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Chen C, Guo Y, Fang Y, Shi J, Meng H, Qu L, Zhang X, Zhu B. The maternal phylogenetic insights of Yunnan Miao group revealed by complete mitogenomes. Gene 2024; 901:148046. [PMID: 38081335 DOI: 10.1016/j.gene.2023.148046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024]
Abstract
The Miao group is one of the representative Hmong-Mien-speaking populations and primarily scattered in southern China and Southeast Asia, which has experienced massive migrations in history and thus forms distinctive evolutionary genetics. Yet, the genetic explorations of Miao group are relatively limited based on complete mitochondrial genome (mitogenome), especially for the Miao group from Yunnan Province (YNM). Here, we sequenced complete mitogenomes of 132 Miao individuals from Yunnan Province using massively parallel sequencing method. Total 132 Miao individuals could be allocated to 119 various haplotypes, which were mainly dominated by haplogroups prevalent in southern East Asia (B, F, M7 and R9), and rarely occupied by northern lineages (A, D, G and M8). In order to dissect the genetic background of YNM more comprehensively, we introduced 99 published population data with 7135 complete mitochondrial sequences for population genetic comparisons. YNM exhibited closer genetic relationships with Hmong-Mien, Tai-Kadai, Sino-Tibetan and Austroasiatic populations, especially for Hmong-Mien populations; we further speculated that Miao group might have certain direct or indirect gene exchanges with ancient Baiyue groups. Several maternal lineages, such as B5a1c1a, F1g1, B4a5 and D4e1a3, were found to be specifically shared by YNM and other Hmong-Mien populations, and these matrilineal expansions occurred roughly during the Neolithic period. Eventually, according to the population dynamic analyses of YNM, the population size began to emerge recovery ∼1-0.5 kya after a long-term population reduction ∼1-5 kya, during which the B5a1c1a haplogroup manifested relatively apparent lineage expansion.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; Department of Forensic Medicine, Faculty of Basic Medical Science, Chongqing Medical University, Chongqing 400016, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Anhui 230031, China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China
| | - Li Qu
- Department of Rheumatology and Immunology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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2
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Scott GR, Navega D, Vlemincq-Mendieta T, Dern LL, O'Rourke DH, Hlusko LJ, Hoffecker JF. Peopling of the Americas: A new approach to assessing dental morphological variation in Asian and Native American populations. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 38018312 DOI: 10.1002/ajpa.24878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023]
Abstract
OBJECTIVES Through biodistance analyses, anthropologists have used dental morphology to elucidate how people moved into and throughout the Americas. Here, we apply a method that focuses on individuals rather than sample frequencies through the application rASUDAS2, based on a naïve Bayes' algorithm. MATERIALS AND METHODS Using the database of C.G. Turner II, we calculated the probability that an individual could be assigned to one of seven biogeographic groups (American Arctic, North & South America, East Asia, Southeast Asia & Polynesia, Australo-Melanesia, Western Eurasia, & Sub-Saharan Africa) through rASUDAS2. The frequency of classifications for each biogeographic group was determined for 1418 individuals from six regions across Asia and the Americas. RESULTS Southeast Asians show mixed assignments but rarely to American Arctic or "American Indian." East Asians are assigned to East Asia half the time while 30% are assigned as Native American. People from the American Arctic and North & South America are assigned to Arctic America or non-Arctic America 75%-80% of the time, with 10%-15% classified as East Asian. DISCUSSION All Native American groups have a similar degree of morphological affinity to East Asia, as 10%-15% are classified as East Asian. East Asians are classified as Native American in 30% of cases. Individuals in the Western Hemisphere are decreasingly classified as Arctic the farther south they are located. Equivalent levels of classification as East Asian across all Native American groups suggests one divergence between East Asians and the population ancestral to all Native Americans. Non-arctic Native American groups are derived from the Arctic population, which represents the Native American founder group.
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Affiliation(s)
- G Richard Scott
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - David Navega
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | | | - Laresa L Dern
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - Dennis H O'Rourke
- Department of Anthropology, University of Kansas, Lawrence, Kansas, USA
| | | | - John F Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
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Niedbalski SD, Long JC. Novel alleles gained during the Beringian isolation period. Sci Rep 2022; 12:4289. [PMID: 35277570 PMCID: PMC8917172 DOI: 10.1038/s41598-022-08212-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/09/2022] [Indexed: 01/23/2023] Open
Abstract
During the Last Glacial Maximum, a small band of Siberians entered the Beringian corridor, where they persisted, isolated from gene flow, for several thousand years before expansion into the Americas. The ecological features of the Beringian environment, coupled with an extended period of isolation at small population size, would have provided evolutionary opportunity for novel genetic variation to arise as both rare standing variants and new mutations were driven to high frequency through both neutral and directed processes. Here we perform a full genome investigation of Native American populations in the Thousand Genomes Project Phase 3 to identify unique high frequency alleles that can be dated to an origin in Beringia. Our analyses demonstrate that descendant populations of Native Americans harbor 20,424 such variants, which is on a scale comparable only to Africa and the Out of Africa bottleneck. This is consistent with simulations of a serial founder effects model. Tests for selection reveal that some of these Beringian variants were likely driven to high frequency by adaptive processes, and bioinformatic analyses suggest possible phenotypic pathways that were under selection during the Beringian Isolation period. Specifically, pathways related to cardiac processes and melanocyte function appear to be enriched for selected Beringian variants.
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Affiliation(s)
- Sara D Niedbalski
- Human Evolutionary Genetics Unit, UMR 2000, CNRS, Institut Pasteur, Paris, France.,Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jeffrey C Long
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA.
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4
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Bodner M, Perego UA, Gomez JE, Cerda-Flores RM, Rambaldi Migliore N, Woodward SR, Parson W, Achilli A. The Mitochondrial DNA Landscape of Modern Mexico. Genes (Basel) 2021; 12:genes12091453. [PMID: 34573435 PMCID: PMC8467843 DOI: 10.3390/genes12091453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 12/16/2022] Open
Abstract
Mexico is a rich source for anthropological and population genetic studies with high diversity in ethnic and linguistic groups. The country witnessed the rise and fall of major civilizations, including the Maya and Aztec, but resulting from European colonization, the population landscape has dramatically changed. Today, the majority of Mexicans do not identify themselves as Indigenous but as admixed, and appear to have very little in common with their pre-Columbian predecessors. However, when the maternally inherited mitochondrial (mt)DNA is investigated in the modern Mexican population, this is not the case. Control region sequences of 2021 samples deriving from all over the country revealed an overwhelming Indigenous American legacy, with almost 90% of mtDNAs belonging to the four major pan-American haplogroups A2, B2, C1, and D1. This finding supports a very low European contribution to the Mexican gene pool by female colonizers and confirms the effectiveness of employing uniparental markers as a tool to reconstruct a country’s history. In addition, the distinct frequency and dispersal patterns of Indigenous American and West Eurasian clades highlight the benefit such large and country-wide databases provide for studying the impact of colonialism from a female perspective and population stratification. The importance of geographical database subsets not only for forensic application is clearly demonstrated.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Ugo A. Perego
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- Department of Math and Science, Southeastern Community College, Burlington, IA 52655, USA
| | - J. Edgar Gomez
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
- FamilySearch Int., Salt Lake City, UT 84150, USA
| | | | - Nicola Rambaldi Migliore
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA; (J.E.G.); (S.R.W.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
- Forensic Science Program, Penn State University, University Park, State College, PA 16802, USA
- Correspondence: (W.P.); (A.A.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (U.A.P.); (N.R.M.)
- Correspondence: (W.P.); (A.A.)
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Davis CA, Profico A, Kappelman J. Digital restoration of the Wilson-Leonard 2 Paleoindian skull (~10,000 BP) from central Texas with comparison to other early American and modern crania. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:486-503. [PMID: 34338313 DOI: 10.1002/ajpa.24379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/01/2021] [Accepted: 07/07/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVES Craniofacial morphology (CFM) is often used to address questions about the biological affinities of the earliest Americans, or Paleoindians, but resolution is complicated in part by a lack of well-preserved crania. The Wilson-Leonard 2 (WL-2) Paleoindian skull from Texas has never been fully analyzed because it is crushed and cannot be physically reconstructed. This study employs a digital restoration for comprehensive assessment and analysis of WL-2. MATERIALS AND METHODS High-resolution CT data and geometric morphometrics are used to restore the WL-2 skull and analyze its morphology using 65 craniometric measurements acquired on the restoration. These data allow for a full morphological description and multivariate (Mahalanobis Distance and Principal Component) comparisons to other Paleoindians and recent populations. RESULTS WL-2 has a long, narrow braincase, and a short, modestly prognathic face. Compared with other Paleoindians, she is individually similar to several skulls from Brazil, but aligns most closely with pooled samples from the US and Mexico. WL-2 is most similar to recent populations from Europe, Asia, and the Americas, and markedly different to those from Africa and Australia. DISCUSSION The overall morphology of WL-2 and her association with Asians and Europeans align well with trends identified in other CFM analyses. Her affinity to recent Amerindians contrasts with the findings of many previous CFM studies, but is seemingly consistent with molecular analyses suggesting a close relationship between some Paleoindians and modern American Indians. This study demonstrates the potential for using digital anthropological methods to study other Paleoindian crania whose data value is limited by physical destruction and/or deformation.
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Affiliation(s)
- Christopher A Davis
- Paleocultural Research Group, Broomfield, Colorado, USA.,Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA
| | - Antonio Profico
- PalaeoHub, Department of Archaeology, University of York, York, United Kingdom
| | - John Kappelman
- Department of Anthropology, The University of Texas at Austin, Austin, Texas, USA.,Department of Geological Sciences, The University of Texas at Austin, Austin, Texas, USA
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6
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Friedrich VK, Rubel MA, Schurr TG. Mitochondrial genetic variation in human bioenergetics, adaptation, and adult disease. Am J Hum Biol 2021; 34:e23629. [PMID: 34146380 DOI: 10.1002/ajhb.23629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Mitochondria are critical for the survival of eukaryotic organisms due to their ability to produce cellular energy, which drives virtually all aspects of host biology. However, the effects of mitochondrial DNA (mtDNA) variation in relation to disease etiology and adaptation within contemporary global human populations remains incompletely understood. METHODS To develop a more holistic understanding of the role of mtDNA diversity in human adaptation, health, and disease, we investigated mitochondrial biology and bioenergetics. More specifically, we synthesized details from studies of mitochondrial function and variation in the context of haplogroup background, climatic adaptation, and oxidative disease. RESULTS The majority of studies show that mtDNA variation arose during modern human dispersal around the world. Some of these variants appear to have been positively selected for their adaptiveness in colder climates, with these sequence changes having implications for tissue-specific function and thermogenic capacity. In addition, many variants modulating energy production are also associated with damaging metabolic byproducts and mitochondrial dysfunction, which, in turn, are implicated in the onset and severity of several different adult mitochondrial diseases. Thus, mtDNA variation that governs bioenergetics, metabolism, and thermoregulation may potentially have adverse consequences for human health, depending on the genetic background and context in which it occurs. CONCLUSIONS Our review suggests that the mitochondrial research field would benefit from independently replicating mtDNA haplogroup-phenotype associations across global populations, incorporating potentially confounding environmental, demographic, and disease covariates into studies of mtDNA variation, and extending association-based studies to include analyses of complete mitogenomes and assays of mitochondrial function.
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Affiliation(s)
- Volney K Friedrich
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Translational Imaging and Precision Medicine, University of California - San Diego, La Jolla, California, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Affiliation(s)
- John F. Hoffecker
- Institute of Arctic and Alpine Research, University of Colorado at Boulder, Boulder, CO, USA
| | - Scott A. Elias
- Institute of Arctic and Alpine Research, University of Colorado at Boulder, Boulder, CO, USA
| | - Olga Potapova
- Pleistocene Park Foundation, Philadelphia, PA, USA
- Department of Mammoth Fauna Studies, Academy of Sciences of Sakha, Yakutsk, Russian Federation
- The Mammoth Site of Hot Springs, SD, Inc., Hot Springs, SD, USA
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8
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Lenover MB, Šešelj M. Variation in the fusion sequence of primary and secondary ossification centers in the human skeleton. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 170:373-392. [PMID: 31468509 DOI: 10.1002/ajpa.23921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/28/2019] [Accepted: 08/06/2019] [Indexed: 11/12/2022]
Abstract
OBJECTIVES One of the biggest challenges for biological anthropologists is determining the minimum number of individuals in commingled skeletal samples in forensic or bioarcheological contexts. The fusion sequence of primary and secondary ossification centers is a promising, yet under-explored, process to improve identification of associated remains of subadults and young adults, but is limited by the lack of understanding of population variation in this aspect of human development. While prior studies show within-population variation in fusion sequence, possible geographic variation has not been systematically explored. MATERIALS AND METHODS To explore potential variation in fusion sequence in different populations, we analyzed eight skeletal samples of East Asian, North American, African, and European ancestry. Forty-three epiphyses were cross tabulated to determine the order of beginning and completing fusion for each geographic group. Results were distilled into modal sequence (most common order) trajectories, including the variation around the modal sequence. RESULTS Population variation occurs within and across all geographic groups, especially in later fusing sites. Some sites, such as the acromion and sacral elements, consistently exhibit greater variability. Among outliers from the modal sequence, it is more common for early-fusing sites to fuse late than for later-fusing sites to fuse early. The completing fusion trajectories vary less than the beginning fusion trajectories. DISCUSSION Despite considerable variation within and among different geographic groups, there are shared commonalities across different samples that can facilitate differentiation of multiple individuals. With fewer outliers, the completing fusion trajectories are potentially of greater practical use in forensic and bioarcheological practice.
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Affiliation(s)
- Makenna B Lenover
- Department of Anthropology, Bryn Mawr College, Bryn Mawr, Pennsylvania
| | - Maja Šešelj
- Department of Anthropology, Bryn Mawr College, Bryn Mawr, Pennsylvania
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León-Moreno LC, Saldaña-Cruz AM, Sánchez-Corona J, Mendoza-Carrera F, García-Zapién AG, Revilla-Monsalve C, Islas-Andrade S, Brito-Zurita O, Pérez-Vargas A, Flores-Martínez SE. Distribution of potential risk alleles and haplotypes of the CYP2C9 and CYP2C19 genes in Mexican native populations: A comparative study among Amerindian populations. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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Arias L, Barbieri C, Barreto G, Stoneking M, Pakendorf B. High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:238-255. [DOI: 10.1002/ajpa.23345] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 09/17/2017] [Accepted: 10/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Leonardo Arias
- Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Anthropology; Leipzig D-04103 Germany
- Laboratorio de Genética Molecular Humana; Universidad del Valle; Cali Colombia
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution; Max Planck Institute for the Science of Human History; Jena D-07745 Germany
| | - Guillermo Barreto
- Laboratorio de Genética Molecular Humana; Universidad del Valle; Cali Colombia
| | - Mark Stoneking
- Department of Evolutionary Genetics; Max Planck Institute for Evolutionary Anthropology; Leipzig D-04103 Germany
| | - Brigitte Pakendorf
- Dynamique du Langage; UMR5596, CNRS & Université de Lyon; Lyon Cedex 07 69363 France
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Abstract
PURPOSE OF REVIEW Cardiovascular disease (CVD) is responsible for more morbidity and mortality worldwide than any other ailment. Strategies for reducing CVD prevalence must involve identification of individuals at high risk for these diseases, and the prevention of its initial development. Such preventive efforts are currently limited by an incomplete understanding of the genetic determinants of CVD risk. In this review, evidence for the involvement of inherited mitochondrial mutations in development of CVD is examined. RECENT FINDINGS Several forms of CVD have been documented in the presence of pathogenic mitochondrial DNA (mtDNA) mutations, both in isolation and as part of larger syndromes. Other 'natural' mtDNA polymorphisms not overtly tied to any pathology have also been associated with alterations in mitochondrial function and individual risk for CVD, but until very recently these studies have been merely correlative. Fortunately, novel animal models are now allowing investigators to define a causal relationship between inherited 'natural' mtDNA polymorphisms, and cardiovascular function and pathology. SUMMARY Cardiovascular involvement is highly prevalent among patients with pathogenic mtDNA mutations. The relationship between CVD susceptibility and 'natural' mtDNA polymorphisms requires further investigation, but will be aided in the near future by several novel experimental models.
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Affiliation(s)
- Alexander W. Bray
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham
| | - Scott W. Ballinger
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham
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Di Corcia T, Sanchez Mellado C, Davila Francia TJ, Ferri G, Sarno S, Luiselli D, Rickards O. East of the Andes: The genetic profile of the Peruvian Amazon populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:328-338. [PMID: 28343372 DOI: 10.1002/ajpa.23209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/08/2016] [Accepted: 02/28/2017] [Indexed: 01/22/2023]
Abstract
OBJECTIVES Assuming that the differences between the Andes and the Amazon rainforest at environmental and historical levels have influenced the distribution patterns of genes, languages, and cultures, the maternal and paternal genetic reconstruction of the Peruvian Amazon populations was used to test the relationships within and between these two extreme environments. MATERIALS AND METHODS We analyzed four Peruvian Amazon communities (Ashaninka, Huambisa, Cashibo, and Shipibo) for both Y chromosome (17 STRs and 8 SNPs) and mtDNA data (control region sequences, two diagnostic sites of the coding region, and one INDEL), and we studied their variability against the rest of South America. RESULTS We detected a high degree of genetic diversity in the Peruvian Amazon people, both for mtDNA than for Y chromosome, excepting for Cashibo people, who seem to have had no exchanges with their neighbors, in contrast with the others communities. The genetic structure follows the divide between the Andes and the Amazon, but we found a certain degree of gene flow between these two environments, as particularly emerged with the Y chromosome descent cluster's (DCs) analysis. DISCUSSION The Peruvian Amazon is home to an array of populations with differential rates of genetic exchanges with their neighbors and with the Andean people, depending on their peculiar demographic histories. We highlighted some successful Y chromosome lineages expansions originated in Peru during the pre-Columbian history which involved both Andeans and Amazon Arawak people, showing that at least a part of the Amazon rainforest did not remain isolated from those exchanges.
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Affiliation(s)
- T Di Corcia
- Department of Biology, University of Rome "Tor Vergata,", Via della Ricerca Scientifica n. 1, Roma, 00173, Italy
| | - C Sanchez Mellado
- Faculty of Intercultural Education and Humanity, National Intercultural University of Amazon, Yarinacocha, Coronel Portillo, Ucayali, 25000, Peru
| | - T J Davila Francia
- Faculty of Intercultural Education and Humanity, National Intercultural University of Amazon, Yarinacocha, Coronel Portillo, Ucayali, 25000, Peru
| | - G Ferri
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, 41124, Italy
| | - S Sarno
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - D Luiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - O Rickards
- Department of Biology, University of Rome "Tor Vergata,", Via della Ricerca Scientifica n. 1, Roma, 00173, Italy
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Varano S, Scorrano G, Martínez-Labarga C, Finocchio A, Rapone C, Berti A, Rickards O. Exploring the mitochondrial DNA variability of the Amazonian Yanomami. Am J Hum Biol 2016; 28:846-856. [DOI: 10.1002/ajhb.22877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/29/2016] [Accepted: 05/13/2016] [Indexed: 11/09/2022] Open
Affiliation(s)
- Sara Varano
- Department of Biology, Center of Molecular Anthropology for Ancient DNA Studies; University of Rome ‘Tor Vergata’; Via della Ricerca Scientifica n. 1 Rome Italy
| | - Gabriele Scorrano
- Department of Biology, Center of Molecular Anthropology for Ancient DNA Studies; University of Rome ‘Tor Vergata’; Via della Ricerca Scientifica n. 1 Rome Italy
| | - Cristina Martínez-Labarga
- Department of Biology, Center of Molecular Anthropology for Ancient DNA Studies; University of Rome ‘Tor Vergata’; Via della Ricerca Scientifica n. 1 Rome Italy
| | - Andrea Finocchio
- Department of Biology, Center of Molecular Anthropology for Ancient DNA Studies; University of Rome ‘Tor Vergata’; Via della Ricerca Scientifica n. 1 Rome Italy
| | - Cesare Rapone
- Carabinieri, Scientific Investigation Department; Viale di Tor di Quinto n. 151 Rome Italy
| | - Andrea Berti
- Carabinieri, Scientific Investigation Department; Viale di Tor di Quinto n. 151 Rome Italy
| | - Olga Rickards
- Department of Biology, Center of Molecular Anthropology for Ancient DNA Studies; University of Rome ‘Tor Vergata’; Via della Ricerca Scientifica n. 1 Rome Italy
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Foulds HJA, Rodgers CD, Duncan V, Ferguson LJ. A systematic review and meta-analysis of screen time behaviour among North American indigenous populations. Obes Rev 2016; 17:455-66. [PMID: 26990323 DOI: 10.1111/obr.12389] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 11/29/2022]
Abstract
Screen time (computer, television, video game and smartphone/tablet activity) is associated with increased obesity and other health risks. This systematic review evaluates screen time among North American Indigenous populations and compares it with that of North American Europeans. Electronic databases (e.g. MEDLINE and EMBASE) were searched, and citations cross-referenced. Included articles reported screen time among First Nations/American Indians, Métis, Inuit/Alaskan Natives or Native Hawaiians. From 788 citations evaluated, 40 identified articles report television, video game, computer and/or overall screen time. Overall screen time was 3.65 ± 1.26 h day(-1) (n = 2,242, 8 articles) among Indigenous children/youth and 3.61 ± 2.95 h day(-1) (n = 155, 1 article) among adults. Among children/youth, 66.0% (n = 11 256, 9 articles) reported less than 2 h day(-1) of television screen time, while only 52.8% (n = 2,458, 1 article) of adults reported this volume. Screen time was generally greater among male population, youth, First Nations/American Indians and overweight/obese individuals. Indigenous children/youth reported greater overall screen time than North American Europeans (4.81 ± 2.84 h day(-1) , n = 1,182 vs. 3.40 ± 2.81 h day(-1) , n = 2,785; 3 articles; p < 0.0001). Screen time is common among North American Indigenous populations. Further research evaluating interventions to reduce screen time and chronic disease risks is required.
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Affiliation(s)
- H J A Foulds
- College of Kinesiology, University of Saskatchewan, Saskatoon, Canada
| | - C D Rodgers
- College of Kinesiology, University of Saskatchewan, Saskatoon, Canada
| | - V Duncan
- Health Sciences Library, University of Saskatchewan, Saskatoon, Canada
| | - L J Ferguson
- College of Kinesiology, University of Saskatchewan, Saskatoon, Canada
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Maley B. Examining biological continuity across the late holocene occupation of the Aleutian Islands using cranial morphometrics and quantitative genetic permutation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:71-85. [PMID: 27075865 DOI: 10.1002/ajpa.22944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/09/2015] [Accepted: 01/01/2016] [Indexed: 11/08/2022]
Abstract
OBJECTIVES The number of distinct human migrations into the Aleutian Islands during the Holocene has been a recurrent debate in the anthropological literature. Stemming from Hrdlička's sorting of the prehistoric remains into two distinct populations based on archaeological context and cranial measurements, the human occupation of the Aleutian Islands has long been thought to be the consequence of two distinct human migrations, a Paleo-Aleut migration that provided the initial settlement of the islands, and a Neo-Aleut migration that replaced the original settlers around 1000 BP. This study examines the relationship of the Aleut cranial assemblages in the context of greater Alaskan population variability to assess the evidence for a substantial migration into the Aleutian Islands during the late Holocene. MATERIALS AND METHODS A battery of 29 cranial measurements that quantify global cranial shape were analyzed using Euclidean morphometric methods and quantitative genetic permutation methods to examine the plausibility for two distinct Aleut occupations ("Paleo-Aleut" and "Neo-Aleut"), the latter of which is held to share closer phenetic affinities to mainland Alaskan populations than the former. The Aleut skeletal assemblages were arranged according to temporal association, geographic location, and cranial typology, and analyzed within a comparative framework of mainland Alaskan samples using principal coordinates, biological distance and random skewers permutation methods. RESULTS Regardless of how the Aleut assemblages are divided, they show greater similarity to each other than to any of the mainland Alaskan assemblages. These findings are consistent across the methodological approaches. DISCUSSION The results obtained in this study provide no support for a cranial morphology-based subdivision of the Aleuts into two distinct samples, Hence, there is no evidence for a substantial population migration of so-called Neo-Aleuts, nor for a population replacement event of an extant Paleo-Aleut population by a mainland-affiliated Neo-Aleuts population at or after 1000 BP.
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Affiliation(s)
- Blaine Maley
- Department of Biomedical Sciences, Marian University, Indianapolis, IN, 46222
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18
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Céspedes-Garro C, Fricke-Galindo I, Naranjo MEG, Rodrigues-Soares F, Fariñas H, de Andrés F, López-López M, Peñas-Lledó EM, LLerena A. Worldwide interethnic variability and geographical distribution of CYP2C9 genotypes and phenotypes. Expert Opin Drug Metab Toxicol 2015; 11:1893-905. [DOI: 10.1517/17425255.2015.1111871] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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de Azevedo S, Bortolini MC, Bonatto SL, Hünemeier T, Santos FR, González-José R. Ancient remains and the first peopling of the Americas: Reassessing the Hoyo Negro skull. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:514-21. [PMID: 26174009 DOI: 10.1002/ajpa.22801] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE A noticeably well-preserved ∼12.500 years-old skeleton from the Hoyo Negro cave, Yucatán, México, was recently reported, along with its archaeological, genetic and skeletal characteristics. Based exclusively on an anatomical description of the skull (HN5/48), Chatters and colleagues stated that this specimen can be assigned to a set of ancient remains that differ from modern Native Americans, the so called "Paleoamericans". Here, we aim to further explore the morphological affinities of this specimen with a set of comparative cranial samples covering ancient and modern periods from Asia and the Americas. METHODS Images published in the original article were analyzed using geometric morphometrics methods. Shape variables were used to perform Principal Component and Discriminant analysis against the reference samples. RESULTS Even thought the Principal Component Analysis suggests that the Hoyo Negro skull falls in a subregion of the morphospace occupied by both "Paleoamericans" and some modern Native Americans, the Discriminant analyses suggest greater affinity with a modern Native American sample. DISCUSSION These results reinforce the idea that the original population that first occupied the New World carried high levels of within-group variation, which we have suggested previously on a synthetic model for the settlement of the Americas. Our results also highlight the importance of developing formal classificatory test before deriving settlement hypothesis purely based on macroscopic descriptions.
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Affiliation(s)
- Soledad de Azevedo
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Bvd. Brown 2915, U9120ACD, Puerto Madryn, Argentina
| | - Maria C Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Sandro L Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul. Av. Ipiranga 6681, 90610-001, Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Fabrício R Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-910, Belo Horizonte, MG, Brazil
| | - Rolando González-José
- Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Bvd. Brown 2915, U9120ACD, Puerto Madryn, Argentina
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20
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Maddux SD, Sporleder AN, Burns CE. Geographic Variation in Zygomaxillary Suture Morphology and its Use in Ancestry Estimation. J Forensic Sci 2015; 60:966-73. [PMID: 25817798 DOI: 10.1111/1556-4029.12774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 07/19/2014] [Accepted: 07/27/2014] [Indexed: 11/30/2022]
Abstract
Angled/curved zygomaxillary suture coding is widely employed in cranial assessments of ancestry. However, the efficacy of this method has not been extensively evaluated across diverse populations. In this study, zygomaxillary suture morphology was assessed on a total of 411 human crania from six populations (European, Native American, African, Asian, Arctic Circle, and Aboriginal Australian) using a novel 3D coordinate landmark method. Our results indicate a predominance of angled sutures among native peoples of the Arctic and North America (85-86%), a prevalence of curved sutures among Africans and Aboriginal Australians (77-81%), and essentially equal proportions of both configurations in Asians and Europeans (50-56%). Statistically, angled/curved coding generally discriminates poorly between groups, except when populations with antithetically high frequencies of the two configurations (e.g., African vs. Native American) are compared. Moreover, comparisons across previous studies reveal conflicting frequencies for many populations, further suggesting limited utility of this trait in ancestry estimation.
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Affiliation(s)
- Scott D Maddux
- Department of Pathology and Anatomical Sciences, University of Missouri, M263 Medical Sciences Building, Columbia, MO, MO 65212, USA
| | - Alexandria N Sporleder
- Department of Pathology and Anatomical Sciences, University of Missouri, M263 Medical Sciences Building, Columbia, MO, MO 65212, USA.,College of Osteopathic Medicine, University of Pikeville, 147 Sycamore Street, Pikeville, KY, 41501, USA
| | - Casey E Burns
- Department of Pathology and Anatomical Sciences, University of Missouri, M263 Medical Sciences Building, Columbia, MO, MO 65212, USA
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21
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Lippold S, Xu H, Ko A, Li M, Renaud G, Butthof A, Schröder R, Stoneking M. Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. INVESTIGATIVE GENETICS 2014; 5:13. [PMID: 25254093 PMCID: PMC4174254 DOI: 10.1186/2041-2223-5-13] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 02/07/2023]
Abstract
Background Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias. Results We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm. Conclusions The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.
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Affiliation(s)
- Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Hongyang Xu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Department of Computational Genetics, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Albert Ko
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Fondation Mérieux, 17 rue Bourgelat, Lyon 69002, France
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany ; Present address: Institute of Biochemistry, Faculty of Medicine, University of Leipzig, Leipzig D04103, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig D04103, Germany
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22
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Vilar MG, Melendez C, Sanders AB, Walia A, Gaieski JB, Owings AC, Schurr TG. Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 155:352-68. [PMID: 25043798 DOI: 10.1002/ajpa.22569] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 01/05/2023]
Abstract
Puerto Rico and the surrounding islands rest on the eastern fringe of the Caribbean's Greater Antilles, located less than 100 miles northwest of the Lesser Antilles. Puerto Ricans are genetic descendants of pre-Columbian peoples, as well as peoples of European and African descent through 500 years of migration to the island. To infer these patterns of pre-Columbian and historic peopling of the Caribbean, we characterized genetic diversity in 326 individuals from the southeastern region of Puerto Rico and the island municipality of Vieques. We sequenced the mitochondrial DNA (mtDNA) control region of all of the samples and the complete mitogenomes of 12 of them to infer their putative place of origin. In addition, we genotyped 121 male samples for 25 Y-chromosome single nucleotide polymorphism and 17 STR loci. Approximately 60% of the participants had indigenous mtDNA haplotypes (mostly from haplogroups A2 and C1), while 25% had African and 15% European haplotypes. Three A2 sublineages were unique to the Greater Antilles, one of which was similar to Mesoamerican types, while C1b haplogroups showed links to South America, suggesting that people reached the island from the two distinct continental source areas. However, none of the male participants had indigenous Y-chromosomes, with 85% of them instead being European/Mediterranean and 15% sub-Saharan African in origin. West Eurasian Y-chromosome short tandem repeat haplotypes were quite diverse and showed similarities to those observed in southern Europe, North Africa and the Middle East. These results attest to the distinct, yet equally complex, pasts for the male and female ancestors of modern day Puerto Ricans.
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Affiliation(s)
- Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, 19104-6398
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23
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Menéndez L, Bernal V, Novellino P, Perez SI. Effect of bite force and diet composition on craniofacial diversification of Southern South American human populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 155:114-27. [DOI: 10.1002/ajpa.22560] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 06/03/2014] [Accepted: 06/16/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Lumila Menéndez
- CONICET; División Antropología; Museo de La Plata (UNLP), Paseo del Bosque S/N; La Plata 1900 Buenos Aires Argentina
| | - Valeria Bernal
- CONICET; División Antropología; Museo de La Plata (UNLP), Paseo del Bosque S/N; La Plata 1900 Buenos Aires Argentina
| | - Paula Novellino
- CONICET, Laboratorio de Bioarqueología, Museo de Ciencias Naturales y Antropológicas “J.C.Moyano,” Mendoza; Argentina
| | - S. Ivan Perez
- CONICET; División Antropología; Museo de La Plata (UNLP), Paseo del Bosque S/N; La Plata 1900 Buenos Aires Argentina
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24
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Pettersson JHO, Fiz-Palacios O. Dating the origin of the genus Flavivirus in the light of Beringian biogeography. J Gen Virol 2014; 95:1969-1982. [PMID: 24914065 DOI: 10.1099/vir.0.065227-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Flavivirus includes some of the most important human viral pathogens, and its members are found in all parts of the populated world. The temporal origin of diversification of the genus has long been debated due to the inherent problems with dating deep RNA virus evolution. A generally accepted hypothesis suggests that Flavivirus emerged within the last 10 000 years. However, it has been argued that the tick-borne Powassan flavivirus was introduced into North America some time between the opening and closing of the Beringian land bridge that connected Asia and North America 15 000-11 000 years ago, indicating an even older origin for Flavivirus. To determine the temporal origin of Flavivirus, we performed Bayesian relaxed molecular clock dating on a dataset with high coverage of the presently available Flavivirus diversity by combining tip date calibrations and internal node calibration, based on the Powassan virus and Beringian land bridge biogeographical event. Our analysis suggested that Flavivirus originated ~85 000 (64 000-110 000) or 120 000 (87 000-159 000) years ago, depending on the circumscription of the genus. This is significantly older than estimated previously. In light of our results, we propose that it is likely that modern humans came in contact with several members of the genus Flavivirus much earlier than suggested previously, and that it is possible that the spread of several flaviviruses coincided with, and was facilitated by, the migration and population expansion of modern humans out of Africa.
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Affiliation(s)
- John H-O Pettersson
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Omar Fiz-Palacios
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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25
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The blood pressure and hypertension experience among North American Indigenous populations. J Hypertens 2014; 32:724-34. [DOI: 10.1097/hjh.0000000000000084] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Bernal V, Béguelin M, Gordón F, Cobos VA, Gonzalez PN, Lotto FP. Craniofacial variation, body size and ecological factors in aboriginal populations from central Patagonia (2000–200 years B.P.). HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2014; 65:101-14. [DOI: 10.1016/j.jchb.2013.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/17/2013] [Indexed: 01/08/2023]
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27
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Herrera B, Hanihara T, Godde K. Comparability of multiple data types from the bering strait region: Cranial and dental metrics and nonmetrics, mtDNA, and Y-chromosome DNA. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 154:334-48. [DOI: 10.1002/ajpa.22513] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Brianne Herrera
- Department of Anthropology; The Ohio State University; Columbus OH
| | - Tsunehiko Hanihara
- Department of Anatomy and Biological Anthropology; Saga Medical School; Saga Japan
| | - Kanya Godde
- Sociology and Anthropology Department; University of La Verne; La Verne CA
- Department of Anthropology; University of Tennessee; Knoxville TN
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28
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Da-Gloria P, Larsen CS. Oral health of the Paleoamericans of Lagoa Santa, central Brazil. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 154:11-26. [DOI: 10.1002/ajpa.22467] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 12/18/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Pedro Da-Gloria
- Laboratório de Estudos Evolutivos Humanos; Departamento de Genética e Biologia Evolutiva; Universidade de São Paulo; CP11461 São Paulo Brazil
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29
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Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 2013; 505:87-91. [PMID: 24256729 DOI: 10.1038/nature12736] [Citation(s) in RCA: 438] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 10/04/2013] [Indexed: 12/19/2022]
Abstract
The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.
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Affiliation(s)
- Maanasa Raghavan
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark [2]
| | - Pontus Skoglund
- 1] Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden [2]
| | - Kelly E Graf
- Center for the Study of the First Americans, Texas A&M University, TAMU-4352, College Station, Texas 77845-4352, USA
| | - Mait Metspalu
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Integrative Biology, University of California, Berkeley, California 94720, USA [3] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark
| | - Ida Moltke
- 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark [2] Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Thomas W Stafford
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark [2] AMS 14C Dating Centre, Department of Physics and Astronomy, University of Aarhus, Ny Munkegade 120, Aarhus DK-8000, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Monika Karmin
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia
| | - Oleg Balanovsky
- 1] Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia [2] Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, Moscow 119991, Russia
| | - Elza Khusnutdinova
- 1] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia [2] Biology Department, Bashkir State University, Ufa, Bashkorostan 450074, Russia
| | - Sergey Litvinov
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia
| | - Ludmila P Osipova
- The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia
| | - Sardana A Fedorova
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Sakha (Yakutia) 677010, Russia
| | - Mikhail I Voevoda
- 1] The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia [2] Institute of Internal Medicine, Siberian Branch of the Russian Academy of Medical Sciences, Borisa Bogatkova 175/1, Novosibirsk 630089, Russia
| | - Michael DeGiorgio
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Thomas Sicheritz-Ponten
- 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Søren Brunak
- 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | | | - Toomas Kivisild
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Richard Villems
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [3] Estonian Academy of Sciences, Tallinn 10130, Estonia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Mattias Jakobsson
- 1] Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden [2] Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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Mitochondrial genetic background modulates bioenergetics and susceptibility to acute cardiac volume overload. Biochem J 2013; 455:157-67. [PMID: 23924350 DOI: 10.1042/bj20130029] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dysfunctional bioenergetics has emerged as a key feature in many chronic pathologies such as diabetes and cardiovascular disease. This has led to the mitochondrial paradigm in which it has been proposed that mtDNA sequence variation contributes to disease susceptibility. In the present study we show a novel animal model of mtDNA polymorphisms, the MNX (mitochondrial-nuclear exchange) mouse, in which the mtDNA from the C3H/HeN mouse has been inserted on to the C57/BL6 nuclear background and vice versa to test this concept. Our data show a major contribution of the C57/BL6 mtDNA to the susceptibility to the pathological stress of cardiac volume overload which is independent of the nuclear background. Mitochondria harbouring the C57/BL6J mtDNA generate more ROS (reactive oxygen species) and have a higher mitochondrial membrane potential relative to those with C3H/HeN mtDNA, independent of nuclear background. We propose this is the primary mechanism associated with increased bioenergetic dysfunction in response to volume overload. In summary, these studies support the 'mitochondrial paradigm' for the development of disease susceptibility, and show that the mtDNA modulates cellular bioenergetics, mitochondrial ROS generation and susceptibility to cardiac stress.
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Martínez-Cortés G, Salazar-Flores J, Haro-Guerrero J, Rubi-Castellanos R, Velarde-Félix JS, Muñoz-Valle JF, López-Casamichana M, Carrillo-Tapia E, Canseco-Avila LM, Bravi CM, López-Armenta M, Rangel-Villalobos H. Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:526-37. [PMID: 23754474 DOI: 10.1002/ajpa.22293] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/23/2013] [Indexed: 12/16/2022]
Abstract
The maternal ancestry (mtDNA) has important applications in different research fields, such as evolution, epidemiology, identification, and human population history. This is particularly interesting in Mestizos, which constitute the main population in Mexico (∼93%) resulting from post-Columbian admixture between Spaniards, Amerindians, and African slaves, principally. Consequently, we conducted minisequencing analysis (SNaPshot) of 11 mitochondrial single-nucleotide polymorphisms in 742 Mestizos of 10 populations from different regions in Mexico. The predominant maternal ancestry was Native American (92.9%), including Haplogroups A, B, C, and D (47, 23.7, 15.9, and 6.2%, respectively). Conversely, European and African ancestries were less frequent (5.3 and 1.9%, respectively). The main characteristics of the maternal lineages observed in Mexican-Mestizos comprised the following: 1) contrasting geographic gradient of Haplogroups A and C; 2) increase of European lineages toward the Northwest; 3) low or absent, but homogeneous, African ancestry throughout the Mexican territory; 4) maternal lineages in Mestizos roughly represent the genetic makeup of the surrounding Amerindian groups, particularly toward the Southeast, but not in the North and West; 5) continuity over time of the geographic distribution of Amerindian lineages in Mayas; and 6) low but significant maternal population structure (FST = 2.8%; P = 0.0000). The average ancestry obtained from uniparental systems (mtDNA and Y-chromosome) in Mexican-Mestizos was correlated with previous ancestry estimates based on autosomal systems (genome-wide single-nucleotide polymorphisms and short tandem repeats). Finally, the comparison of paternal and maternal lineages provided additional information concerning the gender bias admixture, mating patterns, and population structure in Mestizos throughout the Mexican territory.
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Affiliation(s)
- Gabriela Martínez-Cortés
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán, Jalisco, México
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Roewer L, Nothnagel M, Gusmão L, Gomes V, González M, Corach D, Sala A, Alechine E, Palha T, Santos N, Ribeiro-Dos-Santos A, Geppert M, Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B, González-Andrade F, Fagundes de Carvalho E, da Silva DA, Builes JJ, Turbón D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U, Borjas L, Barletta C, Ewart E, Santos S, Krawczak M. Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans. PLoS Genet 2013; 9:e1003460. [PMID: 23593040 PMCID: PMC3623769 DOI: 10.1371/journal.pgen.1003460] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/04/2013] [Indexed: 01/07/2023] Open
Abstract
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. In the largest population genetic study of South Americans to date, we analyzed the Y-chromosomal makeup of more than 1,000 male natives. We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships. This finding is consistent with a rapid initial peopling of South America, followed by long periods of isolation in small tribal groups. The observed continent-wide decoupling of geography, spoken language, and genetics contrasts strikingly with previous reports of such correlation from many parts of Europe and Asia. Moreover, we identified a cluster of Native American founding lineages of Y chromosomes, called C-M217 (C3*), within a restricted area of Ecuador in North-Western South America. The same haplogroup occurs at high frequency in Central, East, and North East Asia, but is virtually absent from North (except Alaska) and Central America. Possible scenarios for the introduction of C-M217 (C3*) into Ecuador may thus include a coastal or trans-Pacific route, an idea also supported by occasional archeological evidence and the recent coalescence of the C3* haplotypes, estimated from our data to have occurred some 6,000 years ago.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Melton PE, Baldi NF, Barrantes R, Crawford MH. Microevolution, migration, and the population structure of five Amerindian populations from Nicaragua and Costa Rica. Am J Hum Biol 2013; 25:480-90. [PMID: 23559443 DOI: 10.1002/ajhb.22382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This research examines the coevolution of languages and uniparental genetic marker (mitochondrial DNA [mtDNA] and nonrecombining Y-chromosome [NRY]) variation within five Lower Central American (Rama, Chorotega, Maléku, Zapatón-Huetar, and Abrojo-Guaymí) Amerindian groups. This pattern occurred since European contact. METHODS We examined mtDNA sequence variation from the hypervariable region 1 (HVS-1) and NRY genetic variation using short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, and DYS439) and NRY haplogroups (Q1a3a, Q1a3*, C3b, R1b1b2, E1b1, G2a2, and I) identified through single-nucleotide polymorphisms. Phylogenetic analysis included multidimensional scaling (MDS), heterozygosity versus rii , and analysis of molecular variance (AMOVA). RESULTS Eighteen mtDNA haplotypes were characterized in 131 participants with 94.6% of these assigned to the Amerindian mtDNA subclades, A2 and B2. The Amerindian NRY haplogroup, Q1a3a, was present in all five groups and ranged from 85% (Zapatón-Huetar) to 35% (Chorotega). Four populations (Rama, Chorotega, Zapatón-Huetar, and Abrojo-Guaymí) were also characterized by the presence of NRY haplogroup R1b1b2 indicative of western European admixture. Seventy NRY STR haplotypes were identified of which 69 (97%) were population specific. MDS plots demonstrated genetic similarities between Mesoamericans and northern Chibchan Amerindian populations, absent in mtDNA analyses, which is further supported by heterozygosity versus rii results. CONCLUSIONS We conclude that although these linguistically related populations in geographic proximity demonstrate a high degree of paternal genetic differentiation, recent demographic events have dramatically altered the paternal genetic structure of the regions Amerindian populations.
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Affiliation(s)
- Phillip E Melton
- Centre for Genetic Origins of Health and Disease, University of Western Australia, Crawley, Australia.
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Influence of admixture components on CYP2C9*2 allele frequency in eight indigenous populations from Northwest Mexico. THE PHARMACOGENOMICS JOURNAL 2013; 13:567-72. [DOI: 10.1038/tpj.2012.52] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/20/2012] [Accepted: 11/16/2012] [Indexed: 11/09/2022]
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Regueiro M, Alvarez J, Rowold D, Herrera RJ. On the origins, rapid expansion and genetic diversity of Native Americans from hunting-gatherers to agriculturalists. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:333-48. [PMID: 23283701 DOI: 10.1002/ajpa.22207] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/08/2012] [Indexed: 11/05/2022]
Abstract
Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices.
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Affiliation(s)
- Maria Regueiro
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes. PLoS One 2012; 7:e51311. [PMID: 23240014 PMCID: PMC3519775 DOI: 10.1371/journal.pone.0051311] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
With analyses of entire mitogenomes, studies of Native American mitochondrial DNA (mtDNA) variation have entered the final phase of phylogenetic refinement: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11–13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.
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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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Salazar-Flores J, Torres-Reyes LA, Martínez-Cortés G, Rubi-Castellanos R, Sosa-Macías M, Muñoz-Valle JF, González-González C, Ramírez A, Román R, Méndez JL, Barrera A, Torres A, Medina R, Rangel-Villalobos H. Distribution of CYP2D6 and CYP2C19 polymorphisms associated with poor metabolizer phenotype in five Amerindian groups and western Mestizos from Mexico. Genet Test Mol Biomarkers 2012; 16:1098-104. [PMID: 22913530 DOI: 10.1089/gtmb.2012.0055] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The distribution of polymorphisms in the CYP2D6 and CYP2C19 genes allows inferring the potential risk for specific adverse drug reactions and lack of therapeutic effects in humans. This variability shows differences among human populations. The aim of this study was to analyze single-nucleotide polymorphisms related to a poor metabolizer (PM) phenotype in nonpreviously studied Amerindian groups and Mestizos (general admixed population) from Mexico. METHODS We detected by SNaPshot(®) different polymorphisms located in CYP2D6 (*3, *4, *6, *7, and *8) and CYP2C19 (*2, *3, *4 and *5) in western Mestizos (n=145) and five Amerindian groups from Mexico: Tarahumaras from the North (n=88); Purépechas from the Center (n=101); and Tojolabales (n=68), Tzotziles (n=88), and Tzeltales (n=20) from the Southeast. Genotypes were observed by capillary electrophoresis. The genetic relationships among these populations were estimated based on these genes. RESULTS AND DISCUSSION The wild-type allele (*1) of both genes was predominant in the Mexican populations studied. The most widely observed alleles were CYP2C19*2 (range, 0%-31%) and CYP2D6*4 (range, 1.2%-7.3%), whereas CYP2D6*3 was exclusively detected in Mestizos. Conversely, CYP2C19*4 and *5, as well as CYP2D6*3, *6, *7, and *8, were not observed in the majority of the Mexican populations. The Tarahumaras presented a high frequency of the allele CYP2C19*2 (31%) and of homozygotes *2/*2 (10.7%), which represent a high frequency of potentially PM phenotypes in this Amerindian group. The genetic distances showed high differentiation of Tarahumaras (principally for CYP2C19 gene). In general, a relative proximity was observed between most of the Amerindian, Mexican-Mestizo, and Latin-American populations. CONCLUSION In general, the wild-type allele (*1) predominates in Mexican populations, outlining a relatively homogeneous distribution for CYP2C19 and CYP2D6. The exception is the Tarahumara group that displays a potentially increased risk for adverse reactions to CYP2C19-metabolized drugs.
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Affiliation(s)
- Joel Salazar-Flores
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán, Jalisco, México
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Theoretical and Methodological Approaches to Understanding Human Migration Patterns and their Utility in Forensic Human Identification Cases. SOCIETIES 2012. [DOI: 10.3390/soc2020042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Revisiting the clinal concept of evolution and dispersal for the tick-borne flaviviruses by using phylogenetic and biogeographic analyses. J Virol 2012; 86:8663-71. [PMID: 22674986 DOI: 10.1128/jvi.01013-12] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tick-borne flaviviruses (TBF) are widely dispersed across Africa, Europe, Asia, Oceania, and North America, and some present a significant threat to human health. Seminal studies on tick-borne encephalitis viruses (TBEV), based on partial envelope gene sequences, predicted a westward clinal pattern of evolution and dispersal across northern Eurasia, terminating in the British Isles. We tested this hypothesis using all available full-length open reading frame (ORF) TBF sequences. Phylogenetic analysis was consistent with current reports. However, linear and nonlinear regression analysis of genetic versus geographic distance combined with BEAST analysis identified two separate clines, suggesting that TBEV spread both east and west from a central point. In addition, BEAST analysis suggested that TBF emerged and dispersed more than 16,000 years ago, significantly earlier than previously predicted. Thus, climatic and ecological changes may have played a greater role in TBF dispersal than humans.
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Burnett S, Wilczak C. Tarsal and tarsometatarsal coalitions from Mound C (Ocmulgee Macon Plateau site, Georgia): Implications for understanding the patterns, origins, and antiquity of pedal coalitions in Native American populations. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2012; 63:167-81. [DOI: 10.1016/j.jchb.2012.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 03/20/2012] [Indexed: 10/28/2022]
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Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations. Proc Natl Acad Sci U S A 2012; 109:8471-6. [PMID: 22586127 DOI: 10.1073/pnas.1118760109] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich'in, and Tłįch populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįch being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized.
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Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong F. Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:422-35. [PMID: 22549307 DOI: 10.1002/ajpa.22068] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 03/06/2012] [Indexed: 11/10/2022]
Abstract
The linguistically distinctive Haida and Tlingit tribes of Southeast Alaska are known for their rich material culture, complex social organization, and elaborate ritual practices. However, much less is known about these tribes from a population genetic perspective. For this reason, we analyzed mtDNA and Y-chromosome variation in Haida and Tlingit populations to elucidate several key issues pertaining to the history of this region. These included the genetic relationships of Haida and Tlingit to other indigenous groups in Alaska and Canada; the relationship between linguistic and genetic data for populations assigned to the Na-Dene linguistic family, specifically, the inclusion of Haida with Athapaskan, Eyak, and Tlingit in the language family; the possible influence of matrilineal clan structure on patterns of genetic variation in Haida and Tlingit populations; and the impact of European entry into the region on the genetic diversity of these indigenous communities. Our analysis indicates that, while sharing a "northern" genetic profile, the Haida and the Tlingit are genetically distinctive from each other. In addition, Tlingit groups themselves differ across their geographic range, in part due to interactions of Tlingit tribes with Athapaskan and Eyak groups to the north. The data also reveal a strong influence of maternal clan identity on mtDNA variation in these groups, as well as the significant influence of non-native males on Y-chromosome diversity. These results yield new details about the histories of the Haida and Tlingit tribes in this region.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104-6398, 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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Rapid coastal spread of First Americans: novel insights from South America's Southern Cone mitochondrial genomes. Genome Res 2012; 22:811-20. [PMID: 22333566 PMCID: PMC3337427 DOI: 10.1101/gr.131722.111] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It is now widely agreed that the Native American founders originated from a Beringian source population ∼15–18 thousand years ago (kya) and rapidly populated all of the New World, probably mainly following the Pacific coastal route. However, details about the migration into the Americas and the routes pursued on the continent still remain unresolved, despite numerous genetic, archaeological, and linguistic investigations. To examine the pioneering peopling phase of the South American continent, we screened literature and mtDNA databases and identified two novel mitochondrial DNA (mtDNA) clades, here named D1g and D1j, within the pan-American haplogroup D1. They both show overall rare occurrences but local high frequencies, and are essentially restricted to populations from the Southern Cone of South America (Chile and Argentina). We selected and completely sequenced 43 D1g and D1j mtDNA genomes applying highest quality standards. Molecular and phylogeographic analyses revealed extensive variation within each of the two clades and possibly distinct dispersal patterns. Their age estimates agree with the dating of the earliest archaeological sites in South America and indicate that the Paleo-Indian spread along the entire longitude of the American double continent might have taken even <2000 yr. This study confirms that major sampling and sequencing efforts are mandatory for uncovering all of the most basal variation in the Native American mtDNA haplogroups and for clarification of Paleo-Indian migrations, by targeting, if possible, both the general mixed population of national states and autochthonous Native American groups, especially in South America.
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Casas-Vargas A, Gómez A, Briceño I, Díaz-Matallana M, Bernal JE, Rodríguez JV. High genetic diversity on a sample of pre-Columbian bone remains from Guane territories in northwestern Colombia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:637-49. [PMID: 21990065 DOI: 10.1002/ajpa.21626] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 08/30/2011] [Indexed: 11/12/2022]
Abstract
Ancient DNA was recovered from 17 individuals found in a rock shelter in the district of "La Purnia" (Santander, Colombia). This region is the homeland of pre-Columbian Guane, whom spread over the "Río Suarez" to the "Río de Oro", and were surrounded to the west by the Central Andes, south and east by foothills of Eastern Andes, and north by the "Chicamocha" river canyon. Guanes established in a region that straddles the Andes and the northern Amazon basin, possibly making it an unavoidable conduit for people moving to and from South America. We amplified mtDNA hypervariable region I (HVI) segments from ancient bone remains, and the resulting sequences were compared with both ancient and modern mitochondrial haplogroups from American and non-American populations. Samples showed a distribution of 35% for haplogroup A, 41% for haplogroup B and 24% for haplogroup D. Nine haplotypes were found in 17 samples, indicating an unusually high genetic diversity on a single site ancient population. Among them, three haplotypes have not been previously found in America, two are shared in Asia, and one is a private haplotype. Despite geographical barriers that eventually isolated them, an important influence of gene flow from neighboring pre-Columbian communities, mainly Muiscas, could explain the high genetic polymorphism of this community before the Spanish conquest, and argues against Guanes as being a genetic isolate.
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Kumar S, Bellis C, Zlojutro M, Melton PE, Blangero J, Curran JE. Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol Biol 2011; 11:293. [PMID: 21978175 PMCID: PMC3217880 DOI: 10.1186/1471-2148-11-293] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 10/07/2011] [Indexed: 01/07/2023] Open
Abstract
Background The Asian origin of Native Americans is largely accepted. However uncertainties persist regarding the source population(s) within Asia, the divergence and arrival time(s) of the founder groups, the number of expansion events, and migration routes into the New World. mtDNA data, presented over the past two decades, have been used to suggest a single-migration model for which the Beringian land mass plays an important role. Results In our analysis of 568 mitochondrial genomes, the coalescent age estimates of shared roots between Native American and Siberian-Asian lineages, calculated using two different mutation rates, are A4 (27.5 ± 6.8 kya/22.7 ± 7.4 kya), C1 (21.4 ± 2.7 kya/16.4 ± 1.5 kya), C4 (21.0 ± 4.6 kya/20.0 ± 6.4 kya), and D4e1 (24.1 ± 9.0 kya/17.9 ± 10.0 kya). The coalescent age estimates of pan-American haplogroups calculated using the same two mutation rates (A2:19.5 ± 1.3 kya/16.1 ± 1.5 kya, B2:20.8 ± 2.0 kya/18.1 ± 2.4 kya, C1:21.4 ± 2.7 kya/16.4 ± 1.5 kya and D1:17.2 ± 2.0 kya/14.9 ± 2.2 kya) and estimates of population expansions within America (~21-16 kya), support the pre-Clovis occupation of the New World. The phylogeography of sublineages within American haplogroups A2, B2, D1 and the C1b, C1c andC1d subhaplogroups of C1 are complex and largely specific to geographical North, Central and South America. However some sub-branches (B2b, C1b, C1c, C1d and D1f) already existed in American founder haplogroups before expansion into the America. Conclusions Our results suggest that Native American founders diverged from their Siberian-Asian progenitors sometime during the last glacial maximum (LGM) and expanded into America soon after the LGM peak (~20-16 kya). The phylogeography of haplogroup C1 suggest that this American founder haplogroup differentiated in Siberia-Asia. The situation is less clear for haplogroup B2, however haplogroups A2 and D1 may have differentiated soon after the Native American founders divergence. A moderate population bottle neck in American founder populations just before the expansion most plausibly resulted in few founder types in America. The similar estimates of the diversity indices and Bayesian skyline analysis in North America, Central America and South America suggest almost simultaneous (~ 2.0 ky from South to North America) colonization of these geographical regions with rapid population expansion differentiating into more or less regional branches across the pan-American haplogroups.
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Affiliation(s)
- Satish Kumar
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, 78227, USA.
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Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:392-405. [PMID: 21994016 DOI: 10.1002/ajpa.21588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/17/2011] [Indexed: 11/09/2022]
Abstract
Discovered in the early 16th century by European colonists, Bermuda is an isolated set of islands located in the mid-Atlantic. Shortly after its discovery, Bermuda became the first English colony to forcibly import its labor by trafficking in enslaved Africans, white ethnic minorities, and indigenous Americans. Oral traditions circulating today among contemporary tribes from the northeastern United States recount these same events, while, in Bermuda, St. David's Islanders consider their histories to be linked to a complex Native American, European, and African past. To investigate the influence of historical events on biological ancestry and native cultural identity, we analyzed genetic variation in 111 members of Bermuda's self-proclaimed St. David's Island Native Community. Our results reveal that the majority of mitochondrial DNA (mtDNA) and Y-chromosome haplotypes are of African and West Eurasian origin. However, unlike other English-speaking New World colonies, most African mtDNA haplotypes appear to derive from central and southeast Africa, reflecting the extent of maritime activities in the region. In light of genealogical and oral historical data from the St. David's community, the low frequency of Native American mtDNA and NRY lineages may reflect the influence of genetic drift, the demographic impact of European colonization, and historical admixture with persons of non-native backgrounds, which began with the settlement of the islands. By comparing the genetic data with genealogical and historical information, we are able to reconstruct the complex history of this Bermudian community, which is unique among New World populations.
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Affiliation(s)
- Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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Krzywanski DM, Moellering DR, Fetterman JL, Dunham-Snary KJ, Sammy MJ, Ballinger SW. The mitochondrial paradigm for cardiovascular disease susceptibility and cellular function: a complementary concept to Mendelian genetics. J Transl Med 2011; 91:1122-35. [PMID: 21647091 PMCID: PMC3654682 DOI: 10.1038/labinvest.2011.95] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While there is general agreement that cardiovascular disease (CVD) development is influenced by a combination of genetic, environmental, and behavioral contributors, the actual mechanistic basis of how these factors initiate or promote CVD development in some individuals while others with identical risk profiles do not, is not clearly understood. This review considers the potential role for mitochondrial genetics and function in determining CVD susceptibility from the standpoint that the original features that molded cellular function were based upon mitochondrial-nuclear relationships established millions of years ago and were likely refined during prehistoric environmental selection events that today, are largely absent. Consequently, contemporary risk factors that influence our susceptibility to a variety of age-related diseases, including CVD were probably not part of the dynamics that defined the processes of mitochondrial-nuclear interaction, and thus, cell function. In this regard, the selective conditions that contributed to cellular functionality and evolution should be given more consideration when interpreting and designing experimental data and strategies. Finally, future studies that probe beyond epidemiologic associations are required. These studies will serve as the initial steps for addressing the provocative concept that contemporary human disease susceptibility is the result of selection events for mitochondrial function that increased chances for prehistoric human survival and reproductive success.
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Affiliation(s)
- David M Krzywanski
- Division of Molecular and Cellular Pathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA
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Barbeito-Andrés J, Pucciarelli H, Sardi M. An ontogenetic approach to facial variation in three Native American populations. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2011; 62:56-67. [DOI: 10.1016/j.jchb.2010.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 10/16/2010] [Indexed: 10/18/2022]
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