Ancient DNA in anthropology: methods, applications, and ethics

Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley

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.

Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia

Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.

Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA

The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from 'wildlife' environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.

Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide

Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.

Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives

Over the past two decades, the study of ancient genomes from Ancestral humans, or human paleogenomic research, has expanded rapidly in both scale and scope. Ethical discourse has subsequently emerged to address issues of social responsibility and scientific robusticity in conducting research. Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among existing guidelines, while addressing core issues such as consent, destructive research methods, and data access and management. Currently, there is a dissonance between guidelines that focus on scientific outcomes and those that hold scientists accountable to stakeholder communities, such as descendants. Thus, we provide additional tools to navigate the complexities of ancient DNA research while centering engagement with stakeholder communities in the scientific process. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Ethics of DNA research on human remains: five globally applicable guidelines

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

A novel method of male sex identification of human ancient skeletal remains

Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.

The problem with petrous? A consideration of the potential biases in the utilization of pars petrosa for ancient DNA analysis

Advances in NGS sequencing technologies, improved laboratory protocols and new bioinformatic workflows have seen huge increases in ancient DNA (aDNA) research on archaeological materials. A large proportion of aDNA work now utilizes the petrous portion of the temporal bone (pars petrosa), which is recognized as an excellent skeletal element for long-term ancient endogenous (host) DNA survival. This has been significant due to the often low endogenous content of other skeletal elements, meaning that large amounts of sequencing are frequently required to obtain sufficient genetic coverage. However, exclusive sampling of the petrous for aDNA analysis introduces a new set of potential biases into our scientific studies - and these issues are yet to be considered by ancient DNA researchers. This paper aims to outline the possible biases of utilizing petrous bones to undertake aDNA analyses and highlight how these complications may potentially be overcome in future research.

[Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA]

INTRODUCTION

Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances.

Biohistorical materials and contemporary privacy concerns-the forensic case of King Albert I

The rapid advancement of technology in genomic analysis increasingly allows researchers to study human biohistorical materials. Nevertheless, little attention has been paid to the privacy of the donor's living relatives and the negative impact they might experience from the (public) availability of genetic results, even in cases of scientific, forensic or historical relevance. This issue has become clear during a cold case investigation of a relic attributed to Belgian King and World War I-hero Albert I who died, according to the official version, in a solo climbing accident in 1934. Authentication of the relic with blood stains assigned to the King and collected on the place where his body was discovered is recognised as one of the final opportunities to test the plausibility of various conspiracy theories on the King's demise. While the historical value and current technological developments allow the genomic analysis of this relic, publication of genetic data would immediately lead to privacy concerns for living descendants and relatives of the King, including the Belgian and British royal families, even after more than 80 years. Therefore, the authentication study of the relic of King Albert I has been a difficult exercise towards balancing public research interests and privacy interests. The identification of the relic was realised by using a strict genetic genealogical approach including Y-chromosome and mitochondrial genome comparison with living relatives, thereby limiting the analysis to genomic regions relevant for identification. The genetic results combined with all available historical elements concerning the relic, provide strong evidence that King Albert I was indeed the donor of the blood stains, which is in line with the official climbing accident hypothesis and contradicts widespread 'mise-en-scène' scenarios. Since publication of the haploid data of the blood stains has the potential to violate the privacy of living relatives, we opted for external and independent reviewing of (the quality of) our data and statistical interpretation by external forensic experts in haploid markers to guarantee the objectivity and scientific accuracy of the identification data analysis as well as the privacy of living descendants and relatives. Although the cold case investigation provided relevant insights into the circumstances surrounding the death of King Albert I, it also revealed the insufficient ethical guidance for current genomic studies of biohistorical material.

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

OBJECTIVES

Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis.

MATERIALS AND METHODS

Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing.

RESULTS

Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth.

DISCUSSION

Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.

A code of ethics for evidence-based research with ancient human remains

As clinical research constantly advances and the concept of evolution becomes a strong and influential part of basic medical research, the absence of a discourse that deals with the use of ancient human remains in evidence-based research is becoming unbearable. While topics such as exhibition and excavation of human remains are established ethical fields of discourse, when faced with instrumentalization of ancient human remains for research (i.e., ancient DNA extractions for disease marker analyses) the answers from traditional ethics or even more practical fields of bio-ethics or more specific biomedical ethics are rare to non-existent. The Centre for Evolutionary Medicine at the University of Zurich solved their needs for discursive action through the writing of a self-given code of ethics which was written in dialogue with the researchers at the Institute and was published online in Sept. 2011: http://evolutionäremedizin.ch/coe/. The philosophico-ethical basis for this a code of conduct and ethics and the methods are published in this article.

Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing

While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.

AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.

Difficulties of sex determination from forensic bone degraded DNA: A comparison of three methods

Sex determination is of paramount importance in forensic anthropology. Numerous anthropological methods have been described, including visual assessments and various measurements of bones. Nevertheless, whatever the method used, the percentage of correct classification of a single bone usually varies between 80% and 95%, due to significant intra- and inter-population variations, and sometimes variations coming from secular trends. DNA is increasingly used in a forensic context. But forensic DNA extraction from bone raises several issues, because the samples are very often badly altered and/or in very small quantity. Nuclear DNA is difficult to get from degraded samples, according to low copy number, at least in comparison with mitochondrial DNA. In a forensic context (as in a paeleoanthropological context) DNA sex determination is usually complicated by the weak amount of DNA, the degraded nature of nucleic acids, the presence of enzymatic inhibitors in DNA extracts, the possible faint amplification of Y band and the risk of contamination during either excavation or manipulation of samples. The aim of this work was to compare three methods of DNA sex determination from bones: procedure #1 using a single PCR amplification, procedure #2 using a double PCR amplification, and procedure #3 adding bleaching for decontamination of the bone, instead of simply rubbing the bone. These processes were applied to samples of bones (49 samples coming from 39 individuals) that were in various states of post mortem alteration. The main results are the following. (i) No DNA could be extracted from three skulls (parietal bones, mastoid process), the compact bone of one rib, and the diaphysis of one femur; (ii) there was a contamination in three skulls; and (iii) the Y band did not appear in two male cases, with one of the three procedures (male tibia, procedure #2) and with procedures #2 and #3 (male femur). This study emphasises the main issue while working with altered bones: the impossibility to extract DNA in some cases, and, worth of all, the contamination of the sample or the faint amplification of Y band which leads to a wrong sex answer. Multiple and significant precautions have to be taken to avoid such difficulties.

Identification of ancient Olea europaea L. and Cornus mas L. seeds by DNA barcoding

The analysis of ancient DNA (aDNA) provides archaeologists and anthropologists with innovative, scientific and accurate data to study and understand the past. In this work, ancient seeds, found in the "Mora Cavorso" archaeological site (Latium, Central Italy), were analyzed to increase information about Italian Neolithic populations (plant use, agriculture, diet, trades, customs and ecology). We performed morphological and genetic techniques to identify fossil botanical species. In particular, this study also suggests and emphasizes the use of DNA barcode method for ancient plant sample analysis. Scanning electron microscope (SEM) observations showed seed compact structure and irregular surface but they did not permit a precise nor empirical classification: so, a molecular approach was necessary. DNA was extracted from ancient seeds and then it was used, as template, for PCR amplifications of standardized barcode genes. Although aDNA could be highly degraded by the time, successful PCR products were obtained, sequenced and compared to nucleotide sequence databases. Positive outcomes (supported by morphological comparison with modern seeds, geographical distribution and historical data) indicated that seeds could be identified as belonging to two plant species: Olea europaea L. and Cornus mas L.

Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA

Museum curators and living communities are sometimes reluctant to permit ancient DNA (aDNA) studies of human skeletal remains because the extraction of aDNA usually requires the destruction of at least some skeletal material. Whether these views stem from a desire to conserve precious materials or an objection to destroying ancestral remains, they limit the potential of aDNA research. To help address concerns about destructive analysis and to minimize damage to valuable specimens, we describe a nondestructive method for extracting DNA from ancient human remains. This method can be used with both teeth and bone, but it preserves the structural integrity of teeth much more effectively than that of bone. Using this method, we demonstrate that it is possible to extract both mitochondrial and nuclear DNA from human remains dating between 300 BC and 1600 AD. Importantly, the method does not expose the remains to hazardous chemicals, allowing them to be safely returned to curators, custodians, and/or owners of the samples. We successfully amplified mitochondrial DNA from 90% of the individuals tested, and we were able to analyze 1-9 nuclear loci in 70% of individuals. We also show that repeated nondestructive extractions from the same tooth can yield amplifiable mitochondrial and nuclear DNA. The high success rate of this method and its ability to yield DNA from samples spanning a wide geographic and temporal range without destroying the structural integrity of the sampled material may make possible the genetic study of skeletal collections that are not available for destructive analysis.

Ancient DNA perspectives on American colonization and population history

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.

A western Eurasian male is found in 2000-year-old elite Xiongnu cemetery in Northeast Mongolia

We analyzed mitochondrial DNA (mtDNA), Y-chromosome single nucleotide polymorphisms (Y-SNP), and autosomal short tandem repeats (STR) of three skeletons found in a 2,000-year-old Xiongnu elite cemetery in Duurlig Nars of Northeast Mongolia. This study is one of the first reports of the detailed genetic analysis of ancient human remains using the three types of genetic markers. The DNA analyses revealed that one subject was an ancient male skeleton with maternal U2e1 and paternal R1a1 haplogroups. This is the first genetic evidence that a male of distinctive Indo-European lineages (R1a1) was present in the Xiongnu of Mongolia. This might indicate an Indo-European migration into Northeast Asia 2,000 years ago. Other specimens are a female with mtDNA haplogroup D4 and a male with Y-SNP haplogroup C3 and mtDNA haplogroup D4. Those haplogroups are common in Northeast Asia. There was no close kinship among them. The genetic evidence of U2e1 and R1a1 may help to clarify the migration patterns of Indo-Europeans and ancient East-West contacts of the Xiongnu Empire. Artifacts in the tombs suggested that the Xiongnu had a system of the social stratification. The West Eurasian male might show the racial tolerance of the Xiongnu Empire and some insight into the Xiongnu society.

The correlation between skeletal weathering and DNA quality and quantity

Mitochondrial DNA analysis of skeletal material is invaluable in forensic identification, although results can vary widely among remains. Previous studies have included bones of different ages, burial conditions, and even species. In the research presented, a collection of human remains that lacked major confounders such as burial age, interment style, and gross environmental conditions, while displaying a very broad range of skeletal degradation, were examined for both mitochondrial DNA (mtDNA) quality and quantity. Overall skeletal weathering, individual bone weathering, and bone variety were considered. Neither skeletal nor bone weathering influenced DNA quality or quantity, indicating that factors that degrade bone do not have the same effect on DNA. In contrast, bone variety, regardless of weathering level, was a significant element in DNA amplification success. Taken together, the results indicate that neither skeletal nor individual bone appearance are reliable indicators of subsequent mtDNA typing outcomes, while the type of bone assayed is.

Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene

Sex identification from skeletal material is of vital importance in order to reconstruct the demographic variables of an individual in forensic genetics and ancient DNA (aDNA) analysis. When the use of conventional methods of sex identification are impossible, molecular analysis of the X and Y chromosomes provides an expedient solution. Two novel systems of molecular sex identification suitable for skeletal material using the amelogenin gene are described, beginning in intron 2-3, spanning exon 3 and ending in intron 3-4. This area was optimal for sexing, as it includes 14 sex-specific polymorphic regions in addition to an indel (insertion or deletion of nucleotides). Once optimised and working with 100% efficiency on the controls, these procedures were applied to a collection of miscellaneous archaeological skeletons (ex situ) sourced from the Raymond Dart Collection of Human Skeletons (Dart Collection). This collection was used to optimise these techniques for skeletal remains derived from an archaeological context. These methods produced 46.66% sex results for the ex situ sample, which is within the normal range for aDNA studies. These new techniques are optimal for sex identification, with both the inherent control of isolating many sex-specific features and combined with the use of sensitive micro-fluidic electrophoresis.

Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age

In 2005 four outstanding multiple burials were discovered near Eulau, Germany. The 4,600-year-old graves contained groups of adults and children buried facing each other. Skeletal and artifactual evidence and the simultaneous interment of the individuals suggest the supposed families fell victim to a violent event. In a multidisciplinary approach, archaeological, anthropological, geochemical (radiogenic isotopes), and molecular genetic (ancient DNA) methods were applied to these unique burials. Using autosomal, mitochondrial, and Y-chromosomal markers, we identified genetic kinship among the individuals. A direct child-parent relationship was detected in one burial, providing the oldest molecular genetic evidence of a nuclear family. Strontium isotope analyses point to different origins for males and children versus females. By this approach, we gain insight into a Late Stone Age society, which appears to have been exogamous and patrilocal, and in which genetic kinship seems to be a focal point of social organization.

Molecular genetic analysis of Wanggu remains, Inner Mongolia, China

The Wanggu tribe, which contributed significantly to the foundation of the Yuan Dynasty, was one of the groups living on the Mongolian steppes during the Jin-Yuan period (AD 1127-1368) of Chinese history. However, there has been both archaeological and historical dispute regarding the origin of the ancient tribe. Recently, we discovered human remains of the Wanggu tribe in the Chengbozi cemetery in the Siziwang Banner of Inner Mongolia, China. To investigate the genetic structure of the Wanggu tribe and to trace the origins of the tribe at a molecular level, we analyzed the control-region sequences and coding regions of mitochondrial DNA (mtDNA) from the remains by direct sequencing and restriction-fragment length polymorphism analysis. In combination with mtDNA data of 15 extant Eurasian populations, we performed phylogenetic analysis and multidimensional scaling analysis. Our results show that the genetic structure of the Wanggu tribe in the Jin-Yuan period is a complex matriline, containing admixture from both Asian and European populations. In addition, we reveal that on the basis of mtDNA data, the ancient tribe may share a recent common ancestor with the Turkic-speaking Uzbeks and Uighurs.

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.

Phenotypic approaches for understanding patterns of intracemetery biological variation

This paper reviews studies of phenotypic inheritance and microevolutionary processes in archaeological populations using data on cranial and dental phenotypic variation, often referred to as paleogenetics or biodistance analysis. The estimation of biological distances between populations, or among individuals within populations, is one component of bioarchaeological research on past populations. In this overview, five approaches that focus on morphological variation within cemeteries are summarized: kinship and cemetery structure analysis, postmarital residence analysis, sample aggregate phenotypic variability, temporal microchronology, and age-structured phenotypic variation. Previous research, theoretical justifications, and methods are outlined for each topic. Case studies are presented that illustrate these theoretical and methodological bases, as well as demonstrate the kinds of inferences possible using these approaches. Kinship and cemetery structure analysis seeks to identify the members of family groups within larger cemeteries or determine whether cemeteries were kin-structured. Analysis of sex-specific phenotypic variation allows estimation of postmarital residence practices, which is important for understanding other aspects of prehistoric social organization. Analysis of aggregate phenotypic variability can be used to infer site formation processes or cemetery catchment area. The study of temporal microchronologies can be used to evaluate provisional archaeological chronologies or study microevolutionary processes such as adaptive selection or changing patterns of gene flow. Finally, age-structured phenotypic variation can be reflective of selection processes within populations or it can be used as a measure of morbidity, growth arrest, and early mortality within past populations. Use of phenotypic data as a genotypic proxy is theoretically sound, even at small scales of analysis.

Use of bleach to eliminate contaminating DNA from the surface of bones and teeth

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.

Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies

The length of the human generation interval is a key parameter when using genetics to date population divergence events. However, no consensus exists regarding the generation interval length, and a wide variety of interval lengths have been used in recent studies. This makes comparison between studies difficult, and questions the accuracy of divergence date estimations. Recent genealogy-based research suggests that the male generation interval is substantially longer than the female interval, and that both are greater than the values commonly used in genetics studies. This study evaluates each of these hypotheses in a broader cross-cultural context, using data from both nation states and recent hunter-gatherer societies. Both hypotheses are supported by this study; therefore, revised estimates of male, female, and overall human generation interval lengths are proposed. The nearly universal, cross-cultural nature of the evidence justifies using these proposed estimates in Y-chromosomal, mitochondrial, and autosomal DNA-based population divergence studies.

Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity

Research into ancient mitochondrial DNA is plagued by contamination, post mortem damage, and other artefacts. The stringent set of controls suggested by Cooper and Poinar a few years ago are, however, rarely followed in practice, and even when applied carefully, these criteria need not be sufficient to guarantee authenticity. The fairly relaxed prerequisites now common for ancient population studies have opened the door for all kinds of contamination and sequencing errors to enter ancient mtDNA data. To reject or question authenticity of particular sequencing results a posteriori, one can follow similar strategies of focused database comparisons that have proven to be effective and successful in the case of flawed modern mtDNA data.

Predictive accuracy of sexing the mandible by ramus flexure

Loth & Henneberg (Am J Phys Anthrop 99 (1996) 473) described a single morphological indicator of sexual dimorphism, namely the presence or absence of flexure on the posterior border of the mandible, with a predictive accuracy of 90.6-99.0%. In the other studies, which have criticized mandibular ramus flexure as sex indicator in adult and fossils specimens by the same method, the accuracy of sexing was found between 59.0% and 80.4% which is well below the reported 90.6-99.0% (Am J Phys Anthrop 107 (1998) 363; Am J Phys Anthrop 111 (2000) 573; Am J Phys Anthrop 111 (2000) 429; Homo 53 (2002) 97). It was indicated that the method sexed males more reliably than females and consistency was low. In the current blind test, 120 mandibles from forensic cases were examined for the presence or absence of mandibular ramus flexure. Virtually identical results were obtained when a second observer examined the same sample of mandibles. The results were then compared to records of the same cases resulting in 85.8% accuracy for the total sample. A marked difference was observed between sexes where the ramus shape was diagnostic for 92.6% of the males but for only 60.0% of the females (p < 0.001). When mandibles with excessive tooth loss (more than two molars missing) (n = 35) were removed from the sample (in normative sample), the overall predictive value increased to 90.6% (95.6% accuracy in males and 70.6% in females). Our results confirm that there are marked differences between the sexes in the predictive accuracy and this indicator is better in mandibles without molar tooth loss as mentioned by Loth & Henneberg. They also pointed out that the tooth loss is a potential source of error. On the other hand, in this study, there were no sexing errors when mandibles which ramus shape scores -1, 0 and +1 were extracted from the normative sample as the "sex indeterminate group". This study suggests that further assessment should be made only when both rami are available for observation, and the mandible shows either bilateral flexure (+2) or bilateral non-flexure (-2). The consideration of this new categorization can also be useful when using Loth & Henneberg's method.

Federal Repatriation Legislation and the Role of Physical Anthropology in Repatriation

Two laws governing the disposition of Native American human remains in museums and institutions have had a profound impact on anthropology, and especially physical anthropology. In contrast to the perception of constant conflict between Native Americans and physical anthropologists, the repatriation process based on these laws has been in large part harmonious between institutions and Native peoples in the US. Despite misconceptions, the Native American Graves Protection and Repatriation Act (NAPGRA; 25 United States Code (U.S.C.) 3001-3013) was not intended to halt further research on Native American remains in museums. In fact, court decisions have affirmed that the documentation of human remains produces information no other methods can provide, and provides necessary evidence to be incorporated and weighed, along with other evidence, in evaluating "cultural affiliation," the legal term for the required connection from federally recognized Native American groups to their ancestors. The wide variety of osteological data collected at the National Museum of Natural History (NMNH), Smithsonian Institution, have proven indispensable when evaluating cultural affiliation, especially when other information sources are unhelpful or ambiguous, and provide an empirical basis for determining the ancestry of individuals whose remains will be discovered in the future. To date, the claim-driven process at the NMNH has resulted in the affiliation and repatriation of more Native American remains than any other institution in the country. Repatriation experiences at the NMNH demonstrate the changing relationships between museums and Native peoples, the continuing important contributions that physical anthropology makes to the repatriation process, and the importance of physical anthropology in understanding the recent and ancient history of North America.

Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA

During the past 10 years palaeomicrobiology, a new scientific discipline, has developed. The study of ancient pathogens by direct detection of their DNA has answered several historical questions and shown changes to pathogens over time. However, ancient DNA (aDNA) continues to be controversial and great care is needed to provide valid data. Here we review the most successful application of the technology, which is the study of tuberculosis. This has provided direct support for the current theory of Mycobacterium tuberculosis evolution, and suggests areas of investigation for the interaction of M tuberculosis with its host.