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Haplogroup M discovered in prehistoric North America
Abstract
We analyzed two mid-Holocene (∼5000 years before present) individuals from North America that belong to mitochondrial DNA (mtDNA) haplogroup M, a common type found in East Asia, but one that has never before been reported in ancient or living indigenous populations in the Americas. This study provides evidence that the founding migrants of the Americas exhibited greater genetic diversity than previously recognized, prompting us to reconsider the widely accepted five-founder model that posits that the Americas were colonized by only five founding mtDNA lineages. Additional genetic studies of prehistoric remains in the Americas are likely to reveal important insights into the early population history of Native Americans. However, the usefulness of this information will be tempered by the ability of researchers to distinguish novel founding lineages from contamination and, as such, we recommend strategies to successfully accomplish this goal.
... To illustrate my semantic point: various contemporary authors have concluded from their genetic data sets that the likeliest point of origin for the peopling of the New World is southern Siberia (Derenko et al. 2007;Wells et al. 2001), or south-central Siberia (Bortolini et al. 2003;Schurr 2004;Schurr and Sherry 2004), or central Siberia (Lell et al. 2002), or eastern Siberia (Wang et al. 2007), or northern Siberia (Forster 2004), or just plain old Siberia (Seielstad et al. 2003). Others point to Asia (O'Rourke 2009), or East Asia (Bandelt et al. 2003;Malhi et al. 2007), or northeast Asia (Battilana et al. 2006;Fagundes et al. 2008), or Mongolia , or the Altai Mountains (Dornelles et al. 2005;Santos et al. 1999, Starikovskaya et al. 2005Zegura et al. 2004), or the ''area around Lake Baikal'' (Derenko et al. 2001;Eshleman et al. 2003). Yet others implicate the Lower Amur/Sea of Okhotsk region (Lell et al. 2002;Starikovskaya et al. 2005) or western Beringia (Derbeneva et al. 2002;Schroeder et al. 2007Schroeder et al. , 2009Tamm et al. 2007). ...
... (A haplogroup is a grouping of similar and ancestrally related haplotypes; a haplotype represents a set of alleles on a single chromosome that are inherited together and thus shared by closely related people.) Indigenous North and South American populations so far sampled collectively exhibit seven mtDNA haplogroups (A, B, C, two variants of D, M, and X) (e.g., Bandelt et al. 2003;Derenko et al. 2001;Fix 2005;Malhi et al. , 2007Perego et al. 2009;Schurr 2004;Schurr and Sherry 2004;Starikovskaya et al. 2005) and four NRY haplogroups (C, P, Q, and R) (e.g., Lell et al. 2002;Santos et al. 1999;Schurr 2004;Seielstad et al. 2003;Tarazona-Santos and Santos 2002;Zegura et al. 2004). Only peoples of the Altai region and the regions southeast and southwest of Lake Baikal express a range of mtDNA haplogroups and NRY haplogroups that encompasses those of First American populations (Derenko et al. 2001;Dornelles et al. 2005;Eshleman et al. 2003;Malhi et al. , 2007Merriwether 2006;Schurr and Sherry 2004;Starikovskaya et al. 2005;Zegura et al. 2004). ...
... Indigenous North and South American populations so far sampled collectively exhibit seven mtDNA haplogroups (A, B, C, two variants of D, M, and X) (e.g., Bandelt et al. 2003;Derenko et al. 2001;Fix 2005;Malhi et al. , 2007Perego et al. 2009;Schurr 2004;Schurr and Sherry 2004;Starikovskaya et al. 2005) and four NRY haplogroups (C, P, Q, and R) (e.g., Lell et al. 2002;Santos et al. 1999;Schurr 2004;Seielstad et al. 2003;Tarazona-Santos and Santos 2002;Zegura et al. 2004). Only peoples of the Altai region and the regions southeast and southwest of Lake Baikal express a range of mtDNA haplogroups and NRY haplogroups that encompasses those of First American populations (Derenko et al. 2001;Dornelles et al. 2005;Eshleman et al. 2003;Malhi et al. , 2007Merriwether 2006;Schurr and Sherry 2004;Starikovskaya et al. 2005;Zegura et al. 2004). ...
This article synthesizes the 2000s-era “peopling of the Americas” data drawn from molecular biology, osteology, and archaeology.
Collectively, they suggest that colonization proceeded in two pulses, both originating in western Beringia, and before that,
south-central and southeastern Siberia. The first pulse occurred circa 16 k–15 k cal. B.P. by watercraft along the coast of
Beringia and western North and South America. The second took place 1,000 years later and involved proto-Clovis hunter-gatherers
who used the ice-free corridor as a conduit south. At least eight North American sites dating as far back as the Last Glacial
Maximum suggest that the peopling picture may eventually need to change to accommodate an earlier than previously thought
migration through the ice-free corridor. For now, the data are not strong enough to support this scenario, but they are tantalizingly
close.
... A relatively small number of human skeletal remains have been identified in the Americas that are in excess of 5000 years old (the mid-Holocene) [20]. Of these, six have yielded analyzable DNA and were published in peer review journals [21][22][23][24][25]. An ancient individual dating to 10300 years before present (BP) from On Your Knees Cave on Prince of Wales Island in Southeast Alaska was analyzed for nearly the entire control region of the mitochondrial genome plus diagnostic sites of the coding region of the mitochondrial genome that assisted in the determination of his mitochondrial genome belonging to sub-haplogroup D4h3a [23]. ...
... Haplogroup B was identified for an individual found in Hourglass Cave in Colorado who died approximately 8000 years BP [21]. Haplogroup A was determined for an individual uncovered at Big Bar Lake, British Columbia with a radiocarbon date of 4975+/240 years BP [24][25]. Two individuals from China Lake, British Columbia, found in the same burial with a radiocarbon date of 4950+/2170 years BP were determined to belong to a form of macrohaplogroup M that has yet to be identified in any extant Native American population [24], [26]. ...
... Haplogroup A was determined for an individual uncovered at Big Bar Lake, British Columbia with a radiocarbon date of 4975+/240 years BP [24][25]. Two individuals from China Lake, British Columbia, found in the same burial with a radiocarbon date of 4950+/2170 years BP were determined to belong to a form of macrohaplogroup M that has yet to be identified in any extant Native American population [24], [26]. The China Lake study suggests that individuals in the early to mid-Holocene may exhibit mitogenomes that have since gone extinct in a specific geographic region or in all of the Americas. ...
To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga'a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor-descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.
... To date, with rare exceptions (Malaspinas et al. 2014;Malhi et al. 2007), the aDNA from pre-Columbian skeletal and mummified remains shares common ancestry with northeastern Asian populations (Casas-Vargas et al. 2011;de la Fuente et al. 2015;Fehren-Schmitz et al. 2014Llamas et al. 2016;Posth et al. 2018;Rasmussen et al. 2014Rasmussen et al. , 2015Shinoda et al. 2010). However, in an ancient mtDNA study by Malhi et al. (2007), two individuals from China Lake, British Colombia, ~5,000 cal BC, are characterized by haplogroup M, an mtDNA haplogroup variant found among Asian populations but no other known Native Americans. ...
... To date, with rare exceptions (Malaspinas et al. 2014;Malhi et al. 2007), the aDNA from pre-Columbian skeletal and mummified remains shares common ancestry with northeastern Asian populations (Casas-Vargas et al. 2011;de la Fuente et al. 2015;Fehren-Schmitz et al. 2014Llamas et al. 2016;Posth et al. 2018;Rasmussen et al. 2014Rasmussen et al. , 2015Shinoda et al. 2010). However, in an ancient mtDNA study by Malhi et al. (2007), two individuals from China Lake, British Colombia, ~5,000 cal BC, are characterized by haplogroup M, an mtDNA haplogroup variant found among Asian populations but no other known Native Americans. Further, Llamas et al. (2016) indicate that none of the 96 mtDNA haplotypes they report for pre-Columbian South Americans are known among modern Native Americans, while Moreno-Mayar et al. (2018) report a previously unknown basic ancient Native American genetic sequence for a Late Pleistocene Alaskan child, thereby confirming that haplogroup extinction and discontinuities have occurred for mtDNA haplogroups and haplotypes. ...
This paper summarizes the current archaeological, physiographic, demographic, molecular, and bioarchaeological understanding of the initial peopling and subsequent population dynamics of South America. Well-dated sites point to a colonization by relatively few broad-spectrum foragers from northeastern Asia between ~13,000 and 12,000 cal BC via the Panamanian Peninsula. By ~11,500–11,000 cal BC, a number of regional, specialized bifacial technologies were developed, with evidence for the seasonal scheduling of resources and the colonization of extreme environments. Restricted mobility, landscape modification, and the cultivation of domesticates were underway by ~8000 cal BC. The early migration routes followed by colonists resulted in a broad east-west population structure among ancient South Americans. Genetic, demographic, and skeletal morphological data indicate that a subsequent demographically driven dispersal into South America largely replaced preexisting central Andeans ~5000 BC, due to increased fertility associated with the shift to agriculture. Beyond the Andes, however, there is little evidence of impact of these later expansions on foragers and horticulturists of the Amazon and Southern Cone who were largely descended from Paleoindians and early Holocene populations.
... To date, with rare exceptions (Malaspinas et al. 2014;Malhi et al. 2007), the aDNA from pre-Columbian skeletal and mummified remains shares common ancestry with northeastern Asian populations (Casas-Vargas et al. 2011;de la Fuente et al. 2015;Fehren-Schmitz et al. 2014Llamas et al. 2016;Posth et al. 2018;Rasmussen et al. 2014Rasmussen et al. , 2015Shinoda et al. 2010). However, in an ancient mtDNA study by Malhi et al. (2007), two individuals from China Lake, British Colombia, ~5,000 cal BC, are characterized by haplogroup M, an mtDNA haplogroup variant found among Asian populations but no other known Native Americans. ...
... To date, with rare exceptions (Malaspinas et al. 2014;Malhi et al. 2007), the aDNA from pre-Columbian skeletal and mummified remains shares common ancestry with northeastern Asian populations (Casas-Vargas et al. 2011;de la Fuente et al. 2015;Fehren-Schmitz et al. 2014Llamas et al. 2016;Posth et al. 2018;Rasmussen et al. 2014Rasmussen et al. , 2015Shinoda et al. 2010). However, in an ancient mtDNA study by Malhi et al. (2007), two individuals from China Lake, British Colombia, ~5,000 cal BC, are characterized by haplogroup M, an mtDNA haplogroup variant found among Asian populations but no other known Native Americans. Further, Llamas et al. (2016) indicate that none of the 96 mtDNA haplotypes they report for pre-Columbian South Americans are known among modern Native Americans, while Moreno-Mayar et al. (2018) report a previously unknown basic ancient Native American genetic sequence for a Late Pleistocene Alaskan child, thereby confirming that haplogroup extinction and discontinuities have occurred for mtDNA haplogroups and haplotypes. ...
... This number will most likely increase if and when further samples are collected. Ripan Mali et al. (2007) argued that researchers may have ignored evidence of founding haplotypes as it did not fit with the prevailing model. ...
... additional founder lineages as contamination and, as such, failed to report the results " (Mali et al. 2007, 647). ...
Abstract
Until very recently, archaeologists argued that the first people to enter the Western Hemisphere walked across the Bering Land Bridge from Siberia after 13,200 calBP, bringing with them fluted Clovis tools. However, there are many problematic areas of this archaeological story: one being that fluted Clovis tools have never been found outside of the Western Hemisphere, another being that in North and South America there are published reports of hundreds of pre-13,200 calBP sites which meet or exceed archaeological standards for dating, stratigraphy, and cultural artifacts. The field of Pleistocene archaeological studies in the Americas has historically been described as a battleground littered with academic causalities. Archaeologists have only recently conceded that Indigenous people were present in the Western Hemisphere a few 1000 years prior to Clovis. This is, however, the same scenario as the Clovis First hypothesis regarding diminishing the time frames of initial migrations; it is just a few 1000 years earlier than Clovis. This scenario reproduces and maintains archaeological power and control over the Indigenous past. Contrary to the traditional discussions of First People in the Western Hemisphere, my research questions are not about where the first people came from and when. I argue that the first people and their descendants are indigenous to the continents of the Western Hemisphere and have been so for thousands of years, this is where they are from. I argue that there is a vast body of evidence for much earlier migrations which is ignored a priori mainly due to embedded “nonfactual” colonially constructed histories which erased an ancient Indigenous presence. I further argue that archaeological discussions which diminish an ancient Indigenous presence in the Western Hemisphere rupture contemporary people’s connections to their ancestral past. I discuss the history of American Anthropology to support my argument that this academic battle is not just about archaeological sites or material remains. The argument reflects an ongoing colonial practice of erasure and denies Indigenous people of the Western Hemisphere a place in ancient world history.
Résumé
Jusqu’à tout récemment, les archéologues ont affirmé que les premiers peuples à avoir pénétré sur l’hémisphère occidental avaient traversé le pont terrestre de la Béringie depuis la Sibérie après 13,200 cal. BP, apportant avec eux les outils cannelés de type Clovis. Il existe cependant de nombreux points problématiques liés à cette histoire archéologique. L’un d’entre eux est que les outils cannelés de type Clovis n’ont jamais été trouvés en dehors de l’hémisphère occidental, l’autre est que plusieurs rapports, en Amérique du Nord et en Amérique du Sud, font état de centaines de sites datant d’avant 13,200 cal. BP, qui répondent ou dépassent les normes archéologiques pour ce qui concerne la datation, la stratigraphie et les artefacts culturels. Le domaine des études archéologiques du pléistocène aux Amériques a toujours été décrit comme un champ de bataille, ponctué de pertes académiques. Les archéologues n’ont que récemment reconnu que les peuples autochtones étaient présents aux Amériques plusieurs milliers d’années avant Clovis. Ceci est cependant le même scénario que la première hypothèse de Clovis à propos de la réduction des durées des migrations initiales, daté simplement quelques milliers d’années plus tôt que Clovis. Ce scénario reproduit et maintient la puissance et le contrôle archéologiques sur le passé indigène. Contrairement aux discussions traditionnelles sur les premiers peuples de l’hémisphère occidental, mes questions de recherche ne portent pas sur d’où ni quand sont arrivés les premiers peuples. Je fais valoir que les premiers peuples et leurs descendants sont des indigènes des continents de l’hémisphère occidental, qu’ils l’ont été pendant des milliers d’années, et que telle est leur origine. Je soutiens qu’il existe une vaste quantité de preuves concernant des migrations beaucoup plus précoces qui est ignorée, a priori, principalement en raison d’histoires ancrées et « non factuelles » construites par les colonies, qui ont effacé une présence autochtone ancienne. De plus, j’affirme que les discussions archéologiques diminuant une présence indigène ancienne sur l’hémisphère occidental, rompent les liens des peuples contemporains avec leur passé ancestral. J’examine l’histoire de l’anthropologie américaine pour étayer mon argument selon lequel cette bataille académique ne concerne pas uniquement des sites archéologiques ou des vestiges matériels, mais qu’elle reflète une pratique néocoloniale pour maintenir l’effacement d’une présence indigène ancienne qui nie la place des peuples autochtones de l’hémisphère occidental dans l’histoire du monde.
Resumen
Hasta hace muy poco, los arqueólogos argumentaban que los primeros pueblos que llegaron al hemisferio occidental atravesaron andando el Puente Terrestre de Bering desde Siberia después de 13.200 años calibrados antes del presente, trayendo consigo herramientas estriadas Clovis. Sin embargo, existen muchas zonas problemáticas en esta historia arqueológica. Una es que las herramientas estriadas clovis nunca han sido encontradas fuera del hemisferio occidental, otra es que en Norteamérica y en Sudamérica hay informes publicados de cientos de emplazamientos anteriores a 13.200 años calibrados antes del presente que satisfacen o superan los estándares arqueológicos de datación, estratigrafia y artefactos culturales. El campo de los estudios arqueológicos del Pleistoceno en ambas Américas ha sido descrito históricamente como un campo de batalla, contaminado con bajas académicas. Sólo recientemente, los arqueólogos han admitido que los pueblos indígenas estaban presentes en las Américas algunos miles de años antes de Clovis. Sin embargo, éste es el mismo escenario ya que la hipótesis del Primer Clovis relativa a la disminución de los marcos de tiempo de las migraciones iniciales, es sólo algunos miles de años anterior a Clovis. Este escenario reproduce y mantiene un poder y control arqueológico sobre el pasado indígena. Al contrario que los debates tradicionales de los Primeros Pueblos en el hemisferio occidental, las preguntas de mi investigación no son sobre cuándo y de dónde vienen los primeros pueblos. Argumento que los primeros pueblos y sus descendientes son indígenas de los continentes del hemisferio occidental y lo han sido así durante miles de años, y es allí de donde proceden. Argumento que existe un vasto corpus de evidencia de migraciones mucho más tempranas que se ignora a priori debido principalmente a historias “irreales”arraigadas construidas colonialmente que borraron una presencia indígena antigua. Asimismo argumento que los debates arqueológicos que disminuyen una presencia indígena antigua en el hemisferio occidental, quiebran las conexiones de los pueblos contemporáneos con su pasado ancestral. Hablo de la historia de la Antropología americana para apoyar mi argumentación de que esta batalla académica no es sólo sobre emplazamientos arqueológicos o restos materiales, sino que refleja una práctica neocolonial de mantener la supresión de una presencia indígena antigua que niega a los pueblos indígenas del hemisferio occidental un lugar en la historia mundial.
... While haplogroup M has been found among prehistoric Native Americans (e.g. Malhi et al., 2007), the haplotype for SFB12 matches an individual from Madagascar for HV1 and since historical evidence shows association with Madagascar during the slave trade to New York, we think this individual is likely to be of Malagasy ancestry rather than Native American. ...
... Historical documents suggest several hundreds of people from Madagascar being imported for the slave labor force by the end of the 17th century as a result of an illegal trade between New York merchants and East African pirates (Matson, 1998;Platt, 1969). While there has been a report of a Native American haplogroup M from British Columbia of approximately 5000 years old (Malhi et al., 2007), based on the historical evidence of the region it seems more likely that these individuals are of Malagasy origin rather than Native American. ...
A burial ground located in the Town of Colonie, NY along the Hudson River revealed fourteen individuals dated from the 17th through the early 19th centuries. Bioarchaeological analysis suggested some of these individuals were of African ancestry who had worked and died on the property owned by the prominent Schuyler family. Mitochondrial DNA (mtDNA) analysis was carried out on skeletal remains of seven adults using restriction fragment length polymorphism typing and direct sequencing of the control region to infer their origins and relatedness. Results show that none of the individuals were maternally related, with four individuals identified as African haplogroup L, one identified as Native American haplogroup X, and two identified as haplogroup M and M7. Individuals of African ancestry correlate with published mtDNA data on African Americans and their geographical origins corroborate with the various exit points during the African slave trade to New York State. Individuals identified as haplogroup M7 and M resemble lineages found in Madagascar. Historical documents suggest several hundred people were imported from Madagascar through illegal trading to New York by the end of the 17th century. This study highlights the diverse origins of the enslaved labor force in colonial New York and contributes to our understanding of African American history in the northeast.
... (e.g.,Lindo et al., 2017;Morales-Arce et al., 2019;Raghavan et al., 2015), in contrast with the first PCR based studies which were prone to false positive haplogroup matches.Malhi et al., 2007 were the only ones to suggest the presence of mtDNA haplogroup M in Native Americans after excluding that this could represent a lineage belonging to haplogroups C or D (both members of the macro-haplogroups M) They advocate that evidence of additional founding mtDNA haplogroups would have been systematically ignored because these resul ...
Objectives
The aim of this study was to create a comprehensive summary of available mtDNA and Y-chromosome data for Native Americans from North, Central, and South America, including both modern and ancient DNA. To illustrate the usefulness of this dataset we present a broad picture of the genetic variation for both markers across the Americas.
Methods
We searched PubMed, ResearchGate, Google Scholar for studies about mtDNA or Y-chromosome variation in Native American populations, including geographic, linguistic, ecological (ecoregion), archeological and chronological information. We used AMOVA to estimate the genetic structure associated with language and ecoregion grouping and Mantel tests to evaluate the correlation between genetic and geographic distances.
Results
Genetic data were obtained from 321 primary sources, including 22,569 individuals from 298 contemporary populations, and 3628 individuals from 202 archeological populations. MtDNA lineages of probable non-Amerindian origin were rare, in contrast with Y-chromosome lineages. Mantel tests showed a statistically significant correlation for the whole continent considering mtDNA but not the Y-chromosome. Genetic structure between groups was always stronger for mtDNA than for the Y-chromosome.
Conclusions
This study summarizes decades of research conducted in Native American populations for both mtDNA and the Y-chromosome. Continental or sub-continental patterns of variation reveal that most of the genetic variation occurs within populations rather than among linguistic or ecoregional groups, and that isolation by distance is barely detectable in most population sets. The genetic structure among groups was always larger for mtDNA than for the Y-chromosome, suggesting between-sex differences in gene flow.
... We successfully determined a highly accurate complete mitogenome sequence of 20,000-year-old Minatogawa 1 (Minato1), a plausible direct descendant of the initial migration into the Japanese Archipelago ( Fig. 1, Table 1 and Supplementary Table S1). Its sequence obtained with average depth of 52 was classified into haplogroup M, and carries no substitutions that are defining subgroups of haplogroup M. Haplogroup M is found at high frequency in present-day Asians, Australasians, and indigenous Americans [13][14][15][16] . The sequence of this ancestral type of haplogroup M is not seen in any of 2,062 present-day Japanese samples newly determined in this study, 672 present-day Japanese 15 , 21,668 Han Chinese 17 . ...
The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.
... Eshleman and colleagues (2003), for instance, deduced that First Americans originated in "the area around Lake Baikal." Neither conclusion precludes the other, nor are there inherent contradictions in genetic studies variously placing the founding population(s) of the Americas in southern Siberia (Derenko et al., 2007), south-central Siberia (Schurr and Sherry, 2004), eastern Siberia (Wang et al., 2007), Siberia (Seielstad et al., 2004, East Asia (Malhi et al., 2007), Mongolia (Malhi et al., 2002), the Altai Mountains (Dornelles et al., 2005), or the Lower Amur/Sea of Okhotsk region (Starikovskaya et al., 2005). ...
This paper argues that the Rocky Mountains played a significantly more important role in the process of the peopling of the New World than archaeologists have traditionally recognized. Although First Americans did not reach the Rockies before they set foot in any other New World region-they could not have, regardless of their point of entry-by Clovis time, evidence suggests that Clovis people knew the Rocky Mountain landscape intimately.Archaeologists should have long anticipated this, given the many resources the Rocky Mountains offer that adjacent, albeit archaeologically better-known regions such as the Plains and some parts of the Far West do not; at least not as ubiquitously. These include plentiful water in the form of streams, lakes, snowpack, and glaciers; high-quality sources of obsidian, chert, quartzite and other knappable stone; and a vertically oriented landscape that maximizes floral and faunal diversity within comparatively condensed space.Two other non-economic characteristics likely contributed significantly to the appeal of the Rocky Mountains to some First Americans: the power and sanctity nearly all humans attribute to mountains, and the seemingly little-recognized fact that northeast Asian Upper Paleolithic people who populated the New World during the terminal Pleistocene occupied mountainous landscapes for some 45,000 years prior to their departure. For many First Americans, mountains-not the flat, windswept tundra of Siberian stereotypes-had always been home.Evidence for the familiarity of Clovis groups with the Rocky Mountain landscapes comes principally from three Clovis caches: Anzick, Fenn, and Mahaffy. All three caches are located in the Rockies, collectively contain artifacts made from ten of the highest-quality stone raw materials available in the Southern, Central and Northern Rockies, and at least one of the caches accompanies the burial of a young child who appears to have been interred intentionally on a prominent and likely sacred landform in a mountain valley.Bringing the paper's argument full circle, that same child's genetic profile shows a direct link to that of another youngster buried thousands of years earlier at the Late Glacial Maximum Mal'ta site in the mountainous Trans-Baikal region of Siberia.
... These data include planked boats (kamul) and related linguistic elements indicating cross-cultural learning of techniques and vocabulary. The presence of mtDNA M haplotypes in two mid-Holocene burials from British Columbia ( Malhi et al., 2007) may indicate the presence in northern North America of Asian-derived haplotypes that disappeared before contact. This could indicate a contact with Asia after the original PaleoAmerind migration. ...
After many years and much effort searching Beringia for the ancestors of Amerinds (PaleoAmerinds), archaeologists are empty-handed. Beringia certainly was the pathway for later peoples (Na-Dene and Inuit), but there is no persuasive evidence of an archaeological culture in Beringia during the last glacial maximum (LGM) when archaeologists expect an early, pre-Clovis culture group and biologists detect a long period of isolation—the “standstill.” In this article, I show that archaeologists defer to biologists for proof of concept, and biologists use that deference to support their outmoded model that Beringia, or even greater Siberia, was the sole route by which all Native American people entered the hemisphere. I propose that the standstill took place in the Americas and that the pathway taken by PaleoAmerinds was by the Pacific Ocean, possibly from Southeast Asia.
... A total of 327 bp mtDNA (positions 16055-16382) was sequenced using three sets of primers (Malhi et al. 2007) that amplified overlapping fragments of the mtDNA hypervariable region I. The length range of the PCR products was 202-212 bp. ...
... Such a possibility is unlikely to be influential for several reasons. First, no ancient DNA study has ever found an allele, mitochondrial or nuclear, in pre-Colombian Native Americans which is not present in modern populations, suggesting that while populations were severely reduced by European influences, their genetic compositions remain similar [37,43,56,57,58,59]. Second, three independent ancient DNA studies have found similar ABO allele compositions in pre-Colombian Native American samples when compared to geographically close modern samples, suggesting the modern ABO geographic pattern reflects its pre-Colombian state [60,61,62]. ...
The ABO locus in humans is characterized by elevated heterozygosity and very similar allele frequencies among populations scattered across the globe. Using knowledge of ABO protein function, we generated a simple model of asymmetric negative frequency dependent selection and genetic drift to explain the maintenance of ABO polymorphism and its loss in human populations. In our models, regardless of the strength of selection, models with large effective population sizes result in ABO allele frequencies that closely match those observed in most continental populations. Populations must be moderately small to fall out of equilibrium and lose either the A or B allele (Ne ≤ 50) and much smaller (Ne ≤ 25) for the complete loss of diversity, which nearly always involved the fixation of the O allele. A pattern of low heterozygosity at the ABO locus where loss of polymorphism occurs in our model is consistent with small populations, such as Native American populations. This study provides a general evolutionary model to explain the observed global patterns of polymorphism at the ABO locus and the pattern of allele loss in small populations. Moreover, these results inform the range of population sizes associated with the recent human colonization of the Americas.
... Moreover, a phylochronological approach, studying genetic patterns across both time and space, permits more accurate assessment of specific changes in population histories than do studies of variation of contemporary gene pools alone (Hadly et al., 2004;Ramakrishnan and Hadly, 2009). Ancient DNA analysis provides a critical dimension because studies of contemporary variation do not detect lineage extinction (e.g., Malhi, et al., 2007), which can be an integral part of a population's history. ...
... The first four haplogroups identified (A, B, C, and D), based on differences from the Anderson or Cambridge Reference Sequence, are found in both modern and ancient native populations. Two more mtDNA lineages have been described in ancient remains from the Americas, haplogroups X (Malhi and Smith, 2002), and M (Malhi et al., 2007) which have so far been reported only in North America, but the latter haplogroup has not been reported in any modern population. Together, these six haplogroups are thought to comprise the vast majority, if not all, of New World mtDNA diversity. ...
Bioarchaeological research must balance scholarly commitment to the generation of new knowledge, descendants' interests in their collective past, and the now common practice of rapid re-interment of excavated human remains. This paper documents the first results of a negotiated protocol built on the retention of one tooth per archaeologically derived skeleton, teeth that can then be used for destructive testing associated with ancient DNA and stable isotope investigations. Seven archaeological sites dating from the 13th to 16th centuries provided 53 teeth, 10 of which were subdivided between DNA and isotope labs. All tooth roots yielded haplogroup results, and five provided more detailed sequence results. Stable isotopes of carbon and nitrogen document heavy reliance on maize among all individuals, as well as reliance on a diverse range of fish. This work establishes baseline mtDNA information for Northern Iroquoians, and confirms the value of using dental tissues for dietary reconstruction. Particularly when human remains are fragmentary or co-mingled, this approach holds promise for ongoing incorporation of bioarchaeology into reconstructions of past peoples' lives.
... The three remaining haplotypes from "area A" were identified in three children (burials 4-6) that were assigned to haplogroup M8 (burials 4 and 6) and C1 (burial 5). While haplogroup M has been identified among prehistoric North Americans (Malhi et al. 2007), M8 has not been found among Native Americans but is frequent among Siberian populations (Starikovskaya et al. 2005). Dental traits of the children in burials 4 and 6 suggest Native American/Asian ancestry, and based on the historical information, it seems more likely these children were of maternal Native American ancestry than Asian. ...
Thirteen burials located on Jackson Street in Youngstown, NY, USA were recovered from a construction site and excavated in 1997. Based on the artifact assemblage, it was suggested that the cemetery was used sometime between the late 1700s and 1840. No historical records existed, and initial assessment of the skeletal remains was not able to determine any cultural affiliation. We carried out osteological and genetic investigations in order to gain insight into ancestral affiliation and kinship of the unknown individuals from the burials. Due to poor preservation of the remains, dental traits and limited osteological observations were available for only a few individuals. We performed DNA extraction and sequenced the mitochondrial DNA (mtDNA) control region following standard ancient DNA procedures. Our results suggest that ten individuals have evidence of biological affiliation with Native Americans, and in particular, four individuals have maternal Native American ancestry. One male individual was determined to be of European ancestry, from both the mtDNA and osteological results. This burial may reflect admixture as a result of frequent contact between Native Americans and Europeans during the eighteenth and nineteenth centuries and attempts by missionaries to convert Native Americans to Christianity. Our study demonstrates the usefulness of a multifaceted approach through archaeological, osteological, and genetic analysis that provides valuable perspectives in understanding the individuals buried at the Jackson Street Burials.
... Gilbert et al. (2008), por ejemplo, identificaron la presencia de los haplogrupos A2 y B2 en al menos tres coprolitos provenientes de una cueva en Oregon que antedatarían en unos 1.000 años 14 C la " cultura " Clovis, mientras que otros estudios han analizado los linajes maternos presentes en individuos recuperados de santuarios inca de altura (Wilson et al. 2007), sambaquís del litoral brasileño (Marinho et al. 2006), poblaciones de Patagonia y Tierra del Fuego (García-Bour et al. 2004), el noroeste argentino (Carnese et al. 2010, Mendisco et al. 2011) o el Caribe (Lalueza-Fox et al. 2003), entre muchos otros. Un interesante aporte a la diversidad de linajes maternos presentes en América fue presentado por Malhi et al. (2007) al describir dos individuos del Holoceno medio de British Columbia (Canadá) portadores de un mismo linaje materno que, aunque asignable al super-haplogrupo M, es distinto de otros linajes M presentes en el continente como los haplogrupos C y D. Por el momento este linaje no ha sido encontrado en otras poblaciones americanas modernas ni antiguas, desconociéndose también sus afinidades filéticas dentro de M. ...
Se revisan someramente los aportes de la arqueología, la lingüística histórica y la
bioantropología al estudio del origen de las poblaciones nativas americanas, y se profundiza en aquellos
aspectos derivados del estudio de la información albergada en macromoléculas biológicas, recuperada tanto
a partir de individuos contemporáneos como de individuos antiguos. Diversas líneas de evidencia confirman
el origen asiático y reciente de las poblaciones indígenas americanas, como así también su escasa diversidad
genética relativa.
... Details of the PCR reactions conducted in this study are summarized in Table 2. Attempts were made to standardize PCR components across kits and make the reactions match as closely to those described by Kemp et al. [26] which used Platinum Taq and has been met with success across a number of additional studies of ancient bones, teeth, and feces (e.g. [9,38,51,58,59]). Complete standardization was not always possible in the cases that cofactors were already premixed in the PCR buffers at various concentrations (i.e., for Herc II and Klentaq, Table 2). ...
DNA from ancient and forensic specimens is often co-extracted with unknown amounts of unknown PCR inhibitors, which can lead to underestimated DNA concentrations, allelic drop-out, and/or false-negative results. It is not surprising, in this case, that numerous methods have been developed to remove PCR inhibitors or subdue their effects. One simple and cost effective approach could be the adoption of a polymerase that overcomes or is less affected by PCR inhibitors. In this study, nine different polymerases were evaluated for their efficacy against PCR inhibitors co-extracted with DNA from 63 ancient salmon vertebrae. These samples were excavated from two archeological sites located at the Dionisio Point locality on the northern end of Galiano Island in coastal southwestern British Columbia, Canada and date to 700-1000 and 1300-1500 years before present. Previously, DNA extracts from samples studied from this locality were determined to be largely inhibited to PCR amplification. In the present study, Omni Klentaq LA (DNA Polymerase Technology, Inc.) outperformed the other 8 polymerases in two measures: (1) its success in genetic species identification of these vertebrae, and (2) its ability to amplify an ancient DNA positive control when spiked with a volume of potentially inhibited extract from the vertebrae.
... This indicates that the first humans to colonize the far north of the American continent were not either the Native Americans or the ancestors of the Neo-Eskimo expansion (Thule culture), which instead started in Alaska around 1 ka (Gilbert et al., 2008b). Moreover, the genetic characterization of samples belonging to two individuals from the China Lake site in British Columbia, dated to 4.95 ka, showed that these individuals belonged to the mtDNA haplogroup M: an Asian haplogroup no longer present in Native American populations (Malhi et al., 2007). This is the first, and so far only, reported case of genetic discontinuity between ancient and modern Americans. ...
Although it is widely recognised that America was the last continent to be populated by our species, researchers' views on various aspects of this process (e.g. the period in which it occurred, the area from which the colonizing populations came, the number of dispersal waves and the routes taken by these migrations) differ significantly. In this paper, we review both classical data and more recent findings from various research fields - including geology, paleoecology, archaeology, skeletal biology, and genetics - that may shed light on the dynamics of the colonization of the American continent, according to a critical reappraisal of the various hypotheses and models that have been advanced over time to explain this process.
... A total of 327 bp mtDNA (positions 16055-16382) was sequenced using three sets of primers (Malhi et al. 2007) that amplified overlapping fragments of the mtDNA hypervariable region I. The length range of the PCR products was 202-212 bp. ...
We report a molecular methodology to obtain and analyse ancient bacterial DNA from archaeological dental calculus. Recent and archaeological DNA samples, as old as 4000 bp, were successfully extracted and amplified with species-specific PCR primers. We propose this approach in order to: detect the presence of specific bacterial species infecting past human populations; compare the composition of ancient oral microbiomes among human populations; and analyse the genetic variability and covariation of bacteria and human host populations. Genomic analysis of bacteria from dental calculus is a promising source of evidence for palaeopathological and micro-evolutionary studies, focused either on micro-organisms or their human hosts.
... In North America, for instance, Younger Dryas age cooling is said to have played a significant role in Paleoindian migration patterns (Faught 2008, p. 689); led to regional abandonment, 'the demise of the Clovis way of life, the emergence of subregional cultural traditions, [and] the extinction of the megafauna' (Anderson and Faught 2000, p. 512); and even obliged Florida Paleoindians to start wearing furs (Dunbar and Vojnovski 2007, p. 179) (see also D.G. Anderson et al. 2002, p. 16; Dansie and Jerrems 2005; Fiedel 1999; Hall et al. 2004; Haynes 2005, 2008; Haynes 2002; Lovvorn et al. 2001; Newby et al. 2005). Geneticists seeking to explain reduced mitochondrial DNA diversity in Native American populations have likewise characterized Younger Dryas age climatic deterioration as 'drastic enough to extinguish [ancestral] northern populations,' creating a population bottleneck in the peopling of the Americas (Forster et al. 1996, p. 941; Malhi et al. 2007; Smith et al. 2005; but see Kemp et al. 2007). But was the impact of cooling on Pleistocene North Americans that pronounced and/or widespread? ...
Paleoindian groups occupied North America throughout the Younger Dryas Chronozone. It is often assumed that cooling temperatures
during this interval, and the impact these would have had on biotic communities, posed significant adaptive challenges to
those groups. That assessment of the nature, severity and abruptness of Younger Dryas changes is largely based on ice core
records from the Greenland ice sheet where changes were indeed dramatic. This paper reviews climatic and environmental records
from this time period in continental North America. We conclude that, on the Great Plains and in the Rocky Mountains, conditions
were in reality less extreme. It therefore follows that conditions during the Younger Dryas interval may not have measurably
added to the challenge routinely faced by Paleoindian groups who, during this interval, successfully (and perhaps rapidly)
dispersed across the diverse habitats of Late Glacial North America.
KeywordsYounger Dryas-Paleoindian-North America-Hunter-gatherer adaptations
... For example, in the Great Lakes region there are relatively high frequencies of haplogroups A, C, and X, and low frequencies of haplogroups B and D (Malhi et al., 2001;Shook, 2005). Pre-contact historic individuals throughout North America belong to these same five haplogroups; however, two individuals from British Colombia dating to approximately 5000 BP, were recently identified as belonging to a sixth haplogroup, M, suggesting that early indigenous peoples exhibited more diversity than was previously thought (Malhi et al., 2007). ...
... It should also be noted that the only evidence of mtDNA haplogroup M in indigenous Americans comes from studies of aDNA from the Pacific Northwest. Malhi et al. (2007Malhi et al. ( , 2010 used RFLP analysis and direct sequencing to identify two individuals from the China Lake site (4,950 14 C YBP) in British Columbia that belong to haplogroup M, an Asian haplogroup not previously found in Native Americans. This haplogroup has yet to be confirmed in other ancient or modern samples from the Americas, but continues to spur interest in identifying potential founder lineages that may be absent from modern populations. ...
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.
... Even populations that are currently extinct, such as the Etruscans from the Italian peninsula, can be studied using this genetic marker [10], solving questions posed more than 2,000 years ago. Sometimes, accepted conventions about the history of a population are shattered by the results of one of these studies, and new and surprising questions arise [11]. The popularity of mitochondrial haplogroups as a genetic marker has even made known to the nonspecialized public due to documentary works by various authors [6,7]. ...
This article describes an easy and cheap laboratory exercise for students to discover their own mitochondrial haplogroup. Students use buccal swabs to obtain mucosa cells as noninvasive tissue samples, extract DNA, and with a simple polymerase chain reaction-restriction fragment length polymorphism analysis they can obtain DNA fragments of different sizes that can be visualized in agarose gels. The analysis of these fragments can reveal the mitochondrial haplogroup of each student. The results of the exercise can be used to provide additional insights into the genetic variation of human populations.
... To fill this sampling gap, they began collaborating with the Shuswap-speaking community of Stswécemc to analyze three ancient individuals (5,000 years before present) from the archaeological sites of China Lake and Big Bar Lake in British Columbia, Canada. A single individual from Big Bar Lake was identified as haplogroup A, whereas two individuals from China Lake, buried together, exhibited the substitution at nucleotide position (np) 10,400, characteristic of haplogroup M, but these two individuals did not exhibit the control region or coding region substitutions for haplogroups C or D (Cybulski et al., 2007; Malhi et al., 2007). We subsequently analyzed the mitochondrial genomes of 31 unrelated (at the grandparent-level) Shuswapspeakers from British Columbia to potentially identify haplogroup M in living individuals that are similar to the mtDNAs identified in the ancient China Lake individuals . ...
Mitochondrial DNA analysis of 31 unrelated Shuswap speakers from a previously poorly sampled region of North America revealed two individuals with haplogroups rarely found in the Americas, C4c and C1d. Comparison of the complete genomes of the two individuals with others found in the literature confirms that C4c is a founding haplotype and gives insight into the evolution of the C1d haplotype. This study demonstrates the importance of collecting and analyzing data from Native North Americans when addressing hypotheses about the peopling of the Americas.
... Because mtDNA is essentially a single locus, it could have been subject to considerable genetic drift, even more than morphological traits [7], during the Pleistocene-Early Holocene. Particularly, some North American aDNA studies suggest that the founding migrants exhibited greater molecular diversity than what has been previously recognized, showing that during the Early-Middle Holocene there were more than five founding mtDNA lineages [46,47]. If the hypothetical Paleoamerican component had a particular mtDNA variation, it could have been modified during the initial South American peopling by founder effect. ...
Currently, one of the major debates about the American peopling focuses on the number of populations that originated the biological diversity found in the continent during the Holocene. The studies of craniometric variation in American human remains dating from that period have shown morphological differences between the earliest settlers of the continent and some of the later Amerindian populations. This led some investigators to suggest that these groups--known as Paleomericans and Amerindians respectively--may have arisen from two biologically different populations. On the other hand, most DNA studies performed over extant and ancient populations suggest a single migration of a population from Northeast Asia. Comparing craniometric and mtDNA data of diachronic samples from East Central Argentina dated from 8,000 to 400 years BP, we show here that even when the oldest individuals display traits attributable to Paleoamerican crania, they present the same mtDNA haplogroups as later populations with Amerindian morphology. A possible explanation for these results could be that the craniofacial differentiation was a local phenomenon resulting from random (i.e. genetic drift) and non-random factors (e.g. selection and plasticity). Local processes of morphological differentiation in America are a probable scenario if we take into consideration the rapid peopling and the great ecological diversity of this continent; nevertheless we will discuss alternative explanations as well.
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.
Entre 1873 et 1884, Florentino Ameghino consacre tous ses efforts à documenter et prouver la coexistence des hommes etde la mégafaune pampéenne dans la valle de Luján. Il identifie ainsi une dizaine des sites en contexte de plaine alluvial desvallées incisés dans le lœss pampéen. Ce sites, caractérises par l’abondance des os modifies de mégafaune et quelquelithiques, ne seront jamais réétudies. L’objectif principal de cette étude est leur réévaluation et validation geoarchéologique.L’analyse séquentielle, et l’étude de l'architecture des séquences fluviolacustres et des facies loessoides associées, et lesdatations par AMS et OSL entre 13 000 AP et 50 000 AP, permettent d’attribuer un âge pléistocène supérieur aux niveauxdécrits au XIX siècle comme porteurs des évidences culturelles. Ces dépôts sont scellés par une couche noire, riche enmatière organique (Terres Noires), qui se corrèlent avec des niveaux similaires des sites Clovis et Monte Verde, signalant unchangement climatique abrupt comme déclencheur du processus d'extinction. Une attention particulière a été donne àl’étude des évidences taphonomiques et à l’expérimentation sur les traces de découpe et percussion. Ainsi sont présentées lesrésultats de ces expériences et des nombreux exemples d’os de mégafaune pampéenne striés et incisés. Ces premièresdécouvertes emmènent à considérer l’'utilisation de technologie osseuse expéditive et à reconsidérer la l’hypothèse d’unpeuplement pampéen antérieur au dernier maximum glaciaire (OIS 2 - OIS 3).
Objectives
The aim of this work is to explore the maternal genetic diversity of hunter‐gatherers of the southern Tierra del Fuego, specifically the north coast of Beagle Channel, the Península Mitre, and Isla de los Estados through ancient mitochondrial DNA analysis.
Materials and Methods
The hypervariable regions 1 and 2 of the mitochondrial genome of five individuals from the north coast of Beagle Channel, six individuals from Península Mitre, and one individual from Isla de los Estados were analyzed. Through diversity statistics, Analysis of Molecular Variance (AMOVA), and Median Joining networks analyses, maternal relationships in the region were evaluated and phylogenetic similarities between ancient and contemporary populations of Tierra del Fuego were determined.
Results
The mitochondrial DNA lineages from the ancient individuals analyzed reveals the presence of subclades C1b and D1g. Pattern of decreasing genetic diversity toward the South is observed. The AMOVAs performed found no statistically significant differences between individuals of the north coast of Beagle Channel and Península Mitre‐Isla de los Estados, and modern Yámana populations. Median joining network of haplotypes of clades C1 and D1g, show the same results.
Discussion
Ethnohistoric and ethnographic records of Península Mitre show that this region was occupied during the 19th century by Haush or Manekenk populations, although their biological, cultural, and subsistence characterization is unclear. We explore their maternal lineages and encounter low levels of genetic diversity and the absence of population differentiation with modern Yámana groups. We suggest that Península Mitre‐Isla de los Estado was part of the same hunting and gathering populations as those of the Beagle Channel.
The rise of more sophisticated forms of analysis has allowed bioarchaeologists to address and answer a wide range of questions regarding past diets, health, mobility, population history, kinship, and taphonomy. However, all of these techniques, e.g. DNA analysis, radiocarbon dating, isotope analysis, and histological analysis require destructive sampling of human remains, which raises ethical issues pertaining to preservation and survival as well as cultural concerns of both past and contemporary societies regarding the post mortem treatment of the dead. This chapter will explore the validity of conducting destructive sampling for the purpose of academic research. It will explore how curators, bioarchaeologists, and archaeologists currently deal with ethical issues surrounding destructive sampling and associated analyses, including the curation of skeletal remains for research purposes, access enquiries, and matters of consent. It is recommended that bioarchaeologists, archaeologists, and curators ensure ethics are at the core of all work carried out when working with human remains. It is thus proposed that these methods should be reserved for focused research questions as opposed to exploratory studies. It is also recommended that researchers and curators receive adequate training in procedures related to destructive sampling as a means of controlling the number of times samples can be taken from bones and teeth which will, in turn, preserve skeletal remains for future generations to study using even more advanced techniques. Following an introduction to the subject matter, this chapter will explore ethics and human remains, technical analyses applied to archaeological human remains, religious and cultural beliefs, and finally makes recommendations for best practice when conducting destructive sampling.
Complex processes in the settling of the Americas
The expansion into the Americas by the ancestors of present day Native Americans has been difficult to tease apart from analyses of present day populations. To understand how humans diverged and spread across North and South America, Moreno-Mayar et al. sequenced 15 ancient human genomes from Alaska to Patagonia. Analysis of the oldest genomes suggests that there was an early split within Beringian populations, giving rise to the Northern and Southern lineages. Because population history cannot be explained by simple models or patterns of dispersal, it seems that people moved out of Beringia and across the continents in a complex manner.
Science , this issue p. eaav2621
A compilation of 63 stratigraphic situations with evidence for human presence and two or more radiocarbon ages older than 10,500 B.P. has been processed to increase the accuracy and precision of the estimated ages and to compare their distributions at hemispheric scale. The compilation was developed to perceive patterns of population expansion and to plot early sites in their temporal and geographic order. The use of radiocarbon dates as data, criteria for inclusion in the compilation, the statistical processing methods used, and effects of controlling for precision and accuracy are described. The results indicate three earliest mean ages with great distance from each other in North and South America by 12,000 B.P., slightly later mean ages in Alaska, and the abrupt occurrence of Fluted and Fishtail Point sites at the beginning of the Younger Dryas climatic reversal (YD). One interpretation of these data is that there were different colonizing groups settling into different parts of the hemisphere in near-contemporaneity. Another is that Fluted and Fishtail Point sites may represent population relocations due to YD related ecological disturbances at the shorelines of those times. Corollary to the conclusions of early population diversity is the possibility of landfalls of people from areas other than Beringia in the late Pleistocene.
Exactly when humans first entered the American Continent, and from where, is still a matter of heated discussion by scientists today. Several migration routes have been proposed to reach the Americas, involving the use of the Bering Land Bridge from Siberia to Alaska or the use of watercraft along the Pacific or Atlantic Coasts; part of the current research involves trying to put times into the potential migration routes into the Americas. Also the role of the arrival of humans in the extinction of megafauna (mammoths, saber-toothed cats, camels, horses, etc.) is discussed against the effect of environmental changes at the end of Pleistocene (~. 10. 000 years ago). Strong archeological evidence suggests that humans arrived in the Americas long before 12. 000 RCYBP and that the Clovis people were not the first group to migrate into the New World. New information derived from linguistics, stone tools, craniometrics, and genetic evidence strongly suggests that the first Americans were very diverse from an ethnic point of view. However, the study of many more early human skeletons is required to construct a real picture.
The earliest practitioners of human skeletal studies in Canada (1848–1958) brought knowledge from England and Scotland and some influence on later works. It was in the 1960s, however, that a tradition of Canadian bioarchaeology took root, nurtured by interactions between Canadian and American archaeologists and physical anthropologists. A commonality of research interests in aboriginal cultural areas bordered by Canada and the USA—the Arctic, the Northwest Coast, and the Northeast (Great Lakes)—stimulated similar approaches to the studies of past peoples. Methodological traditions developed in the 1960s by James E. Anderson are evident in much of contemporary Canadian bioarchaeology. Population relationships studied through the analysis of non-metric skeletal and dental traits are being supplemented by ancient DNA studies. Today’s palaeopathology includes modern diagnostic approaches and classical descriptive methods. Modern histological and morphometric approaches have been added to the traditional gross anatomical methods of physical anthropology. International collaborations have enriched studies of Canadian collections as well as the research questions and methodological approaches of Canadian scholars elsewhere. Ethical approaches to the study of human remains form an integral part of Canada’s bioarchaeological landscape through collaboration and cooperation among archaeologists, physical anthropologists and contemporary indigenous and non-indigenous communities.
This chapter advocates for the development of an ethos (worldview) for bioarchaeologists that embraces an engagement at every level with the larger context within which the human remains and artifacts are connected. This includes descendant populations, local communities, county, state and national legislation, government and local statutes, and repositories and museums that house skeletal collections and related materials. Understanding the historical development of physical anthropology forms a backdrop for the changes that have occurred as the emphasis on descriptive osteological studies shifted to fully realized population-level analyses of processes affecting human adaptation. Native American Graves Protection and Repatriation Act (NAGPRA) and NAGPRA-like legislation is not perfect, and it is important that bioarchaeologists develop an ethos that guides responsible and ethical research instead of relying on laws.
Techniques for the analysis of bone and teeth that get below the anatomical surface to utilize preserved collagen and apatite have become central to understanding aspects of ancestry, kinship, health, diet, disease, growth, and development for ancient and historic groups. Ethical issues abound in this area because it entails genetic and biomedical research using tissues from human remains, and this comes with all the attendant complexities of informed consent and weighing the costs and benefits. A very brief synopsis of what some of these special applications can provide in terms of additional information about identity, ancestry, and migration is provided.
Ancient remains are considered very valuable artefacts, as they allow for the study of ancient cultures, phytogeny, evolution and the reconstruction of demographic history. To obtain all the information contained within remains, the investigation of such samples requires the expertise and various techniques from multiple fields of study. The present review focuses on the molecular biology and radiographic approaches used to identify ancient samples. Studies of ancient remains face various limitations; for example, the quality and quantity of the ancient samples can affect the difficulty of the investigations. Due to these limitations, new sophisticated techniques are being introduced to replace the earlier conventional techniques. A search was conducted using PubMed, Scopus, Science Direct and Science Finder to provide a new and timely review on the molecular mitochondrial DNA and radiographic analysis for human archaeology identification. The present review has determined that molecular biological approaches are very accurate and useful for the use in the ancestral determination of incomplete specimens, whereas observations of the dental pulp chamber are suitable for age at death estimations in both adults and children. However, these techniques are expensive and require expert personnel. Therefore, conventional approaches remain the favourite methods of most institutions, especially in Asia.
A compilation of 63 stratigraphic situations with evidence for human presence and two or more radiocarbon ages older than 10,500 B.P. has been processed to increase the accuracy and precision of the estimated ages and to compare their distributions at hemispheric scale. The compilation was developed to perceive patterns of population expansion and to plot early sites in their temporal and geographic order. The use of radiocarbon dates as data, criteria for inclusion in the compilation, the statistical processing methods used, and effects of controlling for precision and accuracy are described. The results indicate three earliest mean ages with great distance from each other in North and South America by 12,000 B. P., slightly later mean ages in Alaska, and the abrupt occurrence of Fluted and Fishtail Point sites at the beginning of the Younger Dryas climatic reversal (YD). One interpretation of these data is that there were different colonizing groups settling into different parts of the hemisphere in near-contemporaneity. Another is that Fluted and Fishtail Point sites may represent population relocations due to YD related ecological disturbances at the shorelines of those times. Corollary to the conclusions of early population diversity is the possibility of landfalls of people from areas other than Beringia in the late Pleistocene.
One of the most acrimonious debates within archaeological discussion in the United States and Canada has been over the theorized dates of the earliest human presence in the Western Hemisphere (the Americas). Archaeologists have spent untold fortunes seeking answers to questions of who the first people to enter the Western Hemisphere were, where they came from, and when. In this research I want to be very clear that contrary to traditional archaeological studies on early people in the Western Hemisphere, my research focus is not about where the First People came from or when they arrived. First peoples are Indigenous to these lands, this is where they are from. Indigenous people of the Western Hemisphere have their own histories, many of which speak to a genesis in these lands. In this research I argue that there is a vast body of evidence for a much earlier human presence than traditionally accepted in North American archaeology. I present evidence of numerous Pre-Clovis sites dispersed throughout the Western Hemisphere that meet or exceeded the scientific criteria required to be accepted as legitimate. I argue that the long standing academic denial over the legitimacy of Pre-Clovis sites and archaeologists reluctance to consider earlier initial migrations, reflects a colonial practice in North American archaeology which maintains an erasure of an ancient Indigenous presence in the Western Hemisphere. This is a practice which is evident within the documented history of American archaeology over the last century. For many if not all Indigenous people there is no separation between the past and the present, all time and all history is crucial to their culture and well-being. Therefore rupturing the connecting between the present and the past, contemporary and ancestral people, and the people and the land as American archaeology has done, has been a very violent and destructive historic event. For Indigenous peoples, identities weave threads of primordial memories through space and time and acknowledge connections to ancestors, and sacred homelands. I argue that a denial of ancient ancestral connections to the land remains a part of what is at the heart of a lingering intergenerational trauma and individual and community illness. I further argue that American archaeology has an ethical and moral duty to un-erase histories and identities that its academic predecessors erased through violent discursive processes of knowledge production. The existence of Pre 13,200 cal BP sites, and ancestral connections between ancient First Peoples and contemporary Indigenous communities is empowering to these people. The existence of hundreds of ancestral sites in the Pleistocene creates a dialogue from which Indigenous people can challenge erasures of histories, it foregrounds their Indigenous identities and their links to the land and empowers them in seeking justice. To allow that Indigenous people have been present in the Western Hemisphere for a much greater time is to support Indigenous ownership of the past and present, and lands and material heritage. To accept that Indigenous peoples have been in the Western Hemisphere for over 60,000 years and possibly prior to 100,000 ybp is to put them on equal footing with areas of the so called Old World. I concur with Vine Deloria Jr. that Indians will never be accorded full humanity until they are connected with world history.
This research is carried out as ceremony and is framed in Indigenous method and theory and therefore orientated to addressing issues that remain critical to Indigenous populations of the Western Hemisphere (the Americas), healing, emancipation, self-determination and decolonization. The trajectory of Indigenist research is clearly focused on directions of decolonizing, re-writing, re-claiming, and self-determination along paths of “post-colonial” healing in a “neo-colonial” world. To acknowledge connections between contemporary Indigenous people and ancient ancestral landscape and to transfer Indigenous histories to the next generation, is to acknowledge and support cultural continuity and healing. Indigenous Pyro-epistemology cleanses the academic landscape of dehumanizing discussions of Indigenous peoples through a critical scholarship. Thus making academic space for regenerating new thought and discussions which follow paths towards healing within the circle of the eighth fire. I have been fortunate to experience this journey from a bi-cultural lens, and to tell this story from a personal center which is responsible to Indigenous nations yet not bound to any one master. Through a critical Indigenous scholarship I seek to clear away a dense colonial fog which shrouds the Indigenous past in a dark mist of Eurocentric power and control. I come to this journey with a good heart, and with a gift of Two Eyed Seeing and a personal experience of the human cost of colonization. I have listened to many scholars, academics, and ancestors, to the voices which come to mind and the thoughts that question the authority of the status quo. Throughout my research ceremony I quietly listened when the ancestors led my thoughts through forests of solitude and along rippling streams of metaphors which gifted me with renewed thought, new words, and a renewed view of the past, present, and future, which I share in this research and story.
The colonization of the Americas from Siberia after 16kya was one of the most remarkable achievements of early modern humanity. This chapter outlines the archaeological evidence for this dramatic founding human migration into two new continents.Keywords:archaeology;globalization;human evolution;genetics;economics;holocene;indigenous peoples;food
Estrat Crític 5.Vol.1 (2011): 339-351
A multivariate morphometric analysis of two mid and late Holocene human skulls samples, from a prehistoric cemetery in central Chile, was performed. Comparisons with modern populations show that the mid Holocene sample shows morphological affinities with modern groups of Australo-Melanesia, this is, a new case of populations with "paleoamerican" morphology, while the sample from Late Holocene morphologically looks alike to Polynesian and Asian groups. The results of this study are discussed in the context of the historical reconstruction of the evolutionary processes involved in the settlement and dispersal of human populations in the Americas.
Nanocrystalline and amorphous Mg–Ni–Cu–Mn alloys with nominal compositions of Mg–5 wt.% Ni–5 wt.% Cu–x wt.% Mn (x = 0, 1, 3) were synthesized by the melt spinning technique. The structure of the alloys was characterized by scanning electron microscopy and X-ray diffraction analysis. The phase transition during the solidification process was studied by differential scanning calorimetry under an Argon atmosphere. The wheel speed, which is closely associated with the cooling rate, was varied in the production of the melt-spun ribbons. The resultant melt-spun ribbons had various microstructures ranging from dendrite to equiaxed polygonal grains, and finally to an amorphous structure, depending on the wheel speed. The wheel side of the ribbons exhibited a finer microstructure than those on the free or air sides exposed to the atmosphere. Experimental results showed that the mechanical properties of the Mg–Ni–Cu–Mn alloys were enhanced, which can be attributed to significant changes in the microstructure. It was found that the microhardness values of the melt-spun ribbons were strongly dependent on the solidification rate and Mn content. The highest microhardness values were observed on the wheel side of the ribbons.
Previous aDNA research in the Southwest provides a framework to understand the Mimbres population which maintains a unique identity in the archeology of the desert Southwest of North America. Both the mitochondrial DNA (mtDNA) haplogroups and haplotypes of a sample of 46 Mimbres individuals were identified from skeletal remains and compared to those of other ancient and modern populations in the American Southwest and Mexico. The haplogroup frequency distribution of the Mimbres resembles that of other Southwestern populations, suggesting a close relationship between the Mimbres and the neighboring populations and population continuity for a long period of time. However, their relatively low frequency of haplogroup A (11% n = 5) is consistent with a clinal distribution of haplogroup A from Mesoamerica to the Southwest. Moreover, unlike other Southwestern populations, the Mimbres share haplotypes with populations to the south, such as the Cora, Huichol, and Nahua, suggesting gene-flow from Mesoamerica. Here we discuss this data in light of the origin of the Mimbres population and their relationship to other Southwestern and Mexican populations.
The success of ancient DNA (aDNA) studies rests on the preservation of DNA through time, and can be limited by the availability of skeletal samples from particular times and locations. To help overcome this limitation, we sought to extract, amplify, and type human mitochondrial DNA (mtDNA) preserved within 1000- to 2000+-year-old artifacts from the American Southwest. In this study, we successfully typed mtDNA from 21 quids and aprons from Basketmaker II and Mimbres contexts. Recovery and analysis of human DNA from such artifacts will be helpful in confirming and extending genetic characterization of ancient populations for which human remains are scarce or unavailable. To illustrate the potential of these techniques, we tested them as a preliminary and independent line of evidence, relevant to the hypothesis that Western Basketmaker populations in the U S. Southwest were descendants of migrant farmers from central Mexico.
The panel began with an acknowledgment that we were assembled in the traditional territory of the Blood Nation. The panelists were then introduced and, in alphabetical order, gave their initial opening comments.
Molecular genetic studies of Siberian and Native American populations indicate that ancestral Native Americans originated in south-central Siberia and entered the New World between 20 000 and 15 000 years before present (ybp), after thousands of years of isolation in Beringia. These early immigrants probably followed a coastal route into the New World, where they expanded into all continental regions. A second expansion, possibly coming from the same area of Siberia, may have entered the Americas, and genetically influenced North American populations. Beringian populations moved into northern North America after the Last Glacial Maximum (LGM) and gave rise to Aleuts, Eskimos and Na-Dene Indians.
Keywords:
mtDNA;
Y-chromosome;
Asia;
Siberia;
migrations
The last two decades have seen numerous debates in the field of the initial settlement of America and noteworthy was the disagreement between physical and molecular anthropologists. Recently, it has been pointed out that this discordance could partly originate from the description methods and classification labels used in craniometry, which did not account fairly for the within-sample and within-group variance. From there, a federative model for the initial peopling of America has been designed which could now explain the biological variability found at both the craniofacial and genetic level. This is a major step in the study of the initial settlement of America, which deserved to be highlighted. The present paper recalls the two conflicting models that prevailed for the last 20 years of anthropological studies in America before browsing the newly accepted hypothesis about the origin of the first Amerindians as seen by its authors. Lastly, the article evokes some areas of investigations, which could furnish significant fallouts about the dynamics of the peopling of Americas in the future.
Brazilian Amerindians have experienced a drastic population decrease in the past 500 years. Indeed, many native groups from eastern Brazil have vanished. However, their mitochondrial mtDNA haplotypes, still persist in Brazilians, at least 50 million of whom carry Amerindian mitochondrial lineages. Our objective was to test whether, by analyzing extant rural populations from regions anciently occupied by specific Amerindian groups, we could identify potentially authentic mitochondrial lineages, a strategy we have named 'homopatric targeting'.
We studied 173 individuals from Queixadinha, a small village located in a territory previously occupied by the now extinct Botocudo Amerindian nation. Pedigree analysis revealed 74 unrelated matrilineages, which were screened for Amerindian mtDNA lineages by restriction fragment length polymorphism. A cosmopolitan control group was composed of 100 individuals from surrounding cities. All Amerindian lineages identified had their hypervariable segment HVSI sequenced, yielding 13 Amerindian haplotypes in Queixadinha, nine of which were not present in available databanks or in the literature. Among these haplotypes, there was a significant excess of haplogroup C (70%) and absence of haplogroup A lineages, which were the most common in the control group. The novelty of the haplotypes and the excess of the C haplogroup suggested that we might indeed have identified Botocudo lineages. To validate our strategy, we studied teeth extracted from 14 ancient skulls of Botocudo Amerindians from the collection of the National Museum of Rio de Janeiro. We recovered mtDNA sequences from all the teeth, identifying only six different haplotypes (a low haplotypic diversity of 0.8352 ± 0.0617), one of which was present among the lineages observed in the extant individuals studied.
These findings validate the technique of homopatric targeting as a useful new strategy to study the peopling and colonization of the New World, especially when direct analysis of genetic material is not possible.
Our paper "Mitochondrial DNA of Protohistoric Remains of an Arikara Population from South Dakota: Implications for the Macro-Siouan Language Hypothesis" [Lawrence et al. 2010 (this issue)] has been reviewed by two scholars, and although we agree with the comments of the second reviewer, we object to the first reviewer's statement that
the Authors do not use currently accepted methods in ancient DNA studies. the Authors have not followed the now classical stringent standards for the authentications of ancient DNA. Unfortunately, Authors did not do [the following]: (i) test to quantify the preservations of macromolecules (amino acid or collagen), (ii) quantifications of macromolecules, (iii) detections of long amplificates, (iv) amplifications of associated remains (if any), (v) cloning, (vi) independent replications. Further, in this study there is another fundamental question: the impossibility to track down modern DNA human contaminations (see Sampietro et al. 2006) so the results, even though interesting, are not supported by a strong scientific methodology.
We believe that the review was unfair and reflects viewpoints that are potentially stifling to future discoveries and progression of the ancient DNA (aDNA) field as a whole.
Reviewer 1 refers to six "classical stringent standards" to which we did not adhere. Our rebuttal is not to argue that, in fact, we did adhere to any fixed set of "standards" but rather to argue that (1) following these standards cannot alone authenticate aDNA results. Conversely, (2) failing to follow all these standards does not necessarily lead to aberrant and/or unreliable results, and (3) site-specific and/or sample-specific circumstances are suitable for dictating the analytical standards to be followed.
We recognize that the "classical stringent standards" to which the reviewer refers originated from an opinion piece published in Science: Cooper and Poinar's (2000) "Ancient DNA: Do It Right or Not at All." [This was not the first or only list of recommendations; however, according to Google Scholar, this opinion piece has been cited 305 times, making it a classic for the aDNA field (website accessed December 22, 2009). A few years later, Pääbo et al. (2004) expanded on these recommendations and explored them in more detail. Pääbo's review paper was co-authored by Hendrik Poinar, but did not include Alan Cooper. In this letter, we will contrast, where appropriate, the recommendations of Cooper and Poinar (2000) with those put forth by Pääbo et al. (2004).]
The intention of Cooper and Poinar's (2000) paper was to provide some guidelines for the field of aDNA, which had taken a major detour in the early 1990s into what now appears to be a realm of impossibility. During this period, for example, attempts were made to extract and analyze DNA from dinosaurs (Woodward et al. 1994), Miocene chloroplasts (Golenberg et al. 1990; Soltis et al. 1992), and 25-135-million-year-old amber-embedded insects and their gut flora (Cano et al. 1992a, 1992b, 1993, 1994), reports of which were published in leading scientific journals. (Hendrik Poinar was part of the research team that reported on the DNA retrieved from the amber-embedded insects specimens.) Upon reanalysis, the dinosaur DNA was found to closely resemble that of mammals, especially humans (Allard et al. 1995; Hedges and Schweitzer 1995; Henikoff 1995; Zischler et al. 1995) and the chloroplast and insect DNA sequences, collected and analyzed in many cases under substandard conditions, failed to meet evolutionary expectations (Hebsgaard et al. 2005) and/or were not reproducible (Austin et al. 1997). Although it was clearly an opportune time to make some recommendations to ground those practicing in the aDNA field, we object to anyone dictating any methodology that needs to be followed in all circumstances. We dispute that the foremost experts in the study of aDNA, a group in which several of us, in addition to Cooper and Poinar and presumably Reviewer 1, also hold membership, regard these "classical standards" as unequivocally valid requirements or broadly accept them as standards. Although stringent standards are always desirable, unjustifiably stringent standards severely constrain research to specific laboratories and researchers (who may design their standards to their own capability and convenience) and limit the accumulation of knowledge.
As nine such recommendations were made by...
To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171–10659 of the coding region, and we have identified a number of specific coding-region mutations by direct sequencing or restriction-fragment–length–polymorphism tests. This allows us to define new haplogroups (clades of the mtDNA phylogeny) and to dissect the Han mtDNA pool on a phylogenetic basis, which is a prerequisite for any fine-grained phylogeographic analysis, the interpretation of ancient mtDNA, or future complete mtDNA sequencing efforts. Some of the haplogroups under study differ considerably in frequencies across different provinces. The southernmost provinces show more pronounced contrasts in their regional Han mtDNA pools than the central and northern provinces. These and other features of the geographical distribution of the mtDNA haplogroups observed in the Han Chinese make an initial Paleolithic colonization from south to north plausible but would suggest subsequent migration events in China that mainly proceeded from north to south and east to west. Lumping together all regional Han mtDNA pools into one fictive general mtDNA pool or choosing one or two regional Han populations to represent all Han Chinese is inappropriate for prehistoric considerations as well as for forensic purposes or medical disease studies.
The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.
Recent debate has raised serious questions about the viability of the social and ideological reconstruction of prehistoric culture on the basis of mortuary analysis. In recent years bioarchaeology has gained considerable prominence, underscoring the fact that death, burials, and associated mortuary practices are multifaceted phenomena shaped by biological, social, ideological, and taphonomic factors. Few studies attempting social reconstruction through mortuary analysis, including those of a bioarchaeological character, have adequately addressed this multidimensionality. This study shows that social, ideological, and bioarchaeological reconstruction can be productively pursued through tight integration of a multitude of approaches and perspectives set within a long‐term regional study. Focusing on two large 1,000‐year‐old Middle Sicán shaft tombs on the north coast of Peru, it integrates analyses of mitochondrial DNA, inherited dental traits, developmental health, diet, placement of interred individuals and associated grave goods, and data from ground‐penetrating radar surveys. Overall it shows that these tombs reflected the broader social organization and were part of a planned elite cemetery and that the overlying monumental adobe mound served as the physical focus of ancestor worship.
High levels of mitochondrial DNA (mtDNA) diversity were determined for Mongolian populations, represented by the Mongol-speaking Khalkha and Dariganga. Although 103 samples were collected across Mongolia, low levels of genetic substructuring were detected, reflecting the nomadic lifestyle and relatively recent ethnic differentiation of Mongolian populations. mtDNA control region I sequence and seven additional mtDNA polymorphisms were assayed to allow extensive comparison with previous human population studies. Based on a comparative analysis, we propose that indigenous populations in east Central Asia represent the closest genetic link between Old and New World populations. Utilizing restriction/deletion polymorphisms, Mongolian populations were found to carry all four New World founding haplogroups as defined by WALLACE and coworkers. The ubiquitous presence of the four New World haplogroups in the Americas but narrow distribution across Asia weakens support for GREENBERG and coworkers' theory of New World colonization via three independent migrations. The statistical and geographic scarcity of New World haplogroups in Asia makes it improbable that the same four haplotypes would be drawn from one geographic region three independent times. Instead, it is likely that founder effects manifest throughout Asia and the Americas are responsible for differences in mtDNA haplotype frequencies observed in these regions.
Ancient DNA from bones and teeth of 60 individuals from four extinct human populations from Tierra del Fuego-Patagonia (Selknam, Yamana, Kaweskar and Aonikenk) has been extracted and the mitochondrial DNA (mtDNA) amplified by using the polymerase chain reaction. High-resolution analysis of endonuclease restriction site variation in the mtDNA and sequencing of its hypervariable non-coding control region, revealed complete absence of two of the four primary mitochondrial haplotype groups present in contemporary Amerinds, namely A and B. In contrast, haplogroups C and D were found in all but one sample with frequencies of approximately 38% and 60%. These results, together with the decreasing incidence of group A in more southerly latitudes in the American continent and the absence of cluster B above 55 degrees North in America and Asia, argue that the first settlers entering America 21000-14000 years ago already lacked both mtDNA lineages.
Despite considerable investigation, two main questions on the origin of Native Americans remain the topic of intense debate-namely, the number and time of the migration(s) into the Americas. Using the 720 available Amerindian mtDNA control-region sequences, we reanalyzed the nucleotide diversity found within each of the four major mtDNA haplogroups (A-D) thought to have been present in the colonization of the New World. We first verified whether the within-haplogroup sequence diversity could be used as a measure of the haplogroup's age. The pattern of shared polymorphism, the mismatch distribution, the phylogenetic trees, the value of Tajima's D, and the computer simulations all suggested that the four haplogroups underwent a bottleneck followed by a large population expansion. The four haplogroup diversities were very similar to each other, offering a strong support for their single origin. They suggested that the beginning of the Native Americans' ancestral-population differentiation occurred approximately 30,000-40,000 years before the present (ybp), with a 95%-confidence-interval lower bound of approximately 25,000 ybp. These values are in good agreement with the New World-settlement model that we have presented elsewhere, extending the results initially found for haplogroup A to the three other major groups of mtDNA sequences found in the Americas. These results put the peopling of the Americas clearly in an early, pre-Clovis time frame.
Ancient DNA from the bone remains of 25 out of 28 pre-Columbian individuals from the Late Classic-Postclassic Maya site of Xcaret, Quintana Roo, was recovered, and mitochondrial DNA (mtDNA) was amplified by using the polymerase chain reaction. The presence of the four founding Amerindian mtDNA lineages was investigated by restriction analysis and by direct sequencing in selected individuals. The mtDNA lineages A, B, and C were found in this population. Eighty-four percent of the individuals were lineage A, whereas lineages B and C were present at low frequencies, 4% and 8%, respectively. Lineage D was absent from our sample. One individual did not possess any of the four lineages. Six skeletons out of 7 dated from the Late Classic period were haplotype A, whereas 11 skeletons out of 16 dated from the Postclassic period were also haplotype A.
The distribution of mtDNA lineages in the Xcaret population contrasts sharply with that found in ancient Maya from Copán, which lack lineages A and B. On the other hand, our results resemble more closely the frequencies of mtDNA lineages found in contemporary Maya from the Yucatán Peninsula and in other Native American contemporary populations of Mesoamerican origin. Am J Phys Anthropol 116:230–235, 2001.
To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171-10659 of the coding region, and we have identified a number of specific coding-region mutations by direct sequencing or restriction-fragment-length-polymorphism tests. This allows us to define new haplogroups (clades of the mtDNA phylogeny) and to dissect the Han mtDNA pool on a phylogenetic basis, which is a prerequisite for any fine-grained phylogeographic analysis, the interpretation of ancient mtDNA, or future complete mtDNA sequencing efforts. Some of the haplogroups under study differ considerably in frequencies across different provinces. The southernmost provinces show more pronounced contrasts in their regional Han mtDNA pools than the central and northern provinces. These and other features of the geographical distribution of the mtDNA haplogroups observed in the Han Chinese make an initial Paleolithic colonization from south to north plausible but would suggest subsequent migration events in China that mainly proceeded from north to south and east to west. Lumping together all regional Han mtDNA pools into one fictive general mtDNA pool or choosing one or two regional Han populations to represent all Han Chinese is inappropriate for prehistoric considerations as well as for forensic purposes or medical disease studies.
The Aleuts are aboriginal inhabitants of the Aleutian archipelago, including Bering and Copper (Medny) Islands of the Commanders, and seem to be the survivors of the inhabitants of the southern belt of the Bering Land Bridge that connected Chukotka/Kamchatka and Alaska during the end of the Ice Age. Thirty mtDNA samples collected in the Commanders, as well as seven mtDNA samples from Sireniki Eskimos in Chukotka who belong to the Beringian-specific subhaplogroup D2, were studied through complete sequencing. This analysis has provided evidence that all 37 of these mtDNAs are closely related, since they share the founding haplotype for subhaplogroup D2. We also demonstrated that, unlike the Eskimos and Na-Dene, the Aleuts of the Commanders were founded by a single lineage of haplogroup D2, which had acquired the novel transversion mutation 8910A. The phylogeny of haplogroup D complete sequences showed that (1) the D2 root sequence type originated among the latest inhabitants of Beringia and (2) the Aleut 8910A sublineage of D2 is a part of larger radiation of rooted D2, which gave rise to D2a (Na-Dene), D2b (Aleut), and D2c (Eskimo) sublineages. The geographic specificity and remarkable intrinsic diversity of D2 lineages support the refugial hypothesis, which assumes that the founding population of Eskimo-Aleut originated in Beringan/southwestern Alaskan refugia during the early postglacial period, rather than having reached the shores of Alaska as the result of recent wave of migration from interior Siberia.
We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing
both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation
of published mtDNA data on East Asians based on either control region sequencing or restriction fragment length polymorphism
(RFLP) typing. Our results confirm that the East Asian mtDNA pool is locally region-specific and completely covered by the
two superhaplogroups M and N. The phylogenetic partitioning based on complete mtDNA sequences corroborates existing RFLP-based
classification of Asian mtDNA types and supports the distinction between northern and southern populations. We describe new
haplogroups M7, M8, M9, N9, and R9 and demonstrate by way of example that hierarchically subdividing the major branches of
the mtDNA tree aids in recognizing the settlement processes of any particular region in appropriate time scale. This is illustrated
by the characteristically southern distribution of haplogroup M7 in East Asia, whereas its daughter-groups, M7a and M7b2,
specific for Japanese and Korean populations, testify to a presumably (pre-)Jomon contribution to the modern mtDNA pool of
Japan.
We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations.
Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups
constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six
main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual
populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments
of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.
A total of 63 binary polymorphisms and 10 short tandem repeats (STRs) were genotyped on a sample of 2,344 Y chromosomes from 18 Native American, 28 Asian, and 5 European populations to investigate the origin(s) of Native American paternal lineages. All three of Greenberg's major linguistic divisions (including 342 Amerind speakers, 186 Na-Dene speakers, and 60 Aleut-Eskimo speakers) were represented in our sample of 588 Native Americans. Single-nucleotide polymorphism (SNP) analysis indicated that three major haplogroups, denoted as C, Q, and R, accounted for nearly 96% of Native American Y chromosomes. Haplogroups C and Q were deemed to represent early Native American founding Y chromosome lineages; however, most haplogroup R lineages present in Native Americans most likely came from recent admixture with Europeans. Although different phylogeographic and STR diversity patterns for the two major founding haplogroups previously led to the inference that they were carried from Asia to the Americas separately, the hypothesis of a single migration of a polymorphic founding population better fits our expanded database. Phylogenetic analyses of STR variation within haplogroups C and Q traced both lineages to a probable ancestral homeland in the vicinity of the Altai Mountains in Southwest Siberia. Divergence dates between the Altai plus North Asians versus the Native American population system ranged from 10,100 to 17,200 years for all lineages, precluding a very early entry into the Americas.
The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.
Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.
Skeletal remains of 47 individuals from the Great Salt Lake Wetlands, affiliated principally with Bear River (A.D. 400—1000) and Levee Phase (A.D. 1000—1350) Fremont cultural elements, were assessed for four mitochondrial DNA (mtDNA) markers that, in particular association, define four haplogroups (A, B, C, and D) widely shared among contemporary Amerindians groups. The most striking result is the absence of haplogroup A in this Fremont series, despite its predominance in contemporary Amerindian groups. Additionally, haplogroup B, defined by the presence of a 9bp deletion in region V, is present at the moderately high frequency of 60%. Haplogroups C and D are present at low frequencies. An additional haplotype, "N, observed in some modern populations and two other prehistoric samples, is also present in this Fremont skeletal collection. © 1996 Wiley-Liss, Inc.
The distribution of the four founding lineage haplogroups in Native Americans from North, Central, and South America shows a north to south increase in the frequency of lineage B and a North to South decrease in the frequency of lineage A. All four founding lineage haplogroups were detected in North, Central, and South America, and in Greenberg et al.'s ([1986] Curr. Anthropol. 27:477–497) three major linguistic groups (Amerind, NaDene, and Eskaleut), with all four haplogroups often found within a single population. Lineage A was the most common lineage in North America, regardless of language group. This overall distribution is most parsimonious with a single wave of migration into the New World which included multiple variants of all four founding lineage types. Torroni et al.'s ([1993a] Am. J. Hum. Genet. 53:563–590) report that lineage B has a more recent divergence time than theother three lineages can best be explained by multiple variants of lineagesA, C, and D, and fewer variants of lineage B entering the New World. Alternatively, there could have been multiple waves of migration from a single parent population in Asia/Siberia which repeatedly reintroduced the same lineages to the New World. © 1995 Wiley-Liss, Inc.
A decade ago, the first reviews of the collective mitochondrial DNA (mtDNA) data from Native Americans concluded that the Americas were peopled through multiple migrations from different Asian populations beginning more than 30,000 years ago.1 These reports confirmed multiple-wave hypotheses suggested earlier by other sources and rejected the dominant Clovis-first archeological paradigm. Consequently, it appeared that molecular biology had made a significant contribution to the study of American prehistory. As Cann2 comments, the Americas held the greatest promise for genetics to help solve some of the mysteries of prehistoric populations. In particular, mtDNA appeared to offer real potential as a means of better understanding ancient population movements. A decade later, none of the early conclusions remain unequivocal. Nevertheless, in its maturity, the study of Native American mtDNA has produced a volume of reports that still illuminate the nature and timing of the first peopling and postcolonization population movements within the New World.
Polymerase chain reaction (PCR) inhibitors are often co-extracted with ancient DNA (aDNA) and when present make the analysis of aDNA difficult, if not impossible. In this study we review previous research on PCR inhibitors and techniques that address their co-extraction with DNA from sub-optimal samples. Additionally, we introduce a simple extraction technique, “repeat silica extraction,” that effectively removed PCR inhibitors from extracts of 7000–8000-year-old human skeletal remains from the Windover archaeological site in Florida and 700–2000-year-old human coprolites excavated from Fish Slough Cave in southern California. A series of tests on these same samples demonstrates that N-phenacylthiazolium bromide is largely ineffective, despite previously reported success using this compound as part of the DNA extraction process. We also describe a method for demonstrating the presence as well as successful removal of PCR inhibitors by use of a “positive aDNA control,” a test necessary to conclude that negative PCR amplification is the result of the absence of preserved DNA.
mtDNA was successfully extracted from 108 individuals from the Norris Farms Oneota, a prehistoric Native American population, to compare the mtDNA diversity from a pre-Columbian population with contemporary Native American and Asian mtDNA lineages and to examine hypotheses about the peopling of the New World. Haplogroup and hypervariable region I sequence data indicate that the lineages from haplogroups A, B, C, and D are the most common among Native Americans but that they were not the only lineages brought into the New World from Asia. The mtDNA evidence does not support the three-wave hypothesis of migration into the New World but rather suggests a single "wave" of people with considerable mtDNA diversity that exhibits a signature of expansion 23,000-37,000 years ago.
The geographic structure of Y-chromosome variability has been analyzed in native populations of South America, through use of the high-frequency Native American haplogroup defined by the DYS199-T allele and six Y-chromosome–linked microsatellites (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), analyzed in 236 individuals. The following pattern of within- and among-population variability emerges from the analysis of microsatellite data: (1) the Andean populations exhibit significantly higher levels of within-population variability than do the eastern populations of South America; (2) the spatial-autocorrelation analysis suggests a significant geographic structure of Y-chromosome genetic variability in South America, although a typical evolutionary pattern could not be categorically identified; and (3) genetic-distance analyses and the analysis of molecular variance suggest greater homogeneity between Andean populations than between non-Andean ones. On the basis of these results, we propose a model for the evolution of the male lineages of South Amerindians that involves differential patterns of genetic drift and gene flow. In the western part of the continent, which is associated with the Andean area, populations have relatively large effective sizes and gene-flow levels among them, which has created a trend toward homogenization of the gene pool. On the other hand, eastern populations—settled in the Amazonian region, the central Brazilian plateau, and the Chaco region—have exhibited higher rates of genetic drift and lower levels of gene flow, with a resulting trend toward genetic differentiation. This model is consistent with the linguistic and cultural diversity of South Amerindians, the environmental heterogeneity of the continent, and the available paleoecological data.
Sequencing of a 360-nucleotide segment of the mitochondrial control region for 63 individuals from an Amerindian tribe, the Nuu-Chah-Nulth of the Pacific Northwest, revealed the existence of 28 lineages defined by 26 variable positions. This represents a substantial level of mitochondrial diversity for a small local population. Furthermore, the sequence diversity among these Nuu-Chah-Nulth lineages is greater than 60% of the mitochondrial sequence diversity observed in major ethnic groups such as Japanese or sub-Saharan Africans. It was also observed that the majority of the mitochondrial lineages of the Nuu-Chah-Nulth fell into phylogenetic clusters. The magnitude of the sequence difference between the lineage clusters suggests that their origin predates the entry of humans into the Americas. Since a single Amerindian tribe can contain such extensive molecular diversity, it is unnecessary to presume that substantial genetic bottlenecks occurred during the formation of contemporary ethnic groups. In particular, these data do not support the concept of a dramatic founder effect during the peopling of the Americas.
The mitochondrial DNA (mtDNA) sequence variation of the South American Ticuna, the Central American Maya, and the North American Pima was analyzed by restriction-endonuclease digestion and oligonucleotide hybridization. The analysis revealed that Amerindian populations have high frequencies of mtDNAs containing the rare Asian RFLP HincII morph 6, a rare HaeIII site gain, and a unique AluI site gain. In addition, the Asian-specific deletion between the cytochrome c oxidase subunit II (COII) and tRNA(Lys) genes was also prevalent in both the Pima and the Maya. These data suggest that Amerindian mtDNAs derived from at least four primary maternal lineages, that new tribal-specific variants accumulated as these mtDNAs became distributed throughout the Americas, and that some genetic variation may have been lost when the progenitors of the Ticuna separated from the North and Central American populations.
A specific segment of mitochondrial DNA from 18 people was examined by two methods of direct DNA sequencing. This segment includes a small noncoding region (V) shown before by restriction analysis to exhibit length polymorphism. All 11 of the human mtDNAs previously reported to have a deletion in this region proved to lack one of the two adjacent copies of a 9-base-pair sequence normally present in human mtDNAs. Phylogenetic analysis suggests that this deletion occurred only once during the evolution of modern types of human mtDNA and that it will be a valuable anthropological marker for peoples of East Asian origin. The one human mtDNA reported to have an addition in region V differs from the wild type by two mutations in the first copy of the 9-base-pair sequence: one transition and an addition of four cytosines, thereby producing a run of 11 cytosines. One of the direct DNA sequencing methods uses a single oligonucleotide primer to facilitate dideoxy sequencing from purified mtDNA templates. The second, more successful, method first amplifies this mtDNA segment enzymatically with two flanking primers (the "polymerase chain reaction") and then uses a third primer for DNA sequencing. This latter method, which works on the DNA extracted from small amounts of blood as well as on purified mtDNA, is shown to be a rapid means of defining sequence variants without purifying and cloning the same DNA segment from many individuals.
The mtDNA variation of 321 individuals from 17 Native American populations was examined by high-resolution restriction endonuclease analysis. All mtDNAs were amplified from a variety of sources by using PCR. The mtDNA of a subset of 38 of these individuals was also analyzed by D-loop sequencing. The resulting data were combined with previous mtDNA data from five other Native American tribes, as well as with data from a variety of Asian populations, and were used to deduce the phylogenetic relationships between mtDNAs and to estimate sequence divergences. This analysis revealed the presence of four haplotype groups (haplogroups A, B, C, and D) in the Amerind, but only one haplogroup (A) in the Na-Dene, and confirmed the independent origins of the Amerinds and the Na-Dene. Further, each haplogroup appeared to have been founded by a single mtDNA haplotype, a result which is consistent with a hypothesized founder effect. Most of the variation within haplogroups was tribal specific, that is, it occurred as tribal private polymorphisms. These observations suggest that the process of tribalization began early in the history of the Amerinds, with relatively little intertribal genetic exchange occurring subsequently. The sequencing of 341 nucleotides in the mtDNA D-loop revealed that the D-loop sequence variation correlated strongly with the four haplogroups defined by restriction analysis, and it indicated that the D-loop variation, like the haplotype variation, arose predominantly after the migration of the ancestral Amerinds across the Bering land bridge.
Ancient DNA was obtained from skeletal remains from the Norris Farms #36 cemetery, a pre-Columbian archeological site in central Illinois that dates to A.D. 1300. Four mitochondrial DNA (mtDNA) markers were analyzed that delineate the four primary mtDNA lineages found in contemporary Amerindian populations. mtDNA types were determined for 50 individuals; 49 belonged to one of these four lineages. One lineage occurred only in males, suggesting an immigration of maternally related males into this community. There was no significant spatial patterning of mtDNA lineages within the cemetery. This survey of ancient DNA variation in a pre-Columbian population supports the view that the initial colonization of the New World comprised just four primary mtDNA lineages.
Although DNA is the carrier of genetic information, it has limited chemical stability. Hydrolysis, oxidation and nonenzymatic methylation of DNA occur at significant rates in vivo, and are counteracted by specific DNA repair processes. The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments from fossils.
The timing and number of prehistoric migrations involved in the settlement of the American continent is subject to intense debate. Here, we reanalyze Native American control region mtDNA data and demonstrate that only an appropriate phylogenetic analysis accompanied by an appreciation of demographic factors allows us to discern different migrations and to estimate their ages. Reappraising 574 mtDNA control region sequences from aboriginal Siberians and Native Americans, we confirm in agreement with linguistic, archaeological and climatic evidence that (i) the major wave of migration brought one population, ancestral to the Amerinds, from northeastern Siberia to America 20,000-25,000 years ago and (ii) a rapid expansion of a Beringian source population took place at the end of the Younger Dryas glacial phase approximately 11,300 years ago, ancestral to present Eskimo and Na-Dene populations.
mtDNA variation in the Cayapa, an Ecuadorian Amerindian tribe belonging to the Chibcha-Paezan linguistic branch, was analyzed by use of hypervariable control regions I and II along with two linked regions undergoing insertion/deletion mutations. Three major maternal lineage clusters fit into the A, B, and C founding groups first described by Schurr and colleagues in 1990, whereas a fourth lineage, apparently unique to the Cayapa, has ambiguous affinity to known clusters. The time of divergence from a common maternal ancestor of the four lineage groups is of sufficient age that it indicates an origin in Asia and supports the hypothesis that the degree of variability carried by the Asian ancestral populations into the New World was rather high. Spatial autocorrelation analysis points out (a) statistically significant nonrandom distributions of the founding lineages in the Americas, because of north-south population movements that have occurred since the first Asian migrants spread through Beringia into the Americas, and (b) an unusual pattern associated with the D lineage cluster. The values of haplotype and nucleotide diversity that are displayed by the Cayapa appear to differ from those observed in other Chibchan populations but match those calculated for South American groups belonging to various linguistic stocks. These data, together with the results of phylogenetic analysis performed with the Amerinds of Central and South America, highlight the difficulty in the identification of clear coevolutionary patterns between linguistic and genetic relationships in particular human populations.
The Human Genome Project, from one perspective, began in 1981 with the publication1 of the complete sequence of human mitochondrial DNA (mtDNA). The Cambridge reference sequence (CRS), as it is now designated, continues to be indispensable for studies of human evolution, population genetics and mitochondrial diseases. It has been recognized for some time, however, that the CRS differs at several sites from the mtDNA sequences obtained by other investigators2, 3. These discrepancies may reflect either true errors in the original sequencing analysis or rare polymorphisms in the CRS mtDNA. A further complication is that the original mtDNA sequence was principally derived from a single individual of European descent, although it also contained some sequences from both HeLa and bovine mtDNA (1). To resolve these uncertainties, we have completely resequenced the original placental mtDNA sample.
We present mitochondrial haplogroup characterizations of the prehistoric Anasazi of the United States (US) Southwest. These data are part of a long-term project to characterize ancient Great Basin and US Southwest samples for mitochondrial DNA (mtDNA) diversity. Three restriction site polymorphisms (RSPs) and one length polymorphism identify four common Native American matrilines (A, B, C, and D). The Anasazi (n = 27) are shown to have a moderate frequency of haplogroup A (22%), a high frequency of haplogroup B (56%), and a low frequency of C (15%). Haplogroup D has not yet been detected among the Anasazi. In comparison to modern Native American groups from the US Southwest, the Anasazi are shown to have a distribution of haplogroups similar to the frequency pattern exhibited by modern Pueblo groups. A principal component analysis also clusters the Anasazi with some modern (Pueblo) Southwestern populations, and away from other modern (Athapaskan speaking) Southwestern populations. The Anasazi are also shown to have a significantly different distribution of the four haplogroups as compared to the eastern Great Basin Great Salt Lake Fremont (n = 32), although both groups cluster together in a principal component analysis. The context of our data suggests substantial stability within the US Southwest, even in the face of the serious cultural and biological disruption caused by colonization of the region by European settlers. We conclude that although sample numbers are fairly low, ancient DNA (aDNA) data are useful for assessing long-term populational affinities and for discerning regional population structure.
The mitochondrial DNA of modern Native Americans has been shown to fall into one of at least five haplogroups (A, B, C, D, or X) whose frequencies differ among tribal groups. The frequencies of these five haplogroups in a collection of ancient individuals from Western Nevada dating to between approximately 350-9,200 years BP were determined. These data were used to test the hypothesis, supported by archaeological and linguistic data, that the current inhabitants of the Great Basin, the Numic speakers, are recent immigrants into the area who replaced the previous non-Numic inhabitants. The frequency distributions of haplogroups in the ancient and modern Native Americans differed significantly, suggesting that there is a genetic discontinuity between the ancient inhabitants and the modern Numic speakers, providing further support for the Recent Numic Expansion hypothesis. The distribution of mitochondrial haplogroups of the ancient inhabitants of the Great Basin is most similar to those of some of the modern Native American inhabitants of California.
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.
To scrutinize the male ancestry of extant Native American populations, we examined eight biallelic and six microsatellite polymorphisms from the nonrecombining portion of the Y chromosome, in 438 individuals from 24 Native American populations (1 Na Dené and 23 South Amerinds) and in 404 Mongolians. One of the biallelic markers typed is a recently identified mutation (M242) characterizing a novel founder Native American haplogroup. The distribution, relatedness, and diversity of Y lineages in Native Americans indicate a differentiated male ancestry for populations from North and South America, strongly supporting a diverse demographic history for populations from these areas. These data are consistent with the occurrence of two major male migrations from southern/central Siberia to the Americas (with the second migration being restricted to North America) and a shared ancestry in central Asia for some of the initial migrants to Europe and the Americas. The microsatellite diversity and distribution of a Y lineage specific to South America (Q-M19) indicates that certain Amerind populations have been isolated since the initial colonization of the region, suggesting an early onset for tribalization of Native Americans. Age estimates based on Y-chromosome microsatellite diversity place the initial settlement of the American continent at approximately 14,000 years ago, in relative agreement with the age of well-established archaeological evidence.
In search of the ancestors of Native American mitochondrial DNA (mtDNA) haplogroups, we analyzed the mtDNA of 531 individuals from nine indigenous populations in Siberia. All mtDNAs were subjected to high-resolution RFLP analysis, sequencing of the control-region hypervariable segment I (HVS-I), and surveyed for additional polymorphic markers in the coding region. Furthermore, the mtDNAs selected according to haplogroup/subhaplogroup status were completely sequenced. Phylogenetic analyses of the resulting data, combined with those from previously published Siberian arctic and sub-arctic populations, revealed that remnants of the ancient Siberian gene pool are still evident in Siberian populations, suggesting that the founding haplotypes of the Native American A-D branches originated in different parts of Siberia. Thus, lineage A complete sequences revealed in the Mansi of the Lower Ob and the Ket of the Lower Yenisei belong to A1, suggesting that A1 mtDNAs occasionally found in the remnants of hunting-gathering populations of northwestern and northern Siberia belonged to a common gene pool of the Siberian progenitors of Paleoindians. Moreover, lineage B1, which is the most closely related to the American B2, occurred in the Tubalar and Tuvan inhabiting the territory between the upper reaches of the Ob River in the west, to the Upper Yenisei region in the east. Finally, the sequence variants of haplogroups C and D, which are most similar to Native American C1 and D1, were detected in the Ulchi of the Lower Amur. Overall, our data suggest that the immediate ancestors of the Siberian/Beringian migrants who gave rise to ancient (pre-Clovis) Paleoindians have a common origin with aboriginal people of the area now designated the Altai-Sayan Upland, as well as the Lower Amur/Sea of Okhotsk region.
DNA from fossil human bones could provide invaluable information about population migrations, genetic relations between different groups and the spread of diseases. The use of ancient DNA from bones to study the genetics of past populations is, however, very often compromised by the altered and degraded state of preservation of the extracted material. The universally observed postmortem degradation, together with the real possibility of contamination with modern human DNA, makes the acquisition of reliable data, from humans in particular, very difficult. We demonstrate that relatively well preserved DNA is occluded within clusters of intergrown bone crystals that are resistant to disaggregation by the strong oxidant NaOCl. We obtained reproducible authentic sequences from both modern and ancient animal bones, including humans, from DNA extracts of crystal aggregates. The treatment with NaOCl also minimizes the possibility of modern DNA contamination. We thus demonstrate the presence of a privileged niche within fossil bone, which contains DNA in a better state of preservation than the DNA present in the total bone. This counterintuitive approach to extracting relatively well preserved DNA from bones significantly improves the chances of obtaining authentic ancient DNA sequences, especially from human bones.
• ancient DNA
• preservation
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.
The study of ancient DNA has the potential to make significant and unique contributions to ecology and evolution. However, the techniques used contain inherent problems, particularly with regards to the generation of authentic and useful data. The solution currently advocated to reduce contamination and artefactual results is to adopt criteria for authentication. Nevertheless, these criteria are not foolproof, and we believe that they have, in practice, replaced the use of thought and prudence when designing and executing ancient DNA studies. We argue here that researchers in this field must take a more cognitive and self-critical approach. Specifically, in place of checking criteria off lists, researchers must explain, in sufficient enough detail to dispel doubt, how the data were obtained, and why they should be believed to be authentic.
Mitochondrial DNA studies of Native Americans: conceptions and misconceptions of the population pre-history of the Americas Origin and evolution of native American mDNA variation: a reappraisal
- J A Eshleman
- R S Malhi
- D G P F Smith
- R N Lightowlers
- R S Malhi
Eshleman, J.A., Malhi, R.S., Smith, D.G., 2003. Mitochondrial DNA studies of Native Americans: conceptions and misconceptions of the population pre-history of the Americas. Evolutionary Anthropology 12, 7e18. P.F., Lightowlers, R.N., 647 R.S. Malhi et al. / Journal of Archaeological Science 34 (2007) 642e648 rForster, P., Harding, R., Torroni, A., Bandelt, H.-J., 1996. Origin and evolution of native American mDNA variation: a reappraisal. American Journal of Human Genetics 59, 935e945
DNA extraction from Pleistocene bones by a silica-based purification methods Ancient mitochondrial DNA evidence for prehistoric population movement: the Numic expansion
- M Hö
- S Pää
Hö, M., Pää, S., 1993. DNA extraction from Pleistocene bones by a silica-based purification methods. Nucleic Acids Research 21, 3913e3914. Kaestle, F.A., Smith, D.G., 2001. Ancient mitochondrial DNA evidence for prehistoric population movement: the Numic expansion. American Journal of Physical Anthropology 115, 1e12.
Assessing an-cient DNA studies Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo Isopropanol precipi-tation removes PCR inhibitors from ancient bone extracts
- M T P Gilbert
- H.-J Bandelt
- M Hofreiter
- I Barnes
- A Gonzá-Oliver
- L Marquez-Morfin
- J C Jimenez
- A Torre-Blanco
Gilbert, M.T.P., Bandelt, H.-J., Hofreiter, M., Barnes, I., 2005. Assessing an-cient DNA studies. Trends in Ecology and Evolution 20, 541e544. Gonzá-Oliver, A., Marquez-Morfin, L., Jimenez, J.C., Torre-Blanco, A., 2001. Founding Amerindian mitochondrial DNA lineages in ancient Maya from Xcaret, Quintana Roo. American Journal of Physical Anthro-pology 116, 230e235. Hä, C., Brousseau, T., Laudet, V., Stehelin, D., 1995. Isopropanol precipi-tation removes PCR inhibitors from ancient bone extracts. Nucleic Acids Research 23, 881e882. Hey, J., 2005. On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biology 3, e193.
Ancient DNA from a pre-Columbian Am-erindian population Genetic analysis of an 8000 year-old Native American Skeleton Ancient Biomolecules 1, 83e87. Stone, A.C., Stoneking, M., 1998. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World
- A C Stone
- M Stoneking
- A C Stone
- M Stoneking
- E Tarazona-Santos
- D R Carvalho-Silva
- D Pettener
- D Luiselli
- De Stefano
- G F Labarga
- C M Rickards
Stone, A.C., Stoneking, M., 1993. Ancient DNA from a pre-Columbian Am-erindian population. American Journal of Physical Anthropology 92, 463e471. Stone, A.C., Stoneking, M., 1996. Genetic analysis of an 8000 year-old Native American Skeleton. Ancient Biomolecules 1, 83e87. Stone, A.C., Stoneking, M., 1998. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. American Journal of Human Genetics 62, 1153e1170. Tarazona-Santos, E., Carvalho-Silva, D.R., Pettener, D., Luiselli, D., De Stefano, G.F., Labarga, C.M., Rickards, O., Tyler-Smith, C., Pena, S.D., Santos, F.R., 2001. Genetic differentiation in South Amerindians is related to environmental and cultural diversity: evidence from the Y chromosome. American Journal of Human Genetics 68, 1485e1496.
Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders Lack of founding Amerindian mitochondrial DNA lineages in extinct Aborigines from Tierra Del Fuego Patagonia
- C J Kolman
- N Sambuughin
- E Bermingham
Kolman, C.J., Sambuughin, N., Bermingham, E., 1996. Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders. Genetics 142, 1321e1334. Lalueza, C., Perezperez, A., Prats, E., Cornudella, L., Turbon, D., 1997. Lack of founding Amerindian mitochondrial DNA lineages in extinct Aborigines from Tierra Del Fuego Patagonia. Human Molecular Genetics 6, 41e46.
mtDNA history of the Cayapa Amerinds of Ecuador: detection of additional founding lineages for the native American populations
- O Rickards
- C Martinez-Labarga
- J K Lum
- De Stefano
- G F Cann
Rickards, O., Martinez-Labarga, C., Lum, J.K., De Stefano, G.F., Cann, R.L.,
1999. mtDNA history of the Cayapa Amerinds of Ecuador: detection of additional founding lineages for the native American populations. American
Journal of Human Genetics 65, 519e530.