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Weiss KM. The tales genes tell (or not): A century of exploration. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:741-753. [PMID: 29574847 DOI: 10.1002/ajpa.23333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/13/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022]
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Culverhouse RC, Hinrichs AL, Suarez BK. Identifying cryptic population structure in multigenerational pedigrees in a Mexican American sample. BMC Proc 2014; 8:S4. [PMID: 25519323 PMCID: PMC4143674 DOI: 10.1186/1753-6561-8-s1-s4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cryptic population structure can increase both type I and type II errors. This is particularly problematic in case-control association studies of unrelated individuals. Some researchers believe that these problems are obviated in families. We argue here that this may not be the case, especially if families are drawn from a known admixed population such as Mexican Americans. We use a principal component approach to evaluate and visualize the results of three different approaches to searching for cryptic structure in the 20 multigenerational families of the Genetic Analysis Workshop 18 (GAW18). Approach 1 uses all family members in the sample to identify what might be considered "outlier" kindreds. Because families are likely to differ in size (in the GAW18 families, there is about a 4-fold difference in the number of typed individuals), approach 2 uses a weighting system that equalizes pedigree size. Approach 3 concentrates on the founders and the "marry-ins" because, in principle, the entire pedigree can be reconstructed with knowledge of the sequence of these unrelated individuals and genome-wide association study (GWAS) data on everyone else (to identify the position of recombinations). We demonstrate that these three approaches can yield very different insights about cryptic structure in a sample of families.
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Affiliation(s)
- Robert C Culverhouse
- Department of Medicine and Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Anthony L Hinrichs
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Brian K Suarez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, 63110 USA ; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110 USA
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O'Rourke D, Enk J. Genetics, Geography, and Human Variation. Hum Biol 2012. [DOI: 10.1002/9781118108062.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Malhi RS, Gonzalez-Oliver A, Schroeder KB, Kemp BM, Greenberg JA, Dobrowski SZ, Smith DG, Resendez A, Karafet T, Hammer M, Zegura S, Brovko T. Distribution of Y chromosomes among native North Americans: a study of Athapaskan population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 137:412-24. [PMID: 18618732 DOI: 10.1002/ajpa.20883] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this study, 231 Y chromosomes from 12 populations were typed for four diagnostic single nucleotide polymorphisms (SNPs) to determine haplogroup membership and 43 Y chromosomes from three of these populations were typed for eight short tandem repeats (STRs) to determine haplotypes. These data were combined with previously published data, amounting to 724 Y chromosomes from 26 populations in North America, and analyzed to investigate the geographic distribution of Y chromosomes among native North Americans and to test the Southern Athapaskan migration hypothesis. The results suggest that European admixture has significantly altered the distribution of Y chromosomes in North America and because of this caution should be taken when inferring prehistoric population events in North America using Y chromosome data alone. However, consistent with studies of other genetic systems, we are still able to identify close relationships among Y chromosomes in Athapaskans from the Subarctic and the Southwest, suggesting that a small number of proto-Apachean migrants from the Subarctic founded the Southwest Athapaskan populations.
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Affiliation(s)
- Ripan Singh Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, IL 61801, USA.
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Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, Bedoya G, Rojas W, Parra MV, Molina JA, Gallo C, Mazzotti G, Poletti G, Hill K, Hurtado AM, Labuda D, Klitz W, Barrantes R, Bortolini MC, Salzano FM, Petzl-Erler ML, Tsuneto LT, Llop E, Rothhammer F, Excoffier L, Feldman MW, Rosenberg NA, Ruiz-Linares A. Genetic variation and population structure in native Americans. PLoS Genet 2007; 3:e185. [PMID: 18039031 PMCID: PMC2082466 DOI: 10.1371/journal.pgen.0030185] [Citation(s) in RCA: 347] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 09/10/2007] [Indexed: 01/04/2023] Open
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.
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Affiliation(s)
- Sijia Wang
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
| | - Cecil M Lewis
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mattias Jakobsson
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sohini Ramachandran
- Department of Biological Sciences, Stanford University, Stanford, California, United States of America
| | - Nicolas Ray
- Computational and Molecular Population Genetics Lab, University of Bern, Bern, Switzerland
| | - Gabriel Bedoya
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Winston Rojas
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Maria V Parra
- Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
| | - Julio A Molina
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, United States of America
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Guido Mazzotti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Kim Hill
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Ana M Hurtado
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Damian Labuda
- Département de Pédiatrie, CHU Sainte-Justine, Université de Montréal, Montréal, Quebec, Canada
| | - William Klitz
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
- Public Health Institute, Oakland, California, United States of America
| | - Ramiro Barrantes
- Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Luiza T Tsuneto
- Departamento de Genética, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Elena Llop
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Francisco Rothhammer
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Laurent Excoffier
- Computational and Molecular Population Genetics Lab, University of Bern, Bern, Switzerland
| | - Marcus W Feldman
- Department of Biological Sciences, Stanford University, Stanford, California, United States of America
| | - Noah A Rosenberg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrés Ruiz-Linares
- The Galton Laboratory, Department of Biology, University College London, London, United Kingdom
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Mulligan CJ, Hunley K, Cole S, Long JC. POPULATION GENETICS, HISTORY, AND HEALTH PATTERNS IN NATIVE AMERICANS. Annu Rev Genomics Hum Genet 2004; 5:295-315. [PMID: 15485351 DOI: 10.1146/annurev.genom.5.061903.175920] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past two decades, detailed studies of mitochondrial DNA and the Y chromosome have increased our understanding of the history and population genetics of Native American populations. Variation in autosomal DNA has also been investigated, but to a more limited extent. A low level of genetic diversity in Native American populations is a robust finding from all lines of evidence. In contrast to the previous multiple migration scenarios for the Pleistocene peopling of the Americas, it now seems that a single migration satisfactorily explains the genetic data. Native Americans show greater genetic similarity to populations in east central Asia than they do to the current easternmost Siberian populations. Recent studies on the Y chromosome indicate a date of entry (about 17,000 years ago) into the Americas roughly consistent with the archaeological record. Native Americans experienced two episodes of reduced population size: one with the peopling of the Americas and the other with European contact. The former is the more important determinant for the number of gene lineages and founding haplotypes seen in populations. It may also be an important determinant of the genetic variation underlying common complex diseases, and especially diabetes. The tribal structure of contemporary Native American populations is relevant to the distribution of rare Mendelian disorders because most tribes constitute relatively small, semi-independent gene pools. This leads us to expect that the allelic spectrum for Mendelian diseases will be simple within individual tribes but complex for Native Americans as a whole.
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Affiliation(s)
- Connie J Mulligan
- Department of Anthropology, University of Florida , Gainesville, Florida 32611, USA.
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Smith DG, Lorenz J, Rolfs BK, Bettinger RL, Green B, Eshleman J, Schultz B, Malhi R. Implications of the distribution of Albumin Naskapi and Albumin Mexico for new world prehistory. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2000; 111:557-72. [PMID: 10727973 DOI: 10.1002/(sici)1096-8644(200004)111:4<557::aid-ajpa10>3.0.co;2-b] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The known distributions of two mutational variants of the albumin gene that are restricted to Mexico and/or North America, Albumin Mexico (AL*Mexico) and Albumin Naskapi (AL*Naskapi), were expanded by the electrophoretic analysis of sera collected from more than 3, 500 Native Americans representing several dozen tribal groups. With a few exceptions that could be due to recent, isolated cases of admixture, AL*Naskapi is limited to groups that speak Athapaskan and Algonquian, two widely distributed language families not thought to be related, and to several linguistically unrelated groups geographically proximate to its probable ancestral homeland. Similarly, AL*Mexico is limited to groups that speak Yuman or Uto-Aztecan, two language groups in the American Southwest and Baja California not thought to be closely related to each other, and to several linguistically unrelated groups throughout Mexico. The simultaneous consideration of genetic, historical, linguistic, and archaeological evidence suggests that AL*Naskapi probably originated on the northwestern coast of North America, perhaps in some group ancestral to both Athapaskans and Algonquians, and then spread by migration and admixture to contiguous unrelated, or distantly related, tribal groups. AL*Mexico probably originated in Mexico before 3,000 years BP then spread northward along the Tepiman corridor together with cultural influences to several unrelated groups that participated in the Hohokam culture.
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Affiliation(s)
- D G Smith
- Department of Anthropology, University of California at Davis, Davis, California 95616, USA.
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Barbujani G, Pilastro A, De Domenico S, Renfrew C. Genetic variation in North Africa and Eurasia: neolithic demic diffusion vs. Paleolithic colonisation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1994; 95:137-54. [PMID: 7802092 DOI: 10.1002/ajpa.1330950203] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The hypothesis that both genetic and linguistic similarities among Eurasian and North African populations are due to demic diffusion of neolithic farmers is tested against a wide database of allele frequencies. Demic diffusion of farming and languages from the Near East should have determined clines in areas defined by linguistic criteria; the alternative hypothesis of cultural transmission does not predict clines. Spatial autocorrelation analysis shows significant gradients in three of the four linguistic families supposedly affected by neolithic demic diffusion; the Afroasiatic family is the exception. Many such gradients are not observed when populations are jointly analyzed, regardless of linguistic classification. This is incompatible with the hypothesis that major cultural transformations in Eurasia (diffusion of related languages and spread of agriculture) took place without major demographic changes. The model of demic diffusion seems therefore to provide a mechanism explaining coevolution of linguistic and biological traits in much of the Old World. Archaeological, linguistic, and genetic evidence agree in suggesting a multidirectional process of gene flow from the Near East in the neolithic. However, the possibility should be envisaged that some allele frequency patterns can predate the neolithic and depend on the initial spread of Homo sapiens sapiens from Africa into Eurasia.
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Affiliation(s)
- G Barbujani
- Dipartimento di Scienze Statistiche, Università di Bologna, Italy
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Worldwide distribution of phosphoglucomutase 1 (PGM1) polymorphism detected by isoelectric focusing: A review. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf02447599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hazout S, Guasp G, Loirat F, Maurieres P, Larrouy G, Dugoujon JM. A new approach for interpreting the genetic diversity in space: 'Mobile Site Method'. Application to Gm haplotype distribution of twenty-seven Amerindian tribes from North and Central America. Ann Hum Genet 1993; 57:221-37. [PMID: 8257092 DOI: 10.1111/j.1469-1809.1993.tb01598.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We present a new approach, called 'Mobile Site Method' (MSM), to the construction of 'genetic similarity maps' more efficient than that described in a preceding paper (Hazout et al. 1991). After building a triangular mesh between the geographical sites, the method consists of moving these locations at each iteration to reduce the overall differences between the geographic and genetic distances. The genetic similarity map, i.e. the final distorted map, allows the interpretation of the genetic diversity of a population set. We have applied this method to the study of Gm immunoglobulin allotypes of twenty-seven Amerindian groups from North and Central America. By a local weighted linear regression, we have reconstituted the distorted contour of America. This representation completes the observations of the sites during the map distortion. In this study, we have defined a large geographical factor in the genetic data (84% of the variability explained), related to a linguistic factor.
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Affiliation(s)
- S Hazout
- Unité de Recherches Biomathématiques et Biostatistiques, INSERM U 263, Université Paris 7, France
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Callegari-Jacques SM, Salzano FM, Constans J, Maurieres P. Gm haplotype distribution in Amerindians: relationship with geography and language. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1993; 90:427-44. [PMID: 7682769 DOI: 10.1002/ajpa.1330900404] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A review is made of the Gm haplotype distribution in 60 groups of Eskimos, North, Central and South American Indians, totaling 22,808 individuals. Differences were observed in the shapes of the distribution of Gm*ag and the other markers. Nearly identical values for FST and average heterozygosities were obtained in the North+Central/South comparisons. North-South and Southwest/Northeast clinal differences were observed in the Americas using correspondence factorial analysis. The two haplotypes mainly responsible for these differences are Gm*axg and Gm*abOst. When the populations are classified by language groups, besides the recognized differences between Eskimos and Athabaskan (Na-Dene) speakers compared with Amerinds, others are found. For instance, Uto-Aztecan speakers of the United States and Mexico differ in Gm frequencies from the Nuclear Chibchan, Macro-Arawak, and Carib speakers of Central and South America. The notion of a homogeneous Amerind genetic pool does not conform with these and other results.
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Affiliation(s)
- S M Callegari-Jacques
- Departamento de Estatistica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Rothhammer F, Silva C. Gene geography of South America: testing models of population displacement based on archeological evidence. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1992; 89:441-6. [PMID: 1463088 DOI: 10.1002/ajpa.1330890405] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Gene frequencies for 13 marker systems are used to construct synthetic gene frequency maps of South America. The surfaces generated using the first three principal components exhibit clines which validate models of population displacement based on archeological data and a previous analysis of craniometrical variation.
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Affiliation(s)
- F Rothhammer
- Departamento de Biología Celular y Genética, Facultad de Medicina, Universidad de Chile
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Chakraborty R. Gene admixture in human populations: Models and predictions. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1986. [DOI: 10.1002/ajpa.1330290502] [Citation(s) in RCA: 135] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Gene frequency data from six polymorphic blood group systems in 70 South American Indian populations are used to derive synthetic gene frequency maps that document the geographical pattern of genetic variation. Additional analyses are directed toward the elucidation of mechanisms that give rise to or maintain the observed distributions. Variables of local ecology do not appear to explain gene frequency distributions in South America. Instead, local isolation and the action of stochastic forces appears to be the most parsimonious explanation of the observed geographical patterns. This is distinctly different from the geographical patterns of genetic variation seen in other continents.
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Suarez BK, O'Rourke DH, Crouse JD. Genetic variation in North Amerindian populations: association with sociocultural complexity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1985; 67:233-9. [PMID: 4061580 DOI: 10.1002/ajpa.1330670308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A survey of nine polymorphic loci for 82 North Amerindian populations was undertaken to test the hypothesis that increasing levels of sociocultural complexity are ineluctably accompanied by increased heterozygosity. The data reveal a significant relationship in the predicted direction. Moreover, the significant correlation between average heterozygosity and sociocultural complexity is substantially increased by the removal of 19 highly admixed samples. However, this relationship, at least among North Amerindian populations, may be more apparent than real since both mean heterozygosity and the level of sociocultural organization are significantly negatively correlated with latitude. When this latter variable is controlled for, all correlations between heterozygosity and sociocultural complexity are rendered nonsignificant.
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O'Rourke DH, Suarez BK, Crouse JD. Genetic variation in North Amerindian populations: covariance with climate. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 1985; 67:241-50. [PMID: 4061581 DOI: 10.1002/ajpa.1330670309] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Allelic frequencies at seven polymorphic loci in 74 North Amerindian populations are examined relative to patterns of climatic variation. Canonical correlation analysis reveals strong and significant associations of heterozygosity at the ABO, Ss, Duffy, and P loci with climatic variability. Principal component analysis demonstrates that these loci tend to form correlated ensembles. Moreover, canonical correlation analysis of component scores provides support for an association between polymorphism at these loci and environmental variability. The results are concordant with two previous investigations which suggested a relationship between polymorphism for the ABO, Duffy, and Diego systems and climate. It is suggested that the examination of broad geographic patterns of genetic variation at multiple loci is a valuable, but underutilized, method of screening for the effects of long-term systematic pressures.
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