Recommendations for Sustainable Ancient DNA Research in the Global South: Voices From a New Generation of Paleogenomicists.

Paleogenomics - the study of ancient genomes - has made significant contributions, especially to our understanding of the evolutionary history of humans. This knowledge influx has been a direct result of the coupling of next-generation sequencing with improved methods for DNA recovery and analysis of ancient samples. The appeal of ancient DNA studies in the popular media coupled with the trend for such work to be published in "high impact" journals has driven the amassing of ancestral human remains from global collections, often with limited to no engagement or involvement of local researchers and communities. This practice in the paleogenomics literature has led to limited representation of researchers from the Global South at the research design and subsequent stages. Additionally, Indigenous and descendant communities are often alienated from popular and academic narratives that both involve and impact them, sometimes adversely. While some countries have safeguards against 'helicopter science', such as federally regulated measures to protect their biocultural heritage, there is variable oversight in others with regard to sampling and exportation of human remains for destructive research, and differing requirements for accountability or consultation with local researchers and communities. These disparities reveal stark contrasts and gaps in regional policies that lend themselves to persistent colonial practices. While essential critiques and conversations in this sphere are taking place, these are primarily guided through the lens of US-based heritage legislation such as the Native American Graves and Protection Act (NAGPRA). In this article, we aim to expand the scope of ongoing conversations by taking into account diverse regional contexts and challenges drawing from our own research experiences in the field of paleogenomics. We emphasize that true collaborations involve knowledge sharing, capacity building, mutual respect, and equitable participation, all of which take time and the implementation of sustainable research methods; amass-and-publish strategy is simply incompatible with this ethos.

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America.

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes-7 of which are novel-from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago.

A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations.

The rulers of the Inka empire conquered approximately 2 million km2 of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.

Detection of Vibrio cholerae aDNA in human burials from the fifth cholera pandemic in Argentina (1886-1887 AD).

OBJECTIVE: Detecting traces of ancient DNA of Vibrio cholerae to provide genetic information associated with the fifth cholera pandemic. MATERIALS: Sediment samples from the sacral foramina of four individuals were analyzed, recovered from a mass grave near an institution dedicated exclusively to the isolation and treatment of citizens infected with cholera in the late 19th century in the city of Cordoba, Argentina. METHODS: Paleogenetic techniques (ancient DNA extraction, PCR amplification, and Sanger sequencing) were applied. Specific primers for Vibrio cholerae (VCR, ctxA, ctxB, and tcpA) were designed. RESULTS: By amplifying and sequencing the Vibrio cholerae repeats fragment, the infection in at least one individual was confirmed. CONCLUSIONS: The synthesis of the paleogenetic results with the archaeological and historical evidence strongly supports that at least one individual from the mass grave in Cordoba, Argentina, was a victim of the fifth cholera pandemic. SIGNIFICANCE: Confirming the presence of the disease through multiple lines of evidence, including genetic, archaeological, and historical analyses, strengthens and affirms our understanding of the presence, effects, and potential evolutionary paths of the disease in the past. LIMITATIONS: Vibrio cholerae repeats were sequenced in one individual, while the remaining genes could not be amplified, which is likely related to gene copy number. SUGGESTIONS FOR FUTURE RESEARCH: Paleogenetic examination of ancient samples from different locations will broaden our understanding of the origin, evolution, and past dissemination of Vibrio cholerae epidemic strains.

Biological kinship in 750 year old human remains from Central Argentina with signs of interpersonal violence.

Human skeletal remains of an adult male (20-24 years old) and a juvenile (4-8 years old), dated to 750 ± 85 14C years BP, were found on the southern margin of Mar Chiquita Lagoon (Córdoba, Argentina). Both individuals show signs of being victims of interpersonal violence, with arrowheads associated with the remains and perimortem lesions on the juvenile, as well as an unusual form of burial, with the juvenile partially overlapped with the adult. The aim of this work is to study a possible kin relationship between these two individuals through ancient DNA analysis. Biological kinship was evaluated by autosomal and Y-chromosome STR (short tandem repeat) typing, PCR-APLP for SNP determination and hypervariable region I sequencing of the mitochondrial DNA. Genetic analyses indicated that these individuals shared the same Y-chromosomal haplotype but different mitochondrial lineages. The likelihood ratio based on autosomal loci indicates that the genetic profiles of the human remains would be more likely to be that indicating a father-son bond. The paleogenetic approach combined with forensic genetic methods applied to this study allowed us to confirm a hypothesis that originated in bioarchaeological evidence. This study constitutes a unique case in Argentina of kinship determination based on DNA profiles of human remains in an archaeological context of interpersonal violence. It is important to highlight the contribution made by these studies to address topics usually hidden in bioarchaeological studies, such as community organization, cultural customs and mortuary practices.

Ancient mitochondrial DNA and ancestry of Paquimé inhabitants, Casas Grandes (A.D. 1200-1450).

OBJECTIVES: The Casas Grandes (Paquimé) culture, located in the Northwest of Chihuahua, Mexico reached its apogee during the Medio Period (A.D. 1200-1450). Paquimé was abandoned by the end of the Medio Period (A.D. 1450), and the ancestry of its inhabitants remains unsolved. Some authors suggest that waves of Mesoamerican immigrants, possibly merchants, stimulated Paquimé's development during the Medio Period. Archaeological evidence suggests possible ties to groups that inhabited the Southwestern US cultures. This study uses ancient DNA analysis from fourteen samples to estimate genetic affinities of ancient Paquimé inhabitants. MATERIALS AND METHODS: DNA was extracted from 14 dental ancient samples from Paquimé. PCR and Sanger sequencing were used to obtain mitochondrial control region sequences. Networks, PCoA, and Nei genetic distances were estimated to compare Paquimé haplotypes against available past haplotypes data from Southwestern and Mesoamerican groups. RESULTS: Haplogroups were characterized for 11 of the samples, and the results revealed the presence of four distinct Amerindian mitochondrial lineages: B (n = 5; 45%), A (n = 3; 27%), C (n = 2; 18%) and D (n = 1; 10%). Statistical analysis of the haplotypes, haplogroup frequencies, and Nei genetic distances showed close affinity of Paquimé with Mimbres. DISCUSSION: Although our results provide strong evidence of genetic affinities between Paquimé and Mimbres, with the majority of haplotypes shared or derived from ancient Southwest populations, the causes of cultural development at Paquimé still remain a question. These preliminary results provide evidence in support of other bioarchaeological studies, which have shown close biological affinities between Paquimé and Mimbres, a Puebloan culture, in the Southwestern US.