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Haarkötter C, Saiz M, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Álvarez JC, Lorente JA. Evaluation of the usefulness of insertion-null markers in critical skeletal remains. Int J Legal Med 2024; 138:1287-1293. [PMID: 38509248 PMCID: PMC11164766 DOI: 10.1007/s00414-024-03205-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Forensic DNA analysis in compromised skeletal remains may pose challenges due to DNA degradation, often resulting in partial or negative autosomal STRs profiles. To address this issue, alternative approaches such as mitochondrial DNA or SNPs typing may be employed; however, they are labour-intensive and costly. Insertion-null alleles (INNULs), short interspersed nuclear elements, have been suggested as a valuable tool for human identification in challenging samples due to their small amplicon size. A commercial kit including 20 INNULs markers along with amelogenin (InnoTyper® 21) has been developed. This study assesses its utility using degraded skeletal remains, comparing the results obtained (the number of detected alleles, RFU values, PHR, and the number of reportable markers) to those obtained using GlobalFiler™. Subsequently, the random match probability of the two profiles for each sample was determined using Familias version 3 to evaluate the power of discrimination of the results obtained from each kit. In every sample, InnoTyper® 21 yielded more alleles, higher RFU values, and a greater number of reportable loci. However, in most cases, both profiles were similarly informative. In conclusion, InnoTyper® 21 serves as a valuable complement to the analysis of challenging samples in cases where a poor or negative profile was obtained.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain.
| | - Jose Antonio Lorente
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
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Haarkötter C, Saiz M, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Lorente JA, Álvarez JC. Performance comparison of four qPCR and three autosomal STR commercial kits from degraded skeletal remains. Forensic Sci Int 2023; 353:111856. [PMID: 37863006 DOI: 10.1016/j.forsciint.2023.111856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
This research evaluates the current DNA quantification (Quantifiler™ Trio, PowerQuant®, Investigator® Quantiplex® Pro and InnoQuant® HY Fast) and autosomal STRs amplification kits (GlobalFiler™, PowerPlex® Fusion 6 C, Investigator® 24Plex QS) using 62 degraded skeletal remains from armed conflicts (petrous bone, femur, tibia, and tooth) with several parameters (autosomal small, large, and male target, degradation index, probability of degradation, number of alleles above analytical threshold, number of alleles above stochastic threshold, RFU, peak height ratio, number of reportable loci). The best qPCR/autosomal STRs amplification tandem was determined by comparing quantification results by a DNA quantity estimation based on sample average RFU. InnoQuant® HY Fast was the most sensitive kit, and no significative differences were observed among amplification kits; however, Investigator® 24 Plex QS was found to be the most sensitive in our samples. That is why InnoQuant™ and Investigator® 24Plex QS were determined to be the best tandem.
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Affiliation(s)
- Christian Haarkötter
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Saiz
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain.
| | - Xiomara Gálvez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Diana C Vinueza-Espinosa
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Isabel Medina-Lozano
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - José Antonio Lorente
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Juan Carlos Álvarez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
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Uricoechea Patiño D, Collins A, Romero García OJ, Santos Vecino G, Aristizábal Espinosa P, Bernal Villegas JE, Benavides Benitez E, Vergara Muñoz S, Briceño Balcázar I. Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley. Genes (Basel) 2023; 14:2036. [PMID: 38002979 PMCID: PMC10670959 DOI: 10.3390/genes14112036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/18/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area.
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Affiliation(s)
- Daniel Uricoechea Patiño
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
| | - Andrew Collins
- Human Genetics & Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
| | | | - Gustavo Santos Vecino
- Department of Anthropology, Faculty of Social and Human Science, Universidad de Antioquia, Medellín 050010, Colombia;
| | | | | | | | - Saray Vergara Muñoz
- Faculty of Medicine, University of Sinú, Cartagena de Indias 130011, Colombia; (J.E.B.V.); (S.V.M.)
| | - Ignacio Briceño Balcázar
- Doctoral Program in Biosciences, Human Genetics Group, Faculty of Medicine, University of La Sabana, Chía 250001, Colombia;
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Haarkötter C, Vinueza-Espinosa DC, Gálvez X, Saiz M, Medina-Lozano MI, Lorente JA, Álvarez JC. A comparison between petrous bone and tooth, femur and tibia DNA analysis from degraded skeletal remains. Electrophoresis 2023; 44:1559-1568. [PMID: 37469183 DOI: 10.1002/elps.202300097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/07/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Skeletal remains are the only biological material that remains after long periods; however, environmental conditions such as temperature, humidity, and pH affect DNA preservation, turning skeletal remains into a challenging sample for DNA laboratories. Sample selection is a key factor, and femur and tooth have been traditionally recommended as the best substrate of genetic material. Recently, petrous bone (cochlear area) has been suggested as a better option due to its DNA yield. This research aims to evaluate the efficiency of petrous bone compared to other cranium samples (tooth) and postcranial long bones (femur and tibia). A total amount of 88 samples were selected from 38 different individuals. The samples were extracted by using an organic extraction protocol, DNA quantification by Quantifiler Trio kit and amplified with GlobalFiler kit. Results show that petrous bone outperforms other bone remains in quantification data, yielding 15-30 times more DNA than the others. DNA profile data presented likeness between petrous bone and tooth regarding detected alleles; however, the amount of DNA extracted in petrous bones allowed us to obtain more informative DNA profiles with superior quality. In conclusion, petrous bone or teeth sampling is recommended if DNA typing is going to be performed with environmentally degraded skeletal remains.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - José Antonio Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
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Ralston C, Martin DL. Working, Living, and Dying Together: Rethinking Marginality, Sex, and Heterarchy in Kayenta Communities (AD 900–1150). AMERICAN ANTHROPOLOGIST 2020. [DOI: 10.1111/aman.13490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Morales-Arce AY, Snow MH, Kelley JH, Anne Katzenberg M. Ancient mitochondrial DNA and ancestry of Paquimé inhabitants, Casas Grandes (A.D. 1200-1450). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 163:616-626. [PMID: 28382719 DOI: 10.1002/ajpa.23223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/05/2017] [Accepted: 03/18/2017] [Indexed: 11/07/2022]
Abstract
OBJECTIVES The Casas Grandes (Paquimé) culture, located in the Northwest of Chihuahua, Mexico reached its apogee during the Medio Period (A.D. 1200-1450). Paquimé was abandoned by the end of the Medio Period (A.D. 1450), and the ancestry of its inhabitants remains unsolved. Some authors suggest that waves of Mesoamerican immigrants, possibly merchants, stimulated Paquimé's development during the Medio Period. Archaeological evidence suggests possible ties to groups that inhabited the Southwestern US cultures. This study uses ancient DNA analysis from fourteen samples to estimate genetic affinities of ancient Paquimé inhabitants. MATERIALS AND METHODS DNA was extracted from 14 dental ancient samples from Paquimé. PCR and Sanger sequencing were used to obtain mitochondrial control region sequences. Networks, PCoA, and Nei genetic distances were estimated to compare Paquimé haplotypes against available past haplotypes data from Southwestern and Mesoamerican groups. RESULTS Haplogroups were characterized for 11 of the samples, and the results revealed the presence of four distinct Amerindian mitochondrial lineages: B (n = 5; 45%), A (n = 3; 27%), C (n = 2; 18%) and D (n = 1; 10%). Statistical analysis of the haplotypes, haplogroup frequencies, and Nei genetic distances showed close affinity of Paquimé with Mimbres. DISCUSSION Although our results provide strong evidence of genetic affinities between Paquimé and Mimbres, with the majority of haplotypes shared or derived from ancient Southwest populations, the causes of cultural development at Paquimé still remain a question. These preliminary results provide evidence in support of other bioarchaeological studies, which have shown close biological affinities between Paquimé and Mimbres, a Puebloan culture, in the Southwestern US.
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Affiliation(s)
- Ana Y Morales-Arce
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
| | - Meradeth H Snow
- Anthropology, College of Humanities and Sciences, University of Montana, Missoula, Montana, 59812
| | - Jane H Kelley
- Department of Archaeology, University of Calgary (deceased), Calgary, Alberta, Canada, T2N 1N4
| | - M Anne Katzenberg
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada, T2N 1N4
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Byrd RM. Phenotypic variation of transitional forager-farmers in the Sonoran Desert. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 155:579-90. [PMID: 25229162 DOI: 10.1002/ajpa.22613] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 09/02/2014] [Indexed: 11/06/2022]
Abstract
This study examines phenotypic variation and biological distances estimated using morphological traits from three Early Agricultural period (EAP) (2100 BC-AD 50) site-complexes in the Sonoran Desert of southern Arizona and northern Sonora. The hypothesis tested is that EAP forager-farmers were phenotypically homogenous as suggested by patterns in material culture and works to refine inferences regarding gene flow and biological affinity during subsistence transitions. Seven measurements from 62 EAP male and female crania were collected and used to calculate phenotypic variances, biological distances, and FST values with RMET 5.0 software. Analyses were applied to both pooled site-complex samples and to males and females separately. Results show differential variation between site-complex population samples, multiple significant biological distances, and significant FST values for the EAP regional sample that indicate widespread phenotypic heterogeneity rather than homogeneity. Significantly lower than expected variance in the Cienega Creek male sample is inferred to suggest a small closely related population present during the Cienega phase. Greater than expected male variation is attributed to higher frequencies of gene flow in the La Playa and Santa Cruz River site-complex samples. These EAP males are inferred to be more mobile across the Sonoran Desert landscape and representative of multiple biological affinities compared with females. This study provides evidence supporting the canalization of phenotypic variation when associated with human populations becoming increasingly sedentary due to transitioning subsistence practices.
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Affiliation(s)
- Rachael M Byrd
- School of Anthropology, University of Arizona, Tucson, AZ, 85721
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8
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Anastasiou E, Mitchell PD. Evolutionary anthropology and genes: Investigating the genetics of human evolution from excavated skeletal remains. Gene 2013; 528:27-32. [DOI: 10.1016/j.gene.2013.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/23/2013] [Accepted: 06/01/2013] [Indexed: 11/28/2022]
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9
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Monroe C, Kemp BM, Smith DG. Exploring prehistory in the North American southwest with mitochondrial DNA diversity exhibited by Yumans and Athapaskans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:618-31. [DOI: 10.1002/ajpa.22237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 12/23/2012] [Accepted: 01/07/2013] [Indexed: 11/10/2022]
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10
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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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11
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Raff JA, Bolnick DA, Tackney J, O'Rourke DH. Ancient DNA perspectives on American colonization and population history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:503-14. [PMID: 21913177 DOI: 10.1002/ajpa.21594] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 07/07/2011] [Indexed: 11/07/2022]
Abstract
Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.
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Affiliation(s)
- Jennifer A Raff
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA.
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12
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Snow MH, Durand KR, Smith DG. Ancestral Puebloan mtDNA in Context of the Greater Southwest. JOURNAL OF ARCHAEOLOGICAL SCIENCE 2010; 37:1635-1645. [PMID: 20514346 PMCID: PMC2877212 DOI: 10.1016/j.jas.2010.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Ancient DNA (aDNA) was extracted from the human remains of seventy-three individuals from the Tommy and Mine Canyon sites (dated to PI-II and PIII, respectively), located on the B-Square Ranch in the Middle San Juan region of New Mexico. The mitochondrial DNA (mtDNA) haplogroups of forty-eight (65.7%) of these samples were identified, and their frequency distributions were compared with those of other prehistoric and modern populations from the Greater Southwest and Mexico. The haplogroup frequency distributions for the two sites were statistically significantly different from each other, with the Mine Canyon site exhibiting an unusually high frequency of haplogroup A for a Southwestern population, indicating the possible influence of migration or other evolutionary forces. However, both sites exhibited a relatively high frequency of haplogroup B, typical of Southwestern populations, suggesting continuity in the Southwest, as has been hypothesized by others (S. Carlyle 2003; Carlyle, et al. 2000; Kemp 2006; Malhi, et al. 2003; Smith, et al. 2000). The first hypervariable region of twenty-three individuals (31.5%) was also sequenced to confirm haplogroup assignments and compared with other sequences from the region. This comparison further strengthens the argument for population continuity in the Southwest without a detectable influence from Mesoamerica.
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Affiliation(s)
- Meradeth H Snow
- University of California, Davis Anthropology Department, Young Hall One Shields Avenue Davis CA 95616 (530) 848-1432
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13
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Evaluating the Farming/Language Dispersal Hypothesis with genetic variation exhibited by populations in the Southwest and Mesoamerica. Proc Natl Acad Sci U S A 2010; 107:6759-64. [PMID: 20351276 DOI: 10.1073/pnas.0905753107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Farming/Language Dispersal Hypothesis posits that prehistoric population expansions, precipitated by the innovation or early adoption of agriculture, played an important role in the uneven distribution of language families recorded across the world. In this case, the most widely spread language families today came to be distributed at the expense of those that have more restricted distributions. In the Americas, Uto-Aztecan is one such language family that may have been spread across Mesoamerica and the American Southwest by ancient farmers. We evaluated this hypothesis with a large-scale study of mitochondrial DNA (mtDNA) and Y-chromosomal DNA variation in indigenous populations from these regions. Partial correlation coefficients, determined with Mantel tests, show that Y-chromosome variation in indigenous populations from the American Southwest and Mesoamerica correlates significantly with linguistic distances (r = 0.33-0.384; P < 0.02), whereas mtDNA diversity correlates significantly with only geographic distance (r = 0.619; P = 0.002). The lack of correlation between mtDNA and Y-chromosome diversity is consistent with differing population histories of males and females in these regions. Although unlikely, if groups of Uto-Aztecan speakers were responsible for the northward spread of agriculture and their languages from Mesoamerica to the Southwest, this migration was possibly biased to males. However, a recent in situ population expansion within the American Southwest (2,105 years before present; 99.5% confidence interval = 1,273-3,773 YBP), one that probably followed the introduction and intensification of maize agriculture in the region, may have blurred ancient mtDNA patterns, which might otherwise have revealed a closer genetic relationship between females in the Southwest and Mesoamerica.
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Schultz Shook BA, Smith DG. Using ancient mtDNA to reconstruct the population history of northeastern North America. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 137:14-29. [DOI: 10.1002/ajpa.20835] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Mooder KP, Schurr TG, Bamforth FJ, Bazaliiski VI, Savel'ev NA. Population affinities of Neolithic Siberians: a snapshot from prehistoric Lake Baikal. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 129:349-61. [PMID: 16323184 DOI: 10.1002/ajpa.20247] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Archaeological evidence supports the inhabitation of the Lake Baikal region since the Paleolithic. Both metric and nonmetric osteological studies suggest that Neolithic Cis-Baikal populations are the ancestors of contemporary inhabitants of the region. To date, ancient DNA data have not been used to corroborate this biological continuity hypothesis. This study presents a temporal snapshot of the Cis-Baikal Neolithic by examining mtDNA diversity in two cemetery populations situated on the Angara River downstream of Lake Baikal. The 800 years separating the use of the two cemeteries is thought to represent a biocultural hiatus in the Cis-Baikal region, one that ended when a new group migrated into the area. To assess the likelihood that genetic continuity exists between these two Neolithic groups, we examined both mtDNA coding region and hypervariable region I (HVI) polymorphisms from skeletal remains excavated from both cemeteries (Lokomotiv and Ust'-Ida). The mtDNA haplogroup distributions of the two cemetery populations differ significantly, suggesting that they were biologically distinct groups. When the biological distance between these Neolithic groups is compared with modern Siberian and other East Eurasian groups, the posthiatus group (Serovo-Glazkovo) generally aligns with contemporary Siberians, while the prehiatus (Kitoi) individuals are significantly different from all but modern Kets and Shorians living in the Yenisey and Ob River basins to the west of Lake Baikal. These results suggest that the Lake Baikal region experienced a significant depopulation event during the sixth millennium BP, and was reoccupied by a new immigrant population some 800 years later.
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Affiliation(s)
- K P Mooder
- Human Identification Laboratory for Archaeology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada.
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16
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Allard MW, Polanskey D, Wilson MR, Monson KL, Budowle B. Evaluation of Variation in Control Region Sequences for Hispanic Individuals in the SWGDAM mtDNA Data Set. J Forensic Sci 2006; 51:566-73. [PMID: 16696703 DOI: 10.1111/j.1556-4029.2006.00136.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Scientific Working Group on DNA Analysis Methods (SWGDAM) Hispanic data set was analyzed to determine the diversity, phylogeny, and relevant single nucleotide polymorphisms (SNPs) that describe haplogroup patterns for Hispanic Americans (N=686), and to assess the degree of admixture regarding mitochondrial DNA (mtDNA). The largest component of admixture based on mtDNA analysis derives from the four major haplogroups previously observed in Native American ancestry, including A (29.3%), B (15.7%), C (20.6%), and D (4.8%). European (17.8%) and African (11.8%) haplogroups also were observed within this data set. Hispanic SWGDAM samples from the southwest, compared with other SWGDAM Hispanic samples, were observed to have a greater percent of Native American haplogroups present (79.9%), and fewer African American haplogroups (4.5%). A total of 234 SNPs were observed in the data set, including 36 newly reported variable positions. These SWGDAM Hispanic data set SNPs ranged from having 1 to 31 changes (Length=L) on the phylogenetic tree, with site 16519 being the most variable. On average, there were 3.9 character changes for each variable position on the tree. The most variable sites (with 13 or more changes each listed from fastest to slowest) observed were 16519 (L=31), 16189 (L=23), 152 (L=23), 16311 (L=19), 146 (L=17), 195 (L=17), 16093 (L=15), 16362 (L=14), 16129 (L=13), 150 (L=13), and 153 (L=13). These sites are consistent with other reports on highly variable positions. A total of 27 SNPs were chosen to identify all clusters containing 1% (N=7) or more individuals in the SWGDAM Hispanic data set. The descriptive analyses revealed that the SWGDAM Hispanic data set is similar to published Native American and Hispanic data sets.
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Affiliation(s)
- Marc W Allard
- Department of Biological Sciences, George Washington University, Washington, DC 20052, USA.
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17
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Kemp BM, Smith DG. Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Sci Int 2005; 154:53-61. [PMID: 16182949 DOI: 10.1016/j.forsciint.2004.11.017] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 11/24/2004] [Accepted: 11/26/2004] [Indexed: 11/22/2022]
Abstract
The extraction of DNA from archaeological or forensic skeletal remains can provide quite powerful data for analysis, but is plagued by a unique set of methodological problems. One of the most important methodological problems to overcome in such analyses is the presence of modern contamination on the surfaces of bones and teeth, which can lead to false positives and erroneous results unless it is removed before DNA extraction is initiated. Ancient DNA (aDNA) researchers and forensic scientists have employed a number of techniques to minimize such contamination. One such technique is the use of bleach (sodium hypochlorite--NaOCl) to "destroy" contaminating DNA. However, a consensus on the optimum concentration of sodium hypochlorite to be used and the amount of time the bone or tooth should be exposed to it has not emerged. The present study systematically approaches the issue by introducing contamination to ancient bones (from approximately 500 BP) and determining which of several sodium hypochlorite treatments best eliminates surface contamination. The elimination of surface contamination from bone requires immersion in at least 3.0% (w/v) sodium hypochlorite (approximately equal parts of commercial bleach and water) for at least 15 min. Endogenous DNA proved to be quite stable to even extreme sodium hypochlorite treatments (6% for 21 h), suggesting that DNA adsorbs to hydroxyapatite in the bone and that this process facilitates the preservation of DNA in ancient skeletal remains.
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Affiliation(s)
- Brian M Kemp
- Department of Anthropology, University of California, Davis, CA 95616, USA.
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Hunley K, Long JC. Gene flow across linguistic boundaries in Native North American populations. Proc Natl Acad Sci U S A 2005; 102:1312-7. [PMID: 15668380 PMCID: PMC547813 DOI: 10.1073/pnas.0409301102] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cultural and linguistic groups are often expected to represent genetic populations. In this article, we tested the hypothesis that the hierarchical classification of languages proposed by J. Greenberg [(1987) Language in the Americas (Stanford Univ. Press, Stanford, CA)] also represents the genetic structure of Native North American populations. The genetic data are mtDNA sequences for 17 populations gleaned from literature sources and public databases. The hypothesis was rejected. Further analysis showed that departure of the genetic structure from the linguistic classification was pervasive and not due to an outlier population or a problematic language group. Therefore, Greenberg's language groups are at best an imperfect approximation to the genetic structure of these populations. Moreover, we show that the genetic structure among these Native North American populations departs significantly from the best-fitting hierarchical models. Analysis of median joining networks for mtDNA haplotypes provides strong evidence for gene flow across linguistic boundaries. In principle, the language of a population can be replaced more rapidly than its genes because language can be transmitted both vertically from parents to children and horizontally between unrelated people. However, languages are part of a cultural complex, and there may be strong pressure to maintain a language in place whereas genes are free to flow.
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Affiliation(s)
- Keith Hunley
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-0618, USA
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Ousley SD, Billeck WT, Hollinger RE. Federal Repatriation Legislation and the Role of Physical Anthropology in Repatriation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005; Suppl 41:2-32. [PMID: 16369957 DOI: 10.1002/ajpa.20354] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Two laws governing the disposition of Native American human remains in museums and institutions have had a profound impact on anthropology, and especially physical anthropology. In contrast to the perception of constant conflict between Native Americans and physical anthropologists, the repatriation process based on these laws has been in large part harmonious between institutions and Native peoples in the US. Despite misconceptions, the Native American Graves Protection and Repatriation Act (NAPGRA; 25 United States Code (U.S.C.) 3001-3013) was not intended to halt further research on Native American remains in museums. In fact, court decisions have affirmed that the documentation of human remains produces information no other methods can provide, and provides necessary evidence to be incorporated and weighed, along with other evidence, in evaluating "cultural affiliation," the legal term for the required connection from federally recognized Native American groups to their ancestors. The wide variety of osteological data collected at the National Museum of Natural History (NMNH), Smithsonian Institution, have proven indispensable when evaluating cultural affiliation, especially when other information sources are unhelpful or ambiguous, and provide an empirical basis for determining the ancestry of individuals whose remains will be discovered in the future. To date, the claim-driven process at the NMNH has resulted in the affiliation and repatriation of more Native American remains than any other institution in the country. Repatriation experiences at the NMNH demonstrate the changing relationships between museums and Native peoples, the continuing important contributions that physical anthropology makes to the repatriation process, and the importance of physical anthropology in understanding the recent and ancient history of North America.
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Affiliation(s)
- Stephen D Ousley
- Repatriation Office, Department of Anthropology, Smithsonian Institution, Washington, DC 20013-7012, USA.
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Affiliation(s)
- Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6398;
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Mulligan CJ, Hunley K, Cole S, Long JC. POPULATION GENETICS, HISTORY, AND HEALTH PATTERNS IN NATIVE AMERICANS. Annu Rev Genomics Hum Genet 2004; 5:295-315. [PMID: 15485351 DOI: 10.1146/annurev.genom.5.061903.175920] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past two decades, detailed studies of mitochondrial DNA and the Y chromosome have increased our understanding of the history and population genetics of Native American populations. Variation in autosomal DNA has also been investigated, but to a more limited extent. A low level of genetic diversity in Native American populations is a robust finding from all lines of evidence. In contrast to the previous multiple migration scenarios for the Pleistocene peopling of the Americas, it now seems that a single migration satisfactorily explains the genetic data. Native Americans show greater genetic similarity to populations in east central Asia than they do to the current easternmost Siberian populations. Recent studies on the Y chromosome indicate a date of entry (about 17,000 years ago) into the Americas roughly consistent with the archaeological record. Native Americans experienced two episodes of reduced population size: one with the peopling of the Americas and the other with European contact. The former is the more important determinant for the number of gene lineages and founding haplotypes seen in populations. It may also be an important determinant of the genetic variation underlying common complex diseases, and especially diabetes. The tribal structure of contemporary Native American populations is relevant to the distribution of rare Mendelian disorders because most tribes constitute relatively small, semi-independent gene pools. This leads us to expect that the allelic spectrum for Mendelian diseases will be simple within individual tribes but complex for Native Americans as a whole.
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Affiliation(s)
- Connie J Mulligan
- Department of Anthropology, University of Florida , Gainesville, Florida 32611, USA.
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Schurr TG, Sherry ST. Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: Evolutionary and demographic evidence. Am J Hum Biol 2004; 16:420-39. [PMID: 15214060 DOI: 10.1002/ajhb.20041] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A number of important insights into the peopling of the New World have been gained through molecular genetic studies of Siberian and Native American populations. While there is no complete agreement on the interpretation of the mitochondrial DNA (mtDNA) and Y chromosome (NRY) data from these groups, several generalizations can be made. To begin with, the primary migration of ancestral Asians expanded from south-central Siberia into the New World and gave rise to ancestral Amerindians. The initial migration seems to have occurred between 20,000-15,000 calendar years before present (cal BP), i.e., before the emergence of Clovis lithic sites (13,350-12,895 cal BP) in North America. Because an interior route through northern North America was unavailable for human passage until 12,550 cal BP, after the last glacial maximum (LGM), these ancestral groups must have used a coastal route to reach South America by 14,675 cal BP, the date of the Monte Verde site in southern Chile. The initial migration appears to have brought mtDNA haplogroups A-D and NRY haplogroups P-M45a and Q-242/Q-M3 to the New World, with these genetic lineages becoming widespread in the Americas. A second expansion that perhaps coincided with the opening of the ice-free corridor probably brought mtDNA haplogroup X and NRY haplogroups P-M45b, C-M130, and R1a1-M17 to North and Central America. Finally, populations that formerly inhabited Beringia expanded into northern North America after the LGM, and gave rise to Eskimo-Aleuts and Na-Dené Indians.
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MESH Headings
- Americas/epidemiology
- Anthropology, Physical
- Biological Evolution
- Chromosomes, Human, Y/genetics
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/history
- Demography
- Emigration and Immigration/history
- Genetic Variation
- Genetics, Population
- Haplotypes/genetics
- History, Ancient
- History, Early Modern 1451-1600
- Humans
- Indians, North American/genetics
- Indians, North American/history
- Siberia/ethnology
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Bolnick DA, Smith DG. Unexpected patterns of mitochondrial DNA variation among Native Americans from the Southeastern United States. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; 122:336-54. [PMID: 14614755 DOI: 10.1002/ajpa.10284] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mitochondrial DNA (mtDNA) haplogroups were determined by restriction fragment length polymorphism-typing for 66 individuals from four southeastern North American populations, and the HVS I portion of the mtDNA control region was sequenced in 48 of these individuals. Although populations from the same geographic region usually exhibit similar haplogroup frequency distributions (Lorenz and Smith [1996] Am. J. Phys. Anthropol. 101:307-323; Malhi et al. [2001] Hum. Biol. 73:17-55), those from the Southeast instead exhibit haplogroup frequency distributions that differ significantly from one another. Such divergent haplogroup frequency distributions are unexpected for the Muskogean-speaking southeastern populations, which share many sociocultural traits, speak closely related languages, and have experienced extensive admixture both with each other and with other eastern North American populations. Independent origins, genetic isolation from other Native American populations due to matrilocality, differential admixture, or a genetic bottleneck could be responsible for this heterogeneous distribution of haplogroup frequencies. Within a given haplogroup, however, the HVS I sequences from the four Muskogean-speaking populations appear relatively similar to one another, providing evidence for close relationships among them and for reduced diversity within haplogroups in the Southeast. Given additional archaeological, linguistic, and ethnographic evidence, these results suggest that a genetic bottleneck associated with the historical population decline is the most plausible explanation for such patterns of mtDNA variation.
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Affiliation(s)
- Deborah A Bolnick
- Department of Anthropology, University of California, Davis, California 95616, USA.
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Kaestle FA, Horsburgh KA. Ancient DNA in anthropology: methods, applications, and ethics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; Suppl 35:92-130. [PMID: 12653310 DOI: 10.1002/ajpa.10179] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Anthropologists were quick to recognize the potential of new techniques in molecular biology to provide additional lines of evidence on questions long investigated in anthropology, as well as those questions that, while always of interest, could not have been addressed by more traditional techniques. The earliest ancient DNA studies, both within anthropology and in other fields, lacked rigorous hypothesis testing. However, more recently the true value of ancient DNA studies is being realized, and methods are being applied to a wide variety of anthropological questions. We review the most common methods and applications to date, and describe promising avenues of future research. We find that ancient DNA analyses have a valuable place in the array of anthropological techniques, but argue that such studies must not be undertaken merely to demonstrate that surviving DNA is present in organic remains, and that no such work should be performed before a careful consideration of the possible ethical ramifications of the research is undertaken.
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Affiliation(s)
- Frederika A Kaestle
- Department of Anthropology, Indiana University, Bloomington, Indiana 47405-7100, USA.
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Eshleman JA, Malhi RS, Smith DG. Mitochondrial DNA studies of Native Americans: Conceptions and misconceptions of the population prehistory of the Americas. Evol Anthropol 2003. [DOI: 10.1002/evan.10048] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Malhi RS, Mortensen HM, Eshleman JA, Kemp BM, Lorenz JG, Kaestle FA, Johnson JR, Gorodezky C, Smith DG. Native American mtDNA prehistory in the American Southwest. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; 120:108-24. [PMID: 12541329 DOI: 10.1002/ajpa.10138] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This study examines the mtDNA diversity of the proposed descendants of the multiethnic Hohokam and Anasazi cultural traditions, as well as Uto-Aztecan and Southern-Athapaskan groups, to investigate hypothesized migrations associated with the Southwest region. The mtDNA haplogroups of 117 Native Americans from southwestern North America were determined. The hypervariable segment I (HVSI) portion of the control region of 53 of these individuals was sequenced, and the within-haplogroup diversity of 18 Native American populations from North, Central, and South America was analyzed. Within North America, populations in the West contain higher amounts of diversity than in other regions, probably due to a population expansion and high levels of gene flow among subpopulations in this region throughout prehistory. The distribution of haplogroups in the Southwest is structured more by archaeological tradition than by language. Yumans and Pimans exhibit substantially greater genetic diversity than the Jemez and Zuni, probably due to admixture and genetic isolation, respectively. We find no evidence of a movement of mtDNA lineages northward into the Southwest from Central Mexico, which, in combination with evidence from nuclear markers, suggests that the spread of Uto-Aztecan was facilitated by predominantly male migration. Southern Athapaskans probably experienced a bottleneck followed by extensive admixture during the migration to their current homeland in the Southwest.
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Affiliation(s)
- Ripan S Malhi
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Malhi RS, Eshleman JA, Greenberg JA, Weiss DA, Schultz Shook BA, Kaestle FA, Lorenz JG, Kemp BM, Johnson JR, Smith DG. The structure of diversity within New World mitochondrial DNA haplogroups: implications for the prehistory of North America. Am J Hum Genet 2002; 70:905-19. [PMID: 11845406 PMCID: PMC379119 DOI: 10.1086/339690] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2001] [Accepted: 01/10/2002] [Indexed: 11/03/2022] Open
Abstract
The mitochondrial DNA haplogroups and hypervariable segment I (HVSI) sequences of 1,612 and 395 Native North Americans, respectively, were analyzed to identify major prehistoric population events in North America. Gene maps and spatial autocorrelation analyses suggest that populations with high frequencies of haplogroups A, B, and X experienced prehistoric population expansions in the North, Southwest, and Great Lakes region, respectively. Haplotype networks showing high levels of reticulation and high frequencies of nodal haplotypes support these results. The haplotype networks suggest the existence of additional founding lineages within haplogroups B and C; however, because of the hypervariability exhibited by the HVSI data set, similar haplotypes exhibited in Asia and America could be due to convergence rather than common ancestry. The hypervariability and reticulation preclude the use of estimates of genetic diversity within haplogroups to argue for the number of migrations to the Americas.
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Affiliation(s)
- Ripan S Malhi
- Department of Human Genetics, 3726 Medical Science II, University of Michigan, 1301 E. Catherine Street, Ann Arbor, MI 48109-0618, USA.
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28
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Affiliation(s)
- Dennis H. O'Rourke
- Laboratory of Biological Anthropology, University of Utah, Salt Lake City, Utah 84112-0060; e-mail:
| | - M. Geoffrey Hayes
- Laboratory of Biological Anthropology, University of Utah, Salt Lake City, Utah 84112-0060; e-mail:
| | - Shawn W. Carlyle
- Laboratory of Biological Anthropology, University of Utah, Salt Lake City, Utah 84112-0060; e-mail:
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