudio M. Freimer , 37 Alkes L. Maria V. Luis F. Juan C. Claudio M.
Francisco M. Alejandra V. David B. Rem I. Nelson B. Alkes L. Author information Copyright and License information Disclaimer. Copyright notice. The publisher's final edited version of this article is available at Nature. This article has been corrected. See the correction in volume on page See other articles in PMC that cite the published article. Associated Data Supplementary Materials 1. Abstract The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved 1 — 5.
Open in a separate window. Figure 1. Geographic, linguistic and genetic overview of 52 Native American populations A Sampling locations of the populations, with colors corresponding to linguistic groups.
Table 1 Native Americans descend from at least three streams of Asian gene flow. Population groupings tested P-value for this many Asian streams being enough to explain the data Minimum number of streams of Asian gene flow needed to explain the data 1 2 3 E. Figure 2. Distinct streams of gene flow from Asia into America We present an Admixture Graph AG that gives no evidence of being a poor fit to the data and is consistent with three streams of Asian gene flow into America.
Figure 3. A model fitting populations of entirely First American ancestry We show an Admixture Graph AG depicting the relationships among 16 selected Native American populations with entirely First American ancestry along with 2 outgroups Yoruba and Han.
Methods DNA Samples The samples analyzed here were collected for previous studies over several decades. Genotyping All samples were genotyped using Illumina arrays, and the data set analyzed here is the result of merging data from seven different sources Note S1. Correlating geography with population diversity Euclidean distances from the Bering Strait Documentation of at least three streams of gene flow from Asia to America We used the 4 Population Test to assess whether proposed sets of four populations were consistent with a tree.
Admixture Graphs We used the Admixture Graph AG framework 24 to fit models of population separation followed by mixture to the data. Supplementary Material 1 Click here to view. Acknowledgments We are grateful to the volunteers who provided the samples that made this study possible.
Footnotes Author contributions. References 1. Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLoS Genet. Abbi, A. Is Great Andamanese genealogically and typologically distinct from Onge and Jarawa? Language Sciences The International HapMap Consortium. A second generation human haplotype map of over 3. Nature , — Li, J. Worldwide human relationships inferred from genome-wide patterns of variation. Science , — Jakobsson, M.
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Mating systems of the Andhra Pradesh people. Cold Spring Harb. Nei, M. Estimation of fixation indices and gene diversities. Karve, I. Hindu Society—an Interpretation S. Deshmukh, Boivin, N. Book Google Scholar. Dirks, N. Press, Bhasin, M. Campbell, C. Demonstrating stratification in a European American population. Nature Genet.
Haldane, J. A defense of beanbag genetics. Dhandapany, P. Pemberton, T. Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. The jackknife and the bootstrap for general stationary observations. Keinan, A. Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans.
Cavalli-Sforza, L. Phylogenetic analysis. Models and estimation procedures. Pritchard, J. Inference of population structure using multilocus genotype data. Genetics , — Falush, D. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.
Mallory, J. Barik, S. Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. DOI: Patterson and Alkes L. Reich , K. Singh Published 10 August Biology, Medicine Nature India has been underrepresented in genome-wide surveys of human variation. We analyse 25 diverse groups in India to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today.
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