Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes

Human evolutionary genetics gives a chronological framework to interpret the human history. It is based on the molecular clock hypothesis that suppose a straightforward relationship between the mutation rate and the substitution rate with independence of other factors as demography dynamics. Analyzing ancient and modern human complete mitochondrial genomes we show here that, along the time, the substitution rate can be significantly slower or faster than the average germline mutation rate confirming a time dependence effect mainly attributable to changes in the effective population size of the human populations, with an exponential growth in recent times. We also detect that transient polymorphisms play a slowdown role in the evolutionary rate deduced from haplogroup intraspecific trees. Finally, we propose the use of the most divergent lineages within haplogroups as a practical approach to correct these molecular clock mismatches.

Mitochondrial genome diversity on the Central Siberian Plateau with particular reference to the prehistory of northernmost Eurasia

The Central Siberian Plateau was the last geographic area in Eurasia to become habitable by modern humans after the Last Glacial Maximum (LGM). Through a comprehensive dataset of mitochondrial DNA (mtDNA) genomes retained in the remnats of earlier ("Old") Siberians, primarily the Ket, Tofalar, and Todzhi, we explored genetic links between the Yenisei-Sayan region and Northeast Eurasia (best represented by the Yukaghir) over the last 10,000 years. We generated 218 new complete mtDNA sequences and placed them into compound phylogenies with 7 newly obtained and 70 published ancient mitochondrial genomes. We have considerably extended the mtDNA sequence diversity (at the entire mtDNA genome level) of autochthonous Siberians, which remain poorly sampled, and these new data may have a broad impact on the study of human migration. We compared present-day mtDNA diversity in these groups with complete mitochondrial genomes from ancient samples from the region and placed the samples into combined genealogical trees. The resulting components were used to clarify the origins and expansion history of mtDNA lineages that evolved in the refugia of south-central Siberia and beyond, as well as multiple phases of connection between this region and distant parts of Eurasia.

Ancestral mitogenome capture of the Southeast Asian banded linsang

Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.

Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these ‘votive’ mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.

Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia

Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.

Healed impact trauma to a Neolithic cattle frontal bone: A posthuman perspective

Trauma associated with slaughter is identified occasionally archaeologically in the cranial remains of domesticated animals, with evidence for pole-axing occurring in Europe, especially from the Roman period onwards. The injury typically extends through the frontal bone and sinuses to penetrate the braincase, causing haemorrhage, loss of consciousness, brain damage, and death. Evidence for slaughter methods in the British Neolithic, however, is lacking. We report such evidence from a healed blunt-force impact trauma to the frontal bone of a domestic cattle skull from Beckhampton Road Neolithic long barrow, Wiltshire. The injury suggests a failed attempt at slaughter. To our knowledge, this is the first such report for domestic cattle from the British Neolithic. We contextualise this discovery, drawing on research into the role and meaning of faunal remains from Neolithic long barrows in Wiltshire. This work has been undertaken from a posthuman perspective. Thus, we demonstrate the opportunities for paleopathologists to inform and engage within posthumanist interpretative frameworks.

Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management

Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.

Prehistoric mitochondrial DNA of domesticate animals supports a 13th century exodus from the northern US southwest

The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations.

Ancient mtDNA diversity reveals specific population development of wild horses in Switzerland after the Last Glacial Maximum

On large geographical scales, changes in animal population distribution and abundance are driven by environmental change due to climatic and anthropogenic processes. However, so far, little is known about population dynamics on a regional scale. We have investigated 92 archaeological horse remains from nine sites mainly adjacent to the Swiss Jura Mountains dating from c. 41,000-5,000 years BP. The time frame includes major environmental turning points such as the Last Glacial Maximum (LGM), followed by steppe vegetation, afforestation and initial re-opening of the landscape by human agricultural activities. To investigate matrilinear population dynamics, we assembled 240 base pairs of the mitochondrial d-loop. FST values indicate large genetic differentiation of the horse populations that were present during and directly after the LGM. After the retreat of the ice, a highly diverse population expanded as demonstrated by significantly negative results for Tajima's D, Fu's FS and mismatch analyses. At the same time, a different development took place in Asia where populations declined after the LGM. This first comprehensive investigation of wild horse remains on a regional scale reveals a discontinuous colonisation of succeeding populations, a pattern that diverges from the larger Eurasian trend.

Pleistocene aridification cycles shaped the contemporary genetic architecture of Southern African baboons

Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa’s faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons (Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes, are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Nef) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region’s biodiversity.

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

BACKGROUND

Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.

RESULTS

In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya.

CONCLUSIONS

The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.

Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach

The Yuan Dynasty (AD 1271-1368) was the first dynasty in Chinese history where a minority ethnic group (Mongols) ruled. Few cemeteries containing Mongolian nobles have been found owing to their tradition of keeping burial grounds secret and their lack of historical records. Archaeological excavations at the Shuzhuanglou site in the Hebei province of China led to the discovery of 13 skeletons in six separate tombs. The style of the artefacts and burials indicate the cemetery occupants were Mongol nobles. However, the origin, relationships and status of the chief occupant (M1m) are unclear. To shed light on the identity of the principal occupant and resolve the kin relationships between individuals, a multidisciplinary approach was adopted, combining archaeological information, stable isotope data and molecular genetic data. Analysis of autosomal, mitochondrial and Y-chromosomal DNA show that some of the occupants were related. The available evidence strongly suggests that the principal occupant may have been the Mongol noble Korguz. Our study demonstrates the power of a multidisciplinary approach in elucidating information about the inhabitants of ancient historical sites.

The ancient Yakuts: a population genetic enigma

This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages.

Mitochondrial DNA from El Mirador cave (Atapuerca, Spain) reveals the heterogeneity of Chalcolithic populations

Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500–4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760–4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups.

Ancient DNA. Farming's tangled European roots

The transition from foraging to farming in Europe was long and messy, according to two papers published in Science this week.

Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe

Background/Principal Findings

The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe.

Methodology/Significance

Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe.

Conclusion

The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation.

Biological ancestries, kinship connections, and projected identities in four central Anatolian settlements: insights from culturally contextualized genetic anthropology

Previous population genetics studies in Turkey failed to delineate recent historical and social factors that shaped Anatolian cultural and genetic diversity at the local level. To address this shortcoming, we conducted focused ethnohistorical fieldwork and screened biological samples collected from the Yuksekyer region for mitochondrial, Y chromosome, and autosomal markers and then analyzed the data within an ethnohistorical context. Our results revealed that, at the village level, paternal genetic diversity is structured among settlements, whereas maternal genetic diversity is distributed more homogenously, reflecting the strong patrilineal cultural traditions that transcend larger ethnic and religious structures. Local ancestries and origin myths, rather than ethnic or religious affiliations, delineate the social boundaries and projected identities among the villages. Therefore, we conclude that broad, ethnicity-based sampling is inadequate to capture the genetic signatures of recent social and historical dynamics, which have had a profound influence on contemporary genetic and cultural regional diversity.

Historical perspective on mitochondrial medicine

In this review, we trace the origins and follow the development of mitochondrial medicine from the premolecular era (1962-1988) based on clinical clues, muscle morphology, and biochemistry into the molecular era that started in 1988 and is still advancing at a brisk pace. We have tried to stress conceptual advances, such as endosymbiosis, uniparental inheritance, intergenomic signaling and its defects, and mitochondrial dynamics. We hope that this historical review also provides an update on mitochondrial medicine, although we fully realize that the speed of progress in this area makes any such endeavor akin to writing on water.

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius)

BACKGROUND

The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample.

METHODOLOGY

DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences.

CONCLUSIONS

For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.

[Giuseppe Attardi: mitochondrial genetic system and its influence in the study of the mitochondrial diseases]

AIM

To describe the scientific contributions and biography of Giuseppe Attardi (1923-2008), in particular his work on the human mitochondrial genetic system of crucial importance for the discovery and understanding of the mechanisms that produce the mitochondrial diseases.

DEVELOPMENT

Giuseppe Attardi was an Italian-born medical doctor that worked with outstanding researchers as James Watson, Francois Jacob, and Renato Dulbecco, all Nobel Prizes of Medicine until 1963 that was promoted to Professor of the California Institute of Technology in Pasadena (USA). In 1967 discovered the human mitochondrial RNA, a little later the mitochondrial ribosomes and proteins encoded in the genome, in 1981 showed the genetic and transcription map of the mitochondrial DNA, and in 1983 described the proteins codified in this genome, all of them components of the oxidative phosphorylation system, metabolic pathway that leads to the synthesis of ATP. Later, he developed a technique, widely used nowadays, to study the mechanism by which the mutations in the mitochondrial DNA altered the cellular function and originated the mitochondrial diseases. In 1999, demonstrated the role of the mitocondrial DNA, and the mutations produced along the life, in aging.

Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

Genetic variation in prehistoric Sardinia

We sampled teeth from 53 ancient Sardinian (Nuragic) individuals who lived in the Late Bronze Age and Iron Age, between 3,430 and 2,700 years ago. After eliminating the samples that, in preliminary biochemical tests, did not show a high probability to yield reproducible results, we obtained 23 sequences of the mitochondrial DNA control region, which were associated to haplogroups by comparison with a dataset of modern sequences. The Nuragic samples show a remarkably low genetic diversity, comparable to that observed in ancient Iberians, but much lower than among the Etruscans. Most of these sequences have exact matches in two modern Sardinian populations, supporting a clear genealogical continuity from the Late Bronze Age up to current times. The Nuragic populations appear to be part of a large and geographically unstructured cluster of modern European populations, thus making it difficult to infer their evolutionary relationships. However, the low levels of genetic diversity, both within and among ancient samples, as opposed to the sharp differences among modern Sardinian samples, support the hypothesis of the expansion of a small group of maternally related individuals, and of comparatively recent differentiation of the Sardinian gene pools.

mtDNA from hair and nail clarifies the genetic relationship of the 15th century Qilakitsoq Inuit mummies

The 15th century Inuit mummies excavated at Qilakitsoq in Greenland in 1978 were exceptionally well preserved and represent the largest find of naturally mummified specimens from the Arctic. The estimated ages of the individuals, their distribution between two adjacent graves, the results of tissue typing, and incomplete STR results led researchers to conclude that the eight mummies formed two distinct family groups: A grandmother (I/5), two daughters (I/3, I/4), and their two children (I/1, I/2) in one grave, and two sisters (II/6, II/8) and a daughter (II/7) of one of them in the other. Using mtDNA from hair and nail, we have reanalyzed the mummies. The results allowed the unambiguous assignment of each of the mummies to one of three mtDNA haplogroups: A2b (I/5); A2a (I/2, I/3, II/6, II/8); A2a-311 (I/1, I/4, II/7), excluded some of the previous relations, and pointed to new ones. I/5 is not the grandmother/mother of the individuals in Grave I, and she is not maternally related to any of the seven other mummies; I/3 and I/4 are not sisters and II/7 is neither the daughter of II/6 nor of II/8. However, I/1 may be the child of either I/4 or II/7 and these two may be sisters. I/2 may be the son of I/3, who may be the daughter of either II/6 or II/8, and these two may be sisters. The observation of haplogroups A2a and A2b amongst the 550-year-old Inuit puts a lower limit on the age of the two lineages in Greenland.

Peopling of South Asia: investigating the caste-tribe continuum in India

In recent years, mtDNA and Y chromosome studies involving human populations from South Asia and the rest of the world have revealed new insights about the peopling of the world by anatomically modern humans during the late Pleistocene, some 40,000-60,000 years ago, over the southern coastal route from Africa. Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long-term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations. This review attempts to summarize recent genetic studies on Indian caste and tribal populations with the focus on the information embedded in the socially defined structure of Indian populations.

A Romani mitochondrial haplotype in England 500 years before their recorded arrival in Britain

The nomadic Romani (gypsy) people are known for their deep-rooted traditions, but most of their history is recorded from external sources. We find evidence for a Romani genetic lineage in England long before their recorded arrival there. The most likely explanations are that either the historical record is wrong, or that early liaisons between Norse and Romani people during their coincident presence in ninth to tenth century Byzantium led to the spread of the haplotype to England.

A rapid loss of stripes: the evolutionary history of the extinct quagga

Twenty years ago, the field of ancient DNA was launched with the publication of two short mitochondrial (mt) DNA sequences from a single quagga (Equus quagga) museum skin, an extinct South African equid (Higuchi et al. 1984 Nature312, 282-284). This was the first extinct species from which genetic information was retrieved. The DNA sequences of the quagga showed that it was more closely related to zebras than to horses. However, quagga evolutionary history is far from clear. We have isolated DNA from eight quaggas and a plains zebra (subspecies or phenotype Equus burchelli burchelli). We show that the quagga displayed little genetic diversity and very recently diverged from the plains zebra, probably during the penultimate glacial maximum. This emphasizes the importance of Pleistocene climate changes for phylogeographic patterns in African as well as Holarctic fauna.

Population affinities of Neolithic Siberians: a snapshot from prehistoric Lake Baikal

Archaeological evidence supports the inhabitation of the Lake Baikal region since the Paleolithic. Both metric and nonmetric osteological studies suggest that Neolithic Cis-Baikal populations are the ancestors of contemporary inhabitants of the region. To date, ancient DNA data have not been used to corroborate this biological continuity hypothesis. This study presents a temporal snapshot of the Cis-Baikal Neolithic by examining mtDNA diversity in two cemetery populations situated on the Angara River downstream of Lake Baikal. The 800 years separating the use of the two cemeteries is thought to represent a biocultural hiatus in the Cis-Baikal region, one that ended when a new group migrated into the area. To assess the likelihood that genetic continuity exists between these two Neolithic groups, we examined both mtDNA coding region and hypervariable region I (HVI) polymorphisms from skeletal remains excavated from both cemeteries (Lokomotiv and Ust'-Ida). The mtDNA haplogroup distributions of the two cemetery populations differ significantly, suggesting that they were biologically distinct groups. When the biological distance between these Neolithic groups is compared with modern Siberian and other East Eurasian groups, the posthiatus group (Serovo-Glazkovo) generally aligns with contemporary Siberians, while the prehiatus (Kitoi) individuals are significantly different from all but modern Kets and Shorians living in the Yenisey and Ob River basins to the west of Lake Baikal. These results suggest that the Lake Baikal region experienced a significant depopulation event during the sixth millennium BP, and was reoccupied by a new immigrant population some 800 years later.

Comment on "Ancient DNA from the first European farmers in 7500-year-old Neolithic sites"

On the basis of analysis of ancient DNA from early European farmers, Haak et al. (Reports, 11 November 2005, p. 1016) argued for the Paleolithic ancestry of modern Europeans. We stress that the study is more limited in scope than the authors claim, in part because not all of the skeletal samples date to the time of the Neolithic transition in a given area of Europe.

The last Viking King: a royal maternity case solved by ancient DNA analysis

The last of the Danish Viking Kings, Sven Estridsen, died in a.d. 1074 and is entombed in Roskilde Cathedral with other Danish kings and queens. Sven's mother, Estrid, is entombed in a pillar across the chancel. However, while there is no reasonable doubt about the identity of Sven, there have been doubts among historians whether the woman entombed was indeed Estrid. To shed light on this problem, we have extracted and analysed mitochondrial DNA (mtDNA) from pulp of teeth from each of the two royals. Four overlapping DNA-fragments covering about 400bp of hypervariable region 1 (HVR-1) of the D-loop were PCR amplified, cloned and a number of clones with each segment were sequenced. Also a segment containing the H/non-H specific nucleotide 7028 was sequenced. Consensus sequences were determined and D-loop results were replicated in an independent laboratory. This allowed the assignment of King Sven Estridsen to haplogroup H; Estrid's sequence differed from that of Sven at two positions in HVR-1, 16093T-->C and 16304T-->C, indicating that she belongs to subgroup H5a. Given the maternal inheritance of mtDNA, offspring will have the same mtDNA sequence as their mother with the exception of rare cases where the sequence has been altered by a germ line mutation. Therefore, the observation of two sequence differences makes it highly unlikely that the entombed woman was the mother of Sven. In addition, physical examination of the skeleton and the teeth strongly indicated that this woman was much younger (approximately 35 years) at the time of death than the 70 years history records tell. Although the entombed woman cannot be the Estrid, she may well be one of Sven's two daughters-in-law who were also called Estrid and who both became queens.

Molecular characterization of a pre-Columbian mummy and in situ coprolite

The history of Homo sapiens dispersal around the world and inherent interpopulation contacts and conflicts has given rise to several transitions in his relationships with the natural world, with the final result of changes in the patterns of infectious disease (McMichael [2001] Ecosystem Health 7:107-115). Of particular interest, in this context, is the contact between Amerindians and Europeans that started at the end of the 15th century, and the resulting exchange of microbes. We successfully recovered ancient DNA from a pre-Columbian mummy from Cuzco (Peru), radiocarbon-dated to 980-1170 AD, for which consistent mtDNA amplifications and sequences were obtained. The analysis of mtDNA revealed that the mummy's haplogroup was characteristic of Native American populations. We also investigated a sample of feces directly isolated from the intestines of the mummy, using a polymerase chain reaction system designed to detect the broadest spectrum of bacterial DNAs. The analysis of results, following a criterion of "paleoecological consistency" (Rollo and Marota [1998] Philos. Trans. R. Soc. Lond. [Biol.] 354: 111-119), demonstrated that some vestiges of the original microbial flora of the feces were preserved. In particular, we were able to identify the DNA of Haemophylus parainfluenzae, thus suggesting that this recently recognized pathogen was present in precontact Native Americans.

Population origins in Mongolia: Genetic structure analysis of ancient and modern DNA

In the present study, nuclear (autosomal and Y-chromosome short tandem repeats) and mitochondrial (hypervariable region I) ancient DNA data previously obtained from a 2,300-year-old Xiongnu population of the Egyin Gol Valley (south of Lake Baikal in northern Mongolia) (Keyser-Tracqui et al. 2003 Am. J. Hum. Genet. 73:247-260) were compared with data from two contemporary Mongolian populations: one from the same location (Egyin Gol Valley plus a perimeter of less than 100 km around the valley), and one from the whole of Mongolia. The principal objective of this comparative analysis was to assess the likelihood that genetic continuity exists between ancient and present-day Mongolian populations. Since the ancient Xiongnu sample might have been composed of some of the ancestors of the present-day Yakuts, data from a present-day Yakut population, as well as published data from Turkish populations, were also included in the comparative analysis. The main result of our study was the genetic similarity observed among Mongolian samples from different periods and geographic areas. This result supports the hypothesis that the succession over time of different Turkic and Mongolian tribes in the current territory of Mongolia resulted in cultural rather than genetic exchanges. Furthermore, it appears that the Yakuts probably did not find their origin among the Xiongnu tribes, as we previously hypothesized.

mtDNA variation in Inuit populations of Greenland and Canada: Migration history and population structure

We examined 395 mtDNA control-region sequences from Greenlandic Inuit and Canadian Kitikmeot Inuit with the aim of shedding light on the migration history that underlies the present geographic patterns of genetic variation at this locus in the Arctic. In line with previous studies, we found that Inuit populations carry only sequences belonging to haplotype clusters A2 and D3. However, a comparison of Arctic populations from Siberia, Canada, and Greenland revealed considerable differences in the frequencies of these haplotypes. Moreover, large sample sizes and regional information about birthplaces of maternal grandmothers permitted the detection of notable differences in the distribution of haplotypes among subpopulations within Greenland. Our results cast doubt on the prevailing hypothesis that contemporary Inuit trace their all of their ancestry to so-called Thule groups that expanded from Alaska about 800-1,000 years ago. In particular, discrepancies in mutational divergence between the Inuit populations and their putative source mtDNA pool in Siberia/Alaska for the two predominant haplotype clusters, A2a and A2b, are more consistent with the possibility that expanding Thule groups encountered and interbred with existing Dorset populations in Canada and Greenland.

[The origins of dogs: archaeozoology, genetics, and ancient DNA]

The domestication of the dog from the wolf was a key step in the pathway that led to the Neolithic revolution. The earliest fossil dogs, dated to the end of the last glacial period (17,000 to 12,000 years ago), have been found in Russia, Germany and the Middle East. No dogs are represented in the naturalistic art of the European Upper Palaeolithic, suggesting that dogs were introduced at a later date. Genetic studies of extant dog and wolf mitochondrial DNA sequences were interpreted in favour of multiple dog founding events as early as 135-76,000 years ago, or of a single origin in East Asia, 40,000 or 15,000 years ago. Our study included mitochondrial DNA sequences from Italian fossil bones attributed to three Late Pleistocene-Early Holocene wolves (dated from a15,000 to a10,000 14C years ago) and two dogs, dated to a4000 and a3000 14C years ago respectively. Taking paleogeography into account, our phylogenetic data point to a contribution of European wolves to the three major dog clades, in agreement with archaeozoological data. Our phylogeographic studies also suggest genetic differentiation of dogs and wolves related to isolation by geographic distance, supporting multicentric origins of dogs from wolves throughout their vast range of sympatry.

Ancient DNA from the first European farmers in 7500-year-old Neolithic sites

The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans.

Ancient mitochondrial M haplogroups identified in the Southwest Pacific

Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.

Microevolution in prehistoric Andean populations: Chronologic mtDNA variation in the desert valleys of northern Chile

Archeological evidence suggests that the iconographic and technological developments that took place in the highlands around Lake Titicaca in the Central Andean region had an influence on the cultural elaborations of the human groups in the valleys and the Pacific coast of northern Chile. In a previous communication, we were able to show, by means of a distance analysis, that a craniofacial differentiation accompanied the process of cultural evolution in the valleys (Rothhammer and Santoro [2001] Lat. Am. Antiq. 12:59-66). Recently, numerous South Amerindian mtDNA studies were published, and more accurate molecular techniques to study ancient mtDNA are available. In view of these recent developments, we decided 1) to study chronological changes of ancient mtDNA haplogroup frequencies in the nearby Lluta, Azapa, and Camarones Valleys, 2) to identify microevolutionary forces responsible for such changes, and 3) to compare ancient mtDNA haplogroup frequencies with previous data in order to validate craniometrical results and to reconstruct the biological history of the prehistoric valley groups in the context of their interaction with culturally more developed highland populations. From a total of 97 samples from 83 individuals, 68 samples (61 individuals) yielded amplifications for the fragments that harbor classical mtDNA markers. The haplogroup distribution among the total sample was as follows: 26.2%, haplogroup A; 34.4%, haplogroup B; 14.8%, haplogroup C; 3.3%, haplogroup D; and 21.3%, other haplogroups. Haplogroup B tended to increase, and haplogroup A to decrease during a 3,900-year time interval. The sequence data are congruent with the haplogroup analysis. In fact, the sequencing of hypervariable region I of 30 prehistoric individuals revealed 43 polymorphic sites. Sequence alignment and subsequent phylogenetic tree construction showed two major clusters associated with the most common restriction haplogroups. Individuals belonging to haplogroups C and D tended to cluster together with nonclassical lineages.

Genetic analysis of modern and historical burned human remains

Burning of corpses is a well-known funeral procedure that has been performed for a long time in many cultures. Nowadays more and more corpses are burned in crematories and buried in urns, often for practical and financial reasons. In some scientific, criminal or civil cases even after cremation there is the need of genetic investigations for identification or paternity testing. Furthermore, burned remains are the only remains left in North Europe from 1200 BC to 500 AD. This makes genetic investigation of those materials interesting for anthropological reasons. We present on one hand a systematic investigation of 10 corpses before and after the cremation and on the other hand the analysis of seven historical remains representing the bronze age. We chose the ground bone powder and the less destroyed bone parts respectively and employed a slightly modified commercially available DNA extraction method. The presence of human nuclear and mitochondrial DNA was tested by a simple but highly sensitive Duplex-PCR. DNA quantification was done using real time PCR, and genetic typing was tried out using the AmpFISTR Identifiler Multiplex Kit, followed by an automatic analysis on an AbiPrism310.

Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: Evolutionary and demographic evidence

A number of important insights into the peopling of the New World have been gained through molecular genetic studies of Siberian and Native American populations. While there is no complete agreement on the interpretation of the mitochondrial DNA (mtDNA) and Y chromosome (NRY) data from these groups, several generalizations can be made. To begin with, the primary migration of ancestral Asians expanded from south-central Siberia into the New World and gave rise to ancestral Amerindians. The initial migration seems to have occurred between 20,000-15,000 calendar years before present (cal BP), i.e., before the emergence of Clovis lithic sites (13,350-12,895 cal BP) in North America. Because an interior route through northern North America was unavailable for human passage until 12,550 cal BP, after the last glacial maximum (LGM), these ancestral groups must have used a coastal route to reach South America by 14,675 cal BP, the date of the Monte Verde site in southern Chile. The initial migration appears to have brought mtDNA haplogroups A-D and NRY haplogroups P-M45a and Q-242/Q-M3 to the New World, with these genetic lineages becoming widespread in the Americas. A second expansion that perhaps coincided with the opening of the ice-free corridor probably brought mtDNA haplogroup X and NRY haplogroups P-M45b, C-M130, and R1a1-M17 to North and Central America. Finally, populations that formerly inhabited Beringia expanded into northern North America after the LGM, and gave rise to Eskimo-Aleuts and Na-Dené Indians.

Nuclear and mitochondrial DNA analysis of a 2,000-year-old necropolis in the Egyin Gol Valley of Mongolia

DNA was extracted from the skeletal remains of 62 specimens excavated from the Egyin Gol necropolis, in northern Mongolia. This burial site is linked to the Xiongnu period and was used from the 3rd century b.c. to the 2nd century a.d. Three types of genetic markers were used to determine the genetic relationships between individuals buried in the Egyin Gol necropolis. Results from analyses of autosomal and Y chromosome short tandem repeats, as well as mitochondrial DNA, showed close relationships between several specimens and provided additional background information on the social organization within the necropolis as well as the funeral practices of the Xiongnu people. To the best of our knowledge, this is the first study using biparental, paternal, and maternal genetic systems to reconstruct partial genealogies in a protohistoric necropolis.

Native American mtDNA prehistory in the American Southwest

This study examines the mtDNA diversity of the proposed descendants of the multiethnic Hohokam and Anasazi cultural traditions, as well as Uto-Aztecan and Southern-Athapaskan groups, to investigate hypothesized migrations associated with the Southwest region. The mtDNA haplogroups of 117 Native Americans from southwestern North America were determined. The hypervariable segment I (HVSI) portion of the control region of 53 of these individuals was sequenced, and the within-haplogroup diversity of 18 Native American populations from North, Central, and South America was analyzed. Within North America, populations in the West contain higher amounts of diversity than in other regions, probably due to a population expansion and high levels of gene flow among subpopulations in this region throughout prehistory. The distribution of haplogroups in the Southwest is structured more by archaeological tradition than by language. Yumans and Pimans exhibit substantially greater genetic diversity than the Jemez and Zuni, probably due to admixture and genetic isolation, respectively. We find no evidence of a movement of mtDNA lineages northward into the Southwest from Central Mexico, which, in combination with evidence from nuclear markers, suggests that the spread of Uto-Aztecan was facilitated by predominantly male migration. Southern Athapaskans probably experienced a bottleneck followed by extensive admixture during the migration to their current homeland in the Southwest.

Mitochondrial genome diversity of Native Americans supports a single early entry of founder populations into America

There is general agreement that the Native American founder populations migrated from Asia into America through Beringia sometime during the Pleistocene, but the hypotheses concerning the ages and the number of these migrations and the size of the ancestral populations are surrounded by controversy. DNA sequence variations of several regions of the genome of Native Americans, especially in the mitochondrial DNA (mtDNA) control region, have been studied as a tool to help answer these questions. However, the small number of nucleotides studied and the nonclocklike rate of mtDNA control-region evolution impose several limitations to these results. Here we provide the sequence analysis of a continuous region of 8.8 kb of the mtDNA outside the D-loop for 40 individuals, 30 of whom are Native Americans whose mtDNA belongs to the four founder haplogroups. Haplogroups A, B, and C form monophyletic clades, but the five haplogroup D sequences have unstable positions and usually do not group together. The high degree of similarity in the nucleotide diversity and time of differentiation (i.e., approximately 21,000 years before present) of these four haplogroups support a common origin for these sequences and suggest that the populations who harbor them may also have a common history. Additional evidence supports the idea that this age of differentiation coincides with the process of colonization of the New World and supports the hypothesis of a single and early entry of the ancestral Asian population into the Americas.

Authenticating ancient human mitochondrial DNA

The use of ancient DNA techniques in human studies has been hampered by problems of contamination with modern human DNA. The main problem has been that the object of study belongs to the same species as the observer, and the complete elimination of the contamination risk is seemingly unlikely. Contamination has even been detected in the most specialized laboratories in this field. In these kinds of studies it is therefore very important to detect contamination and to distinguish contaminants from authentic results. Here, we report the use of a strategy to authenticate the identity of ancient mitochondrial DNA (mtDNA), based on the previously established relationship between D-loop sequence substitutions and haplogroup-specific restriction site changes. Forty-four individuals from a 16th-century necropolis were analyzed, from which 28 control region sequences were obtained. These sequences were preclassified into haplogroups, according to the observed motifs. Subsequently, the DNA extracts from which the sequences were obtained, along with independent extracts of subsets of the same individuals, were subjected to restriction fragment length polymorphism (RFLP) analysis to compare and corroborate the results. Using this approach, 24 sequences were authenticated, while two were discarded because of result mismatches. The final distribution of the haplogroups in the sample, and the differences in the sequences, are two additional criteria of authentication.

Absence of the 9-bp deletion of mitochondrial DNA in pre-Hispanic inhabitants of Argentina

We investigated the incidence of the Region V mitochondrial DNA 9-base-pair (bp) deletion from human remains recovered from several archaeological sites and contexts throughout Argentina. Of the 34 samples analyzed, 24 yielded DNA extractions that gave clear amplification results. All of the individuals carried two repeats of the 9 bp, one of which has been shown to be deleted in some individuals of Asian origin and defines mitochondrial lineage B. Although most of the modern Amerindian groups in the region exhibit the deletion in high frequencies, the absence of the 9-bp deletion among ancient populations of South America seems to be the rule rather than the exception, as was reported by several studies involving extinct populations. The evidence gathered until now suggests that the earliest settlers of this region of South America did not carry mitochondrial lineage B.

Brief communication: paleoanthropology and the population genetics of ancient genes

The Mezmaiskaya cave mtDNA is similar in many ways to the Feldhofer cave Neandertal sequence and the more recently obtained Vindija cave sequence. If we accept the contention that the Mezmaiskaya cave specimen is a Neandertal infant, its mtDNA provides no new information about the fate of the European Neandertals. However, there is reason to believe that the Mezmaiskaya cave infant is not a Neandertal, and this places its importance in another light, because it delimits the possible hypotheses of Neandertal and recent human genetic relationships. One possibility is a that the pattern found in ancient mtDNA results from the replacement of an isolated gene pool (Neandertals) by one of its contemporaries (modern humans). A second possibility is natural selection expressed as the substitution of an advantageous mtDNA variant within a single large species, including both Neandertals and modern humans. The geologic, archaeological, and dating evidence shows the Mezmaiskaya cave infant to be a burial from a level even more recent than the Upper Paleolithic preserved at the site, and its anatomy does not contradict the assessment that the Mezmaiskaya cave infant is not a Neandertal. Therefore, the second pattern can be favored over the first.

Evolutionary genetics. Europeans trace ancestry to Paleolithic people

Y chromosome data show that living Europeans have deep roots in the region--and researchers say genetic markers may be linked to cultures known from archaeological remains. In a report on page 1155, an international team reports that a wealth of data from the Y chromosome show that more than 80% of European men have inherited their Y chromosomes--which are transmitted only from father to son--from Paleolithic ancestors who lived 25,000 to 40,000 years ago. Thus, the genetic template for European men was set as early as 40,000 years ago, then modified--but not recast--by the Neolithic farmers who arrived in the region about 10,000 years ago.