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Wester JVWC, Vilchez VJS, Torre CEWL, Rodriguez-Delfin LA. Molecular characterization of mitochondrial Amerindian haplogroups and the amelogenin gene in human ancient DNA from three archaeological sites in Lambayeque - Peru. Genet Mol Biol 2020; 43:e20190265. [PMID: 33242324 PMCID: PMC7737099 DOI: 10.1590/1678-4685-gmb-2019-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/05/2020] [Indexed: 11/22/2022] Open
Abstract
Important pre-Inca civilizations, known by their great political and religious
structures, inhabited the northern coast of Peru. Archeological and
anthropological studies have shown that people from these villages have
hierarchical strata, but the genetic structure has been poorly studied. Here, we
aimed to perform a molecular characterization of the Amerindian maternal
lineages and the amelogenin gene in skeletons collected from three archeological
sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional
PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial
haplogroup B and the identification of haplogroups A, C, and D were obtained
with PCR-RFLP experiments. The sex was characterized via amplification of the
AMEL(X/Y) locus. Haplogroup frequencies were compared with
available data from other ancient and modern civilizations from the Peruvian
coast and highlands using statistical methods. Our results showed that
haplogroup C had the highest frequency, while haplogroup B showed variable
diversity in the analyzed populations. The meta-analysis revealed a positive
correlation among some coastal villages. We concluded that ancient populations
analyzed in our study showed the presence of four Amerindian mitochondrial
haplogroups, which is consistent with previous studies.
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Affiliation(s)
- Jorge Victor Wilfredo Cachay Wester
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Laboratório de Genética Humana e Médica, Ribeirão Preto, SP, Brazil
| | - Vanny Judith Soplapuco Vilchez
- Universidad Nacional Pedro Ruiz Gallo, Facultad de Ciencias Biológicas, Departamento de Biología, Laboratorio de Genética y Biología Molecular, Lambayeque, Peru
| | - Carlos Eduardo Wester La Torre
- Museo Nacional de Arqueología y Etnología Brüning, Lambayeque, Peru.,Universidad Nacional Pedro Ruiz Gallo, Facultad de Ciencias Histórico Sociales y Educación, Departamento de Arqueología, Lambayeque, Peru
| | - Luis Alberto Rodriguez-Delfin
- Universidad Nacional Pedro Ruiz Gallo, Facultad de Ciencias Biológicas, Departamento de Biología, Laboratorio de Genética y Biología Molecular, Lambayeque, Peru
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Kolopenuk J. “Pop-Up” Métis and the Rise of Canada's Post-Indigenous Formation. AMERICAN ANTHROPOLOGIST 2018. [DOI: 10.1111/aman.13044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Szathmáry EJE, Zegura SL, Hammer MF. Exceeding Hrdlička's aims: 100 Years of genetics in anthropology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:754-776. [PMID: 29574830 DOI: 10.1002/ajpa.23406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Emőke J E Szathmáry
- Department of Anthropology, St. Paul's College, University of Manitoba, 70 Dysart Road, Winnipeg, Manitoba, R3T 2M6, Canada
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Annotated Draft Genome Assemblies for the Northern Bobwhite ( Colinus virginianus) and the Scaled Quail ( Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size. G3-GENES GENOMES GENETICS 2017; 7:3047-3058. [PMID: 28717047 PMCID: PMC5592930 DOI: 10.1534/g3.117.043083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Northern bobwhite (Colinus virginianus; hereafter bobwhite) and scaled quail (Callipepla squamata) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15-20 KYA.
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Halley YA, Dowd SE, Decker JE, Seabury PM, Bhattarai E, Johnson CD, Rollins D, Tizard IR, Brightsmith DJ, Peterson MJ, Taylor JF, Seabury CM. A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene. PLoS One 2014; 9:e90240. [PMID: 24621616 PMCID: PMC3951200 DOI: 10.1371/journal.pone.0090240] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/27/2014] [Indexed: 11/20/2022] Open
Abstract
Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.
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Affiliation(s)
- Yvette A. Halley
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Scot E. Dowd
- Molecular Research LP, Shallowater, Texas, United States of America
| | - Jared E. Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Paul M. Seabury
- ElanTech Inc., Greenbelt, Maryland, United States of America
| | - Eric Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Charles D. Johnson
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Dale Rollins
- Rolling Plains Quail Research Ranch, Rotan, Texas, United States of America
| | - Ian R. Tizard
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Donald J. Brightsmith
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Markus J. Peterson
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Usme-Romero S, Alonso M, Hernandez-Cuervo H, Yunis EJ, Yunis JJ. Genetic differences between Chibcha and Non-Chibcha speaking tribes based on mitochondrial DNA (mtDNA) haplogroups from 21 Amerindian tribes from Colombia. Genet Mol Biol 2013; 36:149-57. [PMID: 23885195 PMCID: PMC3715279 DOI: 10.1590/s1415-47572013005000011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 12/03/2012] [Indexed: 11/25/2022] Open
Abstract
We analyzed the frequency of four mitochondrial DNA haplogroups in 424 individuals from 21 Colombian Amerindian tribes. Our results showed a high degree of mtDNA diversity and genetic heterogeneity. Frequencies of mtDNA haplogroups A and C were high in the majority of populations studied. The distribution of these four mtDNA haplogroups from Amerindian populations was different in the northern region of the country compared to those in the south. Haplogroup A was more frequently found among Amerindian tribes in northern Colombia, while haplogroup D was more frequent among tribes in the south. Haplogroups A, C and D have clinal tendencies in Colombia and South America in general. Populations belonging to the Chibcha linguistic family of Colombia and other countries nearby showed a strong genetic differentiation from the other populations tested, thus corroborating previous findings. Genetically, the Ingano, Paez and Guambiano populations are more closely related to other groups of south eastern Colombia, as also inferred from other genetic markers and from archeological data. Strong evidence for a correspondence between geographical and linguistic classification was found, and this is consistent with evidence that gene flow and the exchange of customs and knowledge and language elements between groups is facilitated by close proximity.
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Affiliation(s)
- Solangy Usme-Romero
- Grupo de Identificación Humana e Inmunogenética, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
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Mata-Míguez J, Overholtzer L, Rodríguez-Alegría E, Kemp BM, Bolnick DA. The genetic impact of aztec imperialism: Ancient mitochondrial DNA evidence from Xaltocan, Mexico. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:504-16. [DOI: 10.1002/ajpa.22152] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/28/2012] [Indexed: 11/11/2022]
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Stacey A, Sheffield NC, Crandall KA. Calculating expected DNA remnants from ancient founding events in human population genetics. BMC Genet 2008; 9:66. [PMID: 18928554 PMCID: PMC2588638 DOI: 10.1186/1471-2156-9-66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/17/2008] [Indexed: 11/10/2022] Open
Abstract
Background Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters. Conclusion The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible.
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Affiliation(s)
- Andrew Stacey
- Department of Statistics, Brigham Young University, Provo, UT 84602, USA.
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Gilbert MTP, Jenkins DL, Go therstrom A, Naveran N, Sanchez JJ, Hofreiter M, Thomsen PF, Binladen J, Higham TFG, Yohe RM, Parr R, Cummings LS, Willerslev E. DNA from Pre-Clovis Human Coprolites in Oregon, North America. Science 2008; 320:786-9. [DOI: 10.1126/science.1154116] [Citation(s) in RCA: 258] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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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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Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravi CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK, Fedorova SA, Golubenko MV, Stepanov VA, Gubina MA, Zhadanov SI, Ossipova LP, Damba L, Voevoda MI, Dipierri JE, Villems R, Malhi RS. Beringian standstill and spread of Native American founders. PLoS One 2007; 2:e829. [PMID: 17786201 PMCID: PMC1952074 DOI: 10.1371/journal.pone.0000829] [Citation(s) in RCA: 309] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 08/10/2007] [Indexed: 12/19/2022] Open
Abstract
Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the intial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder types all the way to South America. The data also suggest more recent bi-directional gene flow between Siberia and the North American Arctic.
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Affiliation(s)
- Erika Tamm
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
| | - Toomas Kivisild
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Maere Reidla
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
| | - Mait Metspalu
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
| | - David Glenn Smith
- Department of Anthropology, University of California at Davis, Davis, California, United States of America
| | - Connie J. Mulligan
- Department of Anthropology, University of Florida, Gainesville, Florida, United States of America
| | - Claudio M. Bravi
- Instituto Multidisciplinario de Biología Celular, La Plata, Argentina
| | - Olga Rickards
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Elsa K. Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Center, Russian Academy of Sciences, Ufa, Russia
| | - Sardana A. Fedorova
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
- Department of Molecular Genetics, Yakut Research Center, Russian Academy of Medical Sciences, Yakutia, Russia
| | - Maria V. Golubenko
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
- Institute of Medical Genetics, Tomsk Research Center, Russian Academy of Medical Sciences, Tomsk, Russia
| | - Vadim A. Stepanov
- Institute of Medical Genetics, Tomsk Research Center, Russian Academy of Medical Sciences, Tomsk, Russia
| | - Marina A. Gubina
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey I. Zhadanov
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ludmila P. Ossipova
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Larisa Damba
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail I. Voevoda
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Jose E. Dipierri
- Instituto de Biologia de la Altura–Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu, Estonian Biocentre, Tartu, Estonia
| | - Ripan S. Malhi
- Department of Anthropology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- * To whom correspondence should be addressed. E-mail:
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Waguespack NM. Why we're still arguing about the Pleistocene occupation of the Americas. Evol Anthropol 2007. [DOI: 10.1002/evan.20124] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Abstract
Mitochondrial DNA and microsatellite sequences are powerful genetic markers for inferring the genealogy and the population genetic structure of animals but they have only limited resolution for organisms that display low genetic variability due to recent strong bottlenecks. An alternative source of data for deciphering migrations and origins in genetically uniform hosts can be provided by some of their microbes, if their evolutionary history correlates closely with that of the host. In this review, we first discuss how a variety of viruses, and the bacterium Helicobacter pylori, can be used as genetic tracers for one of the most intensively studied species, Homo sapiens. Then, we review statistical problems and limitations that affect the calculation of particular population genetic parameters for these microbes, such as mutation rates, with particular emphasis on the effects of recombination, selection and mode of transmission. Finally, we extend the discussion to other host-parasite systems and advocate the adoption of an integrative approach to both sampling and analysis.
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Affiliation(s)
- Thierry Wirth
- Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University Konstanz, 78457 Konstanz, Germany.
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14
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Fix AG. Rapid deployment of the five founding Amerind mtDNA haplogroups via coastal and riverine colonization. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 128:430-6. [PMID: 15795895 DOI: 10.1002/ajpa.20230] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Numerous studies of variation in mtDNA in Amerindian populations established that four haplogroups are present throughout both North and South America. These four haplogroups (A, B, C, and D) and perhaps a fifth (X) in North America are postulated to be present in the initial founding migration to the Americas. Furthermore, studies of ancient mtDNA in North America suggested long-term regional continuity of the frequencies of these founding haplogroups. Present-day tribal groups possess high frequencies of private mtDNA haplotypes (variants within the major haplogroups), consistent with early establishment of local isolation of regional populations. Clearly these patterns have implications for the mode of colonization of the hemisphere. Recently, the earlier consensus among archaeologists for an initial colonization by Clovis hunters arriving through an ice-free corridor and expanding in a "blitzkrieg " wave was shown to be inconsistent with extensive genetic variability in Native Americans; a coastal migration route avoids this problem. The present paper demonstrates through a computer simulation model how colonization along coasts and rivers could have rapidly spread the founding lineages widely through North America.
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Affiliation(s)
- Alan G Fix
- Department of Anthropology, University of California, Riverside, California 92521, USA.
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Sardi ML, Ramírez Rozzi F, González-José R, Pucciarelli HM. South Amerindian craniofacial morphology: Diversity and implications for Amerindian evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; 128:747-56. [PMID: 16044464 DOI: 10.1002/ajpa.20235] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The most compelling models concerning the peopling of the Americas consider that modern Amerindians share a common biological pattern, showing affinities with populations of the Asian Northeast. The aim of the present study was to assess the degree of variation of craniofacial morphology of South American Amerindians in a worldwide context. Forty-three linear variables were analyzed on crania derived from American, Asian, Australo-Melanesian, European, South-Saharan African, and Polynesian regions. South America was represented by seven Amerindian samples. In order to understand morphologic diversity among Amerindians of South America, variation was estimated using regions and local populations as units of analysis. Variances and F(ST) values were calculated for each unit, respectively. Both analyses indicated that morphologic variation in Southern Amerindians is extremely high: an F(ST) of 0.01531 was obtained for Southern Amerindians, and values from 0.0371-0.1205 for other world regions. Some aspects linked to the time and mode of the peopling of the Americas and various microevolutionary processes undergone by Amerindians are discussed. Some of the alternatives proposed to explain this high variation include: a greater antiquity of the peopling than what is mostly accepted, a peopling by several highly differentiated waves, an important effect of genetic drift, and gene flow with Paleoamericans. A combination of some of these alternatives explains at least some of the variation.
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Affiliation(s)
- Marina L Sardi
- UPR 2147, Dynamique de l'Evolution Humaine, CNRS, 75014 Paris, France.
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Bandelt HJ, Herrnstadt C, Yao YG, Kong QP, Kivisild T, Rengo C, Scozzari R, Richards M, Villems R, Macaulay V, Howell N, Torroni A, Zhang YP. Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Ann Hum Genet 2004; 67:512-24. [PMID: 14641239 DOI: 10.1046/j.1469-1809.2003.00049.x] [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: 11/20/2022]
Abstract
In this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.
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Affiliation(s)
- H-J Bandelt
- Fachbereich Mathematik, Universität Hamburg, Hamburg, Germany.
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Howell N, Elson JL, Turnbull DM, Herrnstadt C. African Haplogroup L mtDNA sequences show violations of clock-like evolution. Mol Biol Evol 2004; 21:1843-54. [PMID: 15190127 DOI: 10.1093/molbev/msh184] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A set of 96 complete mtDNA sequences that belong to the three major African haplogroups (L1, L2, and L3) was analyzed to determine if mtDNA has evolved as a molecular clock. Likelihood ratio tests (LRTs) were carried out with each of the haplogroups and with combined haplogroup sequence sets. Evolution has not been clock-like, neither for the coding region nor for the control region, in combined sets of African haplogroup L mtDNA sequences. In tests of individual haplogroups, L2 mtDNAs showed violations of a molecular clock under all conditions and in both the control and coding regions. In contrast, haplogroup L1 and L3 sequences, both for the coding and control regions, show clock-like evolution. In clock tests of individual L2 subclades, the L2a sequences showed a marked violation of clock-like evolution within the coding region. In addition, the L2a and L2c branch lengths of both the coding and control regions were shorter relative to those of the L2b and L2d sequences, a result that indicates lower levels of sequence divergence. Reduced median network analyses of the L2a sequences indicated the occurrence of marked homoplasy at multiple sites in the control region. After exclusion of the L2a and L2c sequences, African mtDNA coding region evolution has not significantly departed from a molecular clock, despite the results of neutrality tests that indicate the mitochondrial coding region has evolved under nonneutral conditions. In contrast, control region evolution is clock-like only at the haplogroup level, and it thus appears to have evolved essentially independently from the coding region. The results of the clock tests, the network analyses, and the branch length comparisons all caution against the use of simple mtDNA clocks.
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Uinuk-Ool TS, Takezaki N, Klein J. Ancestry and kinships of native Siberian populations: The HLA evidence. Evol Anthropol 2003. [DOI: 10.1002/evan.10124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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