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- Population divergence with or without admixture: selecting models using an ABC approach
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The event will take place on May 25th, at the Novotel Centrum in Katowice. We further removed samples that were outliers in PCA relative to others from their group, showed an excess rate of heterozygotes compared to the expected rate from the frequency in the population, or had evidence of being a second degree relative or closer to another sample in the study Note S1.
Haplotype phase in the ancestral panel, which is necessary for HAPMIX, was determined by phasing both pools of samples together using Beagle Multiple analyses reported in the supplementary materials indicate that our masking procedure produces inferences about history that are consistent with those based on unadmixed samples. Euclidean distances from the Bering Strait We computed a Pearson correlation coefficient between heterozygosity for each population and their least cost distance from the Bering Strait Note S5.
We used the 4 Population Test to assess whether proposed sets of four populations were consistent with a tree. We applied a Hotelling T -test to assess whether the ensemble of all possible f 4 statistics was consistent with zero after taking into account their correlation structure, resulting in a single hypothesis test for whether the Test Population is consistent with having the same relationship to the panel of Asian populations as the set of Southern Native American samples used as a reference group.
We also generalized this test by studying the matrix of all f 4 statistics simultaneously and computing statistics that measure whether the f 4 statistics seen in proposed sets of Native American populations are consistent with deriving from a specified number of Asian migrations. In Note S6 we show that if there have been N distinct streams of gene flow from Asia into the Americas, then the matrix of all possible f 4 statistics can have rank no more than N - 1 ignoring sampling noise. 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.
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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.
Fosroc Conplast P211 Water Reducing Admixture
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.
a glance at my past a past packed with admixture of events and challenges Manual
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 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.
Population divergence with or without admixture: selecting models using an ABC approach
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. The History and Geography of Human Genes. Princeton, UP: Meltzer DJ. First peoples in a new world : colonizing ice age America. University of California Press; The late Pleistocene dispersal of modern humans in the Americas.
Dillehay TD. Probing deeper into first American studies. The human genetic history of the Americas: the final frontier. Tamm E, et al. Beringian standstill and spread of Native American founders. PLos ONE. A three-stage colonization model for the peopling of the Americas. Fagundes NJ, et al. Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas.
Lell JT, et al. The dual origin and Siberian affinities of Native American Y chromosomes.
Bortolini MC, et al. Y-chromosome evidence for differing ancient demographic histories in the Americas. Volodko NV, et al. Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas. Am J Hum Genet. Ray N, et al. A statistical evaluation of models for the initial settlement of the american continent emphasizes the importance of gene flow with Asia. Evaluating microevolutionary models for the early settlement of the New World: the importance of recurrent gene flow with Asia.
Perego UA, et al.
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Fast model-based estimation of ancestry in unrelated individuals. Genome Res. Ruhlen M. A Guide to the World's Languages. Stanford University Press; Schroeder KB, et al.