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https://hdl.handle.net/2440/74194
2024-03-29T07:00:34ZPaleogenomic study of the Mexican past
https://hdl.handle.net/2440/140015
Title: Paleogenomic study of the Mexican past
Author: Llamas, B.; Roca-Rada, X.
Abstract: The discovery that DNA survives in archaeological remains revolutionized archaeology, anthropology, and evolutionary biology, leading to the establishment of paleogenomics as a bona fide field of research (1). In the context of the Americas, paleogenomic researchers have used ancestral genomic information to reconstruct human history with exquisite detail. However, ethical concerns surrounding practices perceived as extractive and colonizing have sometimes overshadowed this endeavor (2). On page 598 of this issue, Villa-Islas et al. (3) set a standard for how paleogenomics can be conducted in an ethical and sustainable manner. They analyzed ancient DNA retrieved from 27 ancestral humans from eight archaeological sites in Mexico, providing insights into the demographic history of Indigenous populations in Central and North Mexico.2023-01-01T00:00:00ZAllelic bias when performing in-solution enrichment of ancient human DNA
https://hdl.handle.net/2440/139555
Title: Allelic bias when performing in-solution enrichment of ancient human DNA
Author: Davidson, R.; Williams, M.P.; Roca-Rada, X.; Kassadjikova, K.; Tobler, R.; Fehren-Schmitz, L.; Llamas, B.
Abstract: In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.
Description: First published: 15 September 20232023-01-01T00:00:00ZMore than dirt: Sedimentary ancient DNA and Indigenous Australia
https://hdl.handle.net/2440/139116
Title: More than dirt: Sedimentary ancient DNA and Indigenous Australia
Author: Lewis, D.A.; Simpson, R.; Hermes, A.; Brown, A.; Llamas, B.
Abstract: The rise of sedimentary ancient DNA (sedaDNA) studies has opened new possibilities for studying past environments. This groundbreaking area of genomics uses sediments to identify organisms, even in cases where macroscopic remains no longer exist. Managing this substrate in Indigenous Australian contexts, however, requires special considerations. Sediments and soils are often considered as waste by-products during archaeological and paleontological excavations and are not typically regulated by the same ethics guidelines utilised in mainstream 'western' research paradigms. Nevertheless, the product of sedaDNA work-genetic information from past fauna, flora, microbial communities and human ancestors-is likely to be of cultural significance and value for Indigenous peoples. This article offers an opinion on the responsibilities of researchers in Australia who engage in research related to this emerging field, particularly when it involves Indigenous communities. One aspect that deserves consideration in such research is the concept of benefit sharing. Benefit sharing refers to the practice of ensuring that the benefits that arise from research are shared equitably with the communities from which the research data were derived. This practice is particularly relevant in research that involves Indigenous communities, who may have unique cultural and spiritual connections to the research material. We argue that the integration of Traditional Knowledges into sedaDNA research would add enormous value to research and its outcomes by providing genomic outputs alongside and within the rich context of multimillennia oral histories.
Description: First published: 12 July 2023.
OnlinePubl2023-01-01T00:00:00ZQuantitative PCR overestimation of DNA in samples contaminated with tin
https://hdl.handle.net/2440/138733
Title: Quantitative PCR overestimation of DNA in samples contaminated with tin
Author: Bonsu, D.N.O.; Higgins, D.; Simon, C.; Goodwin, C.S.; Henry, J.M.; Austin, J.J.
Abstract: Metals can pose challenges while conducting forensic DNA analysis. The presence of metal ions in evidence-related DNA extracts can degrade DNA or inhibit PCR as applied to DNA quantification (real-time PCR or qPCR) and/or STR amplification, leading to low success in STR profiling. Different metal ions were spiked into 0.2 and 0.5 ng of human genomic DNA in an “inhibition study” and the impact was evaluated by qPCR using the Quantifiler™ Trio DNA Quantification Kit (Thermo Fisher Scientific) and an in-house SYBR Green assay. This study reports on a contradictory finding specific to tin (Sn) ions, which caused at least a 38,000-fold overestimation of DNA concentration when utilizing Quantifiler Trio. This was explained by the raw and multicomponent spectral plots, which indicated that Sn suppresses the Quantifiler Trio passive reference dye (Mustang Purple™, MP) at ion concentrations above 0.1 mM. This effect was not observed when DNA was quantified using SYBR Green with ROX™ as the passive reference, nor when DNA was extracted and purified prior to Quantifiler Trio. The results show that metal contaminants can interfere with qPCR-based DNA quantification in unexpected ways and may be assay dependent. The results also highlight the importance of qPCR as a quality check to determine steps for sample cleanup prior to STR amplification that may be similarly impacted by metal ions. Forensic workflows should recognize the risk of inaccurate DNA quantification of samples that are collected from substrates containing tin.
Description: First published: 16 June 20232023-01-01T00:00:00Z