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Gene genealogies within a fixed pedigree, and the robustness of Kingman's coalescent.

https://arctichealth.org/en/permalink/ahliterature128100
Source
Genetics. 2012 Apr;190(4):1433-45
Publication Type
Article
Date
Apr-2012
Author
John Wakeley
Léandra King
Bobbi S Low
Sohini Ramachandran
Author Affiliation
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. wakeley@fas.harvard.edu
Source
Genetics. 2012 Apr;190(4):1433-45
Date
Apr-2012
Language
English
Publication Type
Article
Keywords
Computer simulation
Gene Frequency
Genetic Loci
Genetics, Population - methods
Genome, Human
Humans
Inheritance Patterns
Models, Genetic
Models, Statistical
Mutation Rate
Pedigree
Software
Sweden
Abstract
We address a conceptual flaw in the backward-time approach to population genetics called coalescent theory as it is applied to diploid biparental organisms. Specifically, the way random models of reproduction are used in coalescent theory is not justified. Instead, the population pedigree for diploid organisms--that is, the set of all family relationships among members of the population--although unknown, should be treated as a fixed parameter, not as a random quantity. Gene genealogical models should describe the outcome of the percolation of genetic lineages through the population pedigree according to Mendelian inheritance. Using simulated pedigrees, some of which are based on family data from 19th century Sweden, we show that in many cases the (conceptually wrong) standard coalescent model is difficult to reject statistically and in this sense may provide a surprisingly accurate description of gene genealogies on a fixed pedigree. We study the differences between the fixed-pedigree coalescent and the standard coalescent by analysis and simulations. Differences are apparent in recent past, within ˜
Notes
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PubMed ID
22234858 View in PubMed
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Genetic variation and population structure in native Americans.

https://arctichealth.org/en/permalink/ahliterature160135
Source
PLoS Genet. 2007 Nov;3(11):e185
Publication Type
Article
Date
Nov-2007
Author
Sijia Wang
Cecil M Lewis
Mattias Jakobsson
Sohini Ramachandran
Nicolas Ray
Gabriel Bedoya
Winston Rojas
Maria V Parra
Julio A Molina
Carla Gallo
Guido Mazzotti
Giovanni Poletti
Kim Hill
Ana M Hurtado
Damian Labuda
William Klitz
Ramiro Barrantes
Maria Cátira Bortolini
Francisco M Salzano
Maria Luiza Petzl-Erler
Luiza T Tsuneto
Elena Llop
Francisco Rothhammer
Laurent Excoffier
Marcus W Feldman
Noah A Rosenberg
Andrés Ruiz-Linares
Author Affiliation
The Galton Laboratory, Department of Biology, University College London, London, United Kingdom.
Source
PLoS Genet. 2007 Nov;3(11):e185
Date
Nov-2007
Language
English
Publication Type
Article
Keywords
Alleles
Chromosomes, Human - genetics
Databases, Genetic
Emigration and Immigration
Gene Frequency
Genetic Variation - genetics
Geography
Heterozygote
Humans
Indians, North American - genetics
Language
Linguistics
Phylogeny
Population Dynamics
Abstract
We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.
Notes
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PubMed ID
18039031 View in PubMed
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A test of the influence of continental axes of orientation on patterns of human gene flow.

https://arctichealth.org/en/permalink/ahliterature131361
Source
Am J Phys Anthropol. 2011 Dec;146(4):515-29
Publication Type
Article
Date
Dec-2011
Author
Sohini Ramachandran
Noah A Rosenberg
Author Affiliation
Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA. sramachandran@brown.edu
Source
Am J Phys Anthropol. 2011 Dec;146(4):515-29
Date
Dec-2011
Language
English
Publication Type
Article
Keywords
Americas
Asia
Continental Population Groups - genetics
Emigration and Immigration
Europe
Gene Flow
Genetics, Population
Geography
Humans
Microsatellite Repeats
Models, Genetic
Regression Analysis
Abstract
The geographic distribution of genetic variation reflects trends in past population migrations and can be used to make inferences about these migrations. It has been proposed that the east-west orientation of the Eurasian landmass facilitated the rapid spread of ancient technological innovations across Eurasia, while the north-south orientation of the Americas led to a slower diffusion of technology there. If the diffusion of technology was accompanied by gene flow, then this hypothesis predicts that genetic differentiation in the Americas along lines of longitude will be greater than that in Eurasia along lines of latitude. We use 678 microsatellite loci from 68 indigenous populations in Eurasia and the Americas to investigate the spatial axes that underlie population-genetic variation. We find that genetic differentiation increases more rapidly along lines of longitude in the Americas than along lines of latitude in Eurasia. Distance along lines of latitude explains a sizeable portion of genetic distance in Eurasia, whereas distance along lines of longitude does not explain a large proportion of Eurasian genetic variation. Genetic differentiation in the Americas occurs along both latitudinal and longitudinal axes and has a greater magnitude than corresponding differentiation in Eurasia, even when adjusting for the lower level of genetic variation in the American populations. These results support the view that continental orientation has influenced migration patterns and has played an important role in determining both the structure of human genetic variation and the distribution and spread of cultural traits.
Notes
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PubMed ID
21913175 View in PubMed
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