Ancient nuclear genomes enable repatriation of Indigenous human remains.

After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance. We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods

An assessment of DNA extraction methods from blood-stained soil in forensic science

In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to the presence of inhibitors which limit the effective extraction and amplification of the deoxyribonucleic acid (DNA) required to produce a reportable DNA profile. There are some extraction methods that have been applied to blood-stained soil in forensic science, but these have produced sporadic results. This research has taken a number of different extraction methods from the fields of ancient DNA and environmental DNA and broken them down into the individual steps of pre-treatment, incubation, separation and purification. These steps were assessed independently then combined into various extraction methods to determine the best technique that can effectively and reliably profile human DNA from blood-stained soil. Testing involved assessment of three extraction buffers, (cetyltrimethylammonium bromide, guanidine thiocyanate, and proteinase K), four pre-treatment methods, (polyvinylpyrrolidone, ethylenediaminetetraacetic acid, hydrochloric acid, and sodium hydroxide), three separation steps, (centrifugation, phenol chloroform, and chloroform) and four purification steps, (size exclusion chromatography, bind elute columns, isopropanol precipitation and silica magnetic beads). The most effective procedure was found to be a polyvinylpyrrolidone pre-treatment with a proteinase K extraction buffer followed by magnetic silica bead purification with or without centrifugation. However, centrifugation separation was found to be equally effective after the pre-treatment step as after the incubation step. Our results shows that most of the current forensic procedures would benefit from the addition of a pre-treatment step prior to processing through the automated DNA profiling pipeline.</p

A Community Bioarchaeology Project in the Flinders Group, Queensland, Australia

Bioarchaeological research in Australia has lagged behind that in other regions due to understandable concerns arising from the disregard of Indigenous Australians rights over their ancestors’ remains. To improve this situation, bioarchaeologists working in Australia need to employ more community-oriented approaches to research. This paper reports a project in which we employed such an approach. The project focused on burials in the Flinders Group, Queensland. Traditional Owners played a key role in the excavations and helped devise analyses that would deliver both scientific contributions and socially relevant outcomes. The fieldwork and laboratory analyses yielded a number of interesting results. Most significantly, they revealed that the pattern of mortuary practices recorded by ethnographers in the region in the early 20th century—complex burial of powerful people and simple interment of less important individuals—has a time depth of several hundred years or more. More generally, the project shows that there can be fruitful collaboration between archaeologists and Indigenous communities in relation to the excavation and scientific analysis of Aboriginal ancestral remains.</p

Ancient DNA Insights into Aboriginal Australian Mortuary Practices

Paleogenetics is a relatively new and promising field that has the potential to provide new information about past Indigenous social systems, including insights into the complexity of burial practices. We present results of the first ancient DNA (aDNA) investigation into traditional mortuary practices among Australian Aboriginal people with a focus on North-East Australia. We recovered mitochondrial and Y chromosome sequences from five ancestral Aboriginal Australian remains that were excavated from the Flinders Island group in Cape York, Queensland. Two of these individuals were sampled from disturbed beach burials, while the other three were from bundle burials located in rock shelters. Genomic analyses showed that individuals from all three rock shelter burials and one of the two beach burials had a close genealogical relationship to contemporary individuals from communities from Cape York. In contrast the remaining male individual, found buried on the beach, had a mitochondrial DNA sequence that suggested that he was not from this location but that he was closely related to people from central Queensland or New South Wales. In addition, this individual was associated with a distinctive burial practice to the other four people. It has been suggested that traditionally non-locals or lower status individuals were buried on beaches. Our findings suggest that theories put forward about beach burials being non-local, or less esteemed members of the community, can potentially be resolved through analyses of uniparental genomic data. Generally, these results support the suggestion often derived from ethnohistoric accounts that inequality in Indigenous Australian mortuary practices might be based on the status, sex, and/or age of individuals and may instead relate to place of geographic origin. There is, however, some departure from the traditional ethnohistoric account in that complex mortuary internments were also offered to female individuals of the community, with genomic analyses helping to confirm that the gender of one of the rockshelter internments was that of a young female

A contextualised review of genomic evidence for gene flow events between Papuans and Indigenous Australians in Cape York, Queensland

It has long been accepted that the Indigenous groups of Australia's Cape York Peninsula have numerous cultural traits that were adopted from people in New Guinea and/or the Torres Strait Islands after the formation of the Torres Strait around 8000 years ago. However, opinions differ on whether the movement of the traits in question was accompanied by gene flow events. Some argue for a significant amount of gene flow resulting from voyages from New Guinea and the Torres Strait Islands down the east coast of Cape York. Others contend that there was only contact at the northern end of the Cape and that the cultural traits spread through down-the-line transmission. In recent years partnerships between Australian institutions and Indigenous communities in Cape York have led to new genetic research that provides benefits to both parties. We review the currently available genetic data that have the potential to shed light on this issue, concluding that the data are inconsistent with significant gene flow between Indigenous Australians and Papuan people between 8000 years ago and the colonial period. There are indications of gene flow, but it most likely occurred in the Pleistocene rather than the Holocene. As such, the currently available genomic data do not support the hypothesis that the diffusion of cultural traits from New Guinea and/or the Torres Strait Islands into Cape York was accompanied by gene flow. The data suggest instead that the cultural traits most probably spread via down-the-line trade, exchange, and imitation. Our review highlights the gaps in the available genomic information from contemporary and ancestral descendants of Australia's first settlers, and we suggest that researchers adopt a more collaborative approach, involving Indigenous communities and their knowledge in project design, data collection, and dissemination, in future genomic studies in Australia.</p

A contextualised review of genomic evidence for gene flow events between Papuans and Indigenous Australians in Cape York, Queensland

It has long been accepted that the Indigenous groups of Australia's Cape York Peninsula have numerous cultural traits that were adopted from people in New Guinea and/or the Torres Strait Islands after the formation of the Torres Strait around 8000 years ago. However, opinions differ on whether the movement of the traits in question was accompanied by gene flow events. Some argue for a significant amount of gene flow resulting from voyages from New Guinea and the Torres Strait Islands down the east coast of Cape York. Others contend that there was only contact at the northern end of the Cape and that the cultural traits spread through down-the-line transmission. In recent years partnerships between Australian institutions and Indigenous communities in Cape York have led to new genetic research that provides benefits to both parties. We review the currently available genetic data that have the potential to shed light on this issue, concluding that the data are inconsistent with significant gene flow between Indigenous Australians and Papuan people between 8000 years ago and the colonial period. There are indications of gene flow, but it most likely occurred in the Pleistocene rather than the Holocene. As such, the currently available genomic data do not support the hypothesis that the diffusion of cultural traits from New Guinea and/or the Torres Strait Islands into Cape York was accompanied by gene flow. The data suggest instead that the cultural traits most probably spread via down-the-line trade, exchange, and imitation. Our review highlights the gaps in the available genomic information from contemporary and ancestral descendants of Australia's first settlers, and we suggest that researchers adopt a more collaborative approach, involving Indigenous communities and their knowledge in project design, data collection, and dissemination, in future genomic studies in Australia

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

Revisiting the harem conspiracy and death of Ramesses III : Anthropological, forensic, radiological, and genetic study

Objective: To investigate the true character of the harem conspiracy described in the Judicial Papyrus of Turin and determine whether Ramesses III was indeed killed. Design: Anthropological, forensic, radiological, and genetic study of the mummies of Ramesses III and unknown man E, found together and taken from the 20th dynasty of ancient Egypt (circa 1190-1070 BC). Results: Computed tomography scans revealed a deep cut in Ramesses III's throat, probably made by a sharp knife. During the mummification process, a Horus eye amulet was inserted in the wound for healing purposes, and the neck was covered by a collar of thick linen layers. Forensic examination of unknown man E showed compressed skin folds around his neck and a thoracic inflation. Unknown man E also had an unusual mummification procedure. According to genetic analyses, both mummies had identical haplotypes of the Y chromosome and a common male lineage. Conclusions: This study suggests that Ramesses III was murdered during the harem conspiracy by the cutting of his throat. Unknown man E is a possible candidate as Ramesses III's son Pentawere.</p

Ancestry and pathology in King Tutankhamun's family

Context: The New Kingdom in ancient Egypt, comprising the 18th, 19th, and 20th dynasties, spanned the mid-16th to the early 11th centuries BC. The late 18th dynasty, which included the reigns of pharaohs Akhenaten and Tutankhamun, was an extraordinary time. The identification of a number of royal mummies from this era, the exact relationships between some members of the royal family, and possible illnesses and causes of death have been matters of debate. Objectives: To introduce a new approach to molecular and medical Egyptology, to determine familial relationships among 11 royal mummies of the New Kingdom, and to search for pathological features attributable to possible murder, consanguinity, inherited disorders, and infectious diseases. Design: From September 2007 to October 2009, royal mummies underwent detailed anthropological, radiological, and genetic studies as part of the King Tutankhamun Family Project. Mummies distinct from Tutankhamun's immediate lineage served as the genetic and morphological reference. To authenticate DNA results, analytical steps were repeated and independently replicated in a second ancient DNA laboratory staffed by a separate group of personnel. Eleven royal mummies dating from circa 1410-1324 BC and suspected of being kindred of Tutankhamun and 5 royal mummies dating to an earlier period, circa 1550-1479 BC, were examined. Main Outcome Measures: Microsatellite-based haplotypes in the mummies, generational segregation of alleles within possible pedigree variants, and correlation of identified diseases with individual age, archeological evidence, and the written historical record. Results: Genetic fingerprinting allowed the construction of a 5-generation pedigree of Tutankhamun's immediate lineage. The KV55 mummy and KV35YL were identified as the parents of Tutankhamun. No signs of gynecomastia and craniosynostoses (eg, Antley-Bixler syndrome) or Marfan syndrome were found, but an accumulation of malformations in Tutankhamun's family was evident. Several pathologies including Köhler disease II were diagnosed in Tutankhamun; none alone would have caused death. Genetic testing for STEVOR, AMA1, or MSP1 genes specific for Plasmodium falciparum revealed indications of malaria tropica in 4 mummies, including Tutankhamun's. These results suggest avascular bone necrosis in conjunction with the malarial infection as the most likely cause of death in Tutankhamun. Walking impairment and malarial disease sustained by Tutankhamun is supported by the discovery of canes and an afterlife pharmacy in his tomb. Conclusion: Using a multidisciplinary scientific approach, we showed the feasibility of gathering data on Pharaonic kinship and diseases and speculated about individual causes of death.</p

Giving it a burl: towards the integration of genetics, isotope chemistry, and osteoarchaeology in Cape York, Tropical North Queensland, Australia

In this paper we outline a worked example of the combined use of genetic data and archaeological evidence. The project focuses on Queensland’s Cape York Peninsula and has two goals. One is to shed new light on the population history of the region. The other is to develop a methodology to facilitate repatriation of the remains of Aboriginal Australians. After providing some background to the project and outlining its main activities, we summarize our key findings to date. Subsequently, we discuss what the project has taught us about the prehistory of Cape York, the potential for DNA research and isotope chemistry to assist research institutions and Aboriginal communities with the repatriation of unaffiliated remains, and the process of conducting combined genetic and archaeological research