Australian Centre for Ancient DNA publications
Permanent URI for this collection
Browse
Recent Submissions
Item Metadata only Paleogenomic study of the Mexican past(American Association for the Advancement of Science (AAAS), 2023) Llamas, B.; Roca-Rada, X.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.Item Open Access Allelic bias when performing in-solution enrichment of ancient human DNA(Wiley, 2023) Davidson, R.; Williams, M.P.; Roca-Rada, X.; Kassadjikova, K.; Tobler, R.; Fehren-Schmitz, L.; Llamas, B.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.Item Metadata only More than dirt: Sedimentary ancient DNA and Indigenous Australia(Wiley, 2025) Lewis, D.A.; Simpson, R.; Hermes, A.; Brown, A.; Llamas, B.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.Item Metadata only Quantitative PCR overestimation of DNA in samples contaminated with tin(Wiley, 2023) Bonsu, D.N.O.; Higgins, D.; Simon, C.; Goodwin, C.S.; Henry, J.M.; Austin, J.J.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.Item Open Access Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time(PeerJ, 2023) Eisenhofer Philipona, R.; Brice, K.L.; Blyton, M.D.; Bevins, S.E.; Leigh, K.; Singh, B.K.; Helgen, K.M.; Hough, I.; Daniels, C.B.; Speight, N.; Moore, B.D.Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.Item Open Access Sarcoptic mange changes bacterial and fungal microbiota of bare-nosed wombats (Vombatus ursinus)(BioMed Central, 2022) Næsborg-Nielsen, C.; Eisenhofer, R.; Fraser, T.A.; Wilkinson, V.; Burridge, C.P.; Carver, S.Background: Sarcoptes scabiei is globally distributed and one of the most impactful mammalian ectoparasites. Sarcoptic mange, caused by infection with S. scabiei, causes disruption of the epidermis and its bacterial microbiota, but its effects on host fungal microbiota and on the microbiota of marsupials in general have not been studied. Here, we (i) examine bacterial and fungal microbiota changes associated with mange in wild bare-nosed wombats (BNWs) and (ii) evaluate whether opportunistic pathogens are potentiated by S. scabiei infection in this species. Methods: Using Amplicon Sequencing of the 16S rRNA and ITS2 rDNA genes, we detected skin microbiota changes of the bare-nosed wombat (Vombatus ursinus). We compared the alpha and beta diversity among healthy, moderate, and severe disease states using ANOVA and PERMANOVA with nesting. Lastly, we identified taxa that differed between disease states using analysis of composition of microbes (ANCOM) testing. Results: We detected significant changes in the microbial communities and diversity with mange in BNWs. Severely affected BNWs had lower amplicon sequence variant (ASV) richness compared to that of healthy individuals, and the microbial communities were significantly different between disease states with higher relative abundance of potentially pathogenic microbial taxa in mange-affected BNWs including Staphylococcus sciuri, Corynebacterium spp., Brevibacterium spp., Brachybacterium spp., and Pseudogymnascus spp. and Debaryomyces spp. Conclusion: This study represents the first investigation of microbial changes in association with sarcoptic mange in a marsupial host, as well as the first investigation of fungal microbial changes on the skin of any host suffering from sarcoptic mange. Our results are broadly consistent with bacterial microbiota changes observed in humans, pigs, canids, and Iberian ibex, suggesting the epidermal microbial impacts of mange may be generalisable across host species. We recommend that future studies investigating skin microbiota changes include both bacterial and fungal data to gain a more complete picture of the effects of sarcoptic mange.Item Open Access The immunogenetic impact of European colonization in the Americas(Frontiers Media, 2022) Collen, E.J.; Johar, A.S.; Teixeira, J.C.; Llamas, B.The introduction of pathogens originating from Eurasia into the Americas during early European contact has been associated with high mortality rates among Indigenous peoples, likely contributing to their historical and precipitous population decline. However, the biological impacts of imported infectious diseases and resulting epidemics, especially in terms of pathogenic effects on the Indigenous immunity, remain poorly understood and highly contentious to this day. Here, we examine multidisciplinary evidence underpinning colonization-related immune genetic change, providing contextualization from anthropological studies, paleomicrobiological evidence of contrasting host-pathogen coevolutionary histories, and the timings of disease emergence. We further summarize current studies examining genetic signals reflecting post-contact Indigenous population bottlenecks, admixture with European and other populations, and the putative effects of natural selection, with a focus on ancient DNA studies and immunity-related findings. Considering current genetic evidence, together with a population genetics theoretical approach, we show that post-contact Indigenous immune adaptation, possibly influenced by selection exerted by introduced pathogens, is highly complex and likely to be affected by multifactorial causes. Disentangling putative adaptive signals from those of genetic drift thus remains a significant challenge, highlighting the need for the implementation of population genetic approaches that model the short time spans and complex demographic histories under consideration. This review adds to current understandings of post-contact immunity evolution in Indigenous peoples of America, with important implications for bettering our understanding of human adaptation in the face of emerging infectious diseases.Item Open Access An Outlook for the Acquisition of Marine Sedimentary Ancient DNA (sedaDNA) From North Atlantic Ocean Archive Material(American Geophysical Union (AGU), 2022) Selway, C.A.; Armbrecht, L.; Thornalley, D.Studies incorporating sedimentary ancient DNA (sedaDNA) analyses to investigate paleo-environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field campaigns could unlock an immense resource of sampling material for such paleo-investigations. However, sedaDNA research is at a high risk of contamination by modern environmental DNA, as sub-optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preserved sedaDNA in the sample. Here, we test the feasibility of sedaDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two samples (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryotic sedaDNA from all samples. We characterized the authenticity of each sample through sedaDNA fragment size and damage analyses, which allowed us to disentangle sedaDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most samples were dominated by Emiliania huxleyi, a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non-ideal sampling and sample storage conditions of the investigated samples. Therefore, while we demonstrate that sedaDNA analysis of archival North Atlantic seafloor sediment samples are generally achievable, we stress the importance of best-practice ship-board sampling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.Item Open Access Spectroscopic (analytical) approach to gunshot residue analysis for shooting distance estimation: a systematic review(Springer, 2021) Abedi, M.; Bonsu, D.O.M.; Badu, I.K.; Afoakwah, R.; Ahuja, P.Background: The determination of the shooting distance using gunshot residue (GSR) analysis is crucial in the investigation and reconstruction of firearm-related crimes. However, the conventional chemographic method for GSR analysis is destructive and has limited sensitivity and selectivity. While the spectroscopic method has potential in GSR analysis for crime investigation, there is a current lack of consistency in the spectroscopic results obtained for shooting distance estimation via GSR analysis. Addressing such limitations will enhance the forensic capabilities of law enforcement and provide an added advantage to crime laboratories during an investigation. It will also reinforce the use of such spectroscopic data in a criminal investigation. Main text: We obtained all peer-reviewed articles relevant to shooting distance estimation from searching Scopus, Web of Science, PubMed, and Google Scholar databases. We specifically searched the databases using the keywords “shooting distance,” “range of fire,” “gunshot residue,” “firearm discharge residue,” and “firearm-related crime” and obtained 3811 records. We further filtered these records using a combination of two basic keywords “gunshot residue” and “shooting distance estimations” yielding 108 papers. Following a careful evaluation of the titles, abstracts, and full texts, 40 original peer-reviewed articles on shooting distance estimation via GSR analysis were included in the study. The forgoing included additional sources (n = 5) we obtained from looking through the reference lists of the forensic articles we found. Short conclusion: This paper discusses the current scope of research concerning the chemographic and spectroscopic analysis of GSR for shooting distance estimation. It also examines the challenges of these techniques and provides recommendations for future research.Item Metadata only Comparison of Isohelix™ and Rayon swabbing systems for touch DNA recovery from metal surfaces(Springer, 2021) Bonsu, D.O.M.; Rodie, M.; Higgins, D.; Henry, J.; Austin, J.J.A previous study evaluating two swabbing systems found that DNA was best recovered from sterile metal substrates using an Isohelix™ swab wetted with isopropyl alcohol rather than a Rayon swab with water as the wetting agent. We tested the same swabbing systems on metal (aluminum, brass, and stainless steel) and plastic substrates in a regularly touched environment to simulate the non-deliberate transfer of touch evidence likely seen in a casework scenario, to ascertain the performance of these swabs in an uncontrolled situation. Higher amounts of touch DNA were recovered with Isohelix™ swabs (0.5 – 3.3 ng) compared to Rayon swabs (0.13 – 1.2 ng). The Isohelix™ swabbing system was found to significantly recover more touch DNA (p = 0.04) from the metal substrates than the Rayon swabbing system, consistent with the findings of our previous work. The results contribute to our understanding of the impact of sample collection techniques on touch DNA recovery from problematic metal surfaces and suggest that supplemental cleaning of substrates as a precautionary step against the spread of infections may affect touch DNA persistence and the recovery efficiency of swabs.Item Metadata only Ethics Reporting in Forensic Science Research Publications - A Review(Elsevier, 2022) Bonsu, D.O.M.; Afoakwah, C.B.; Abedi, M.; Higgins, D.; Austin, J.J.An essential element of compliance with ethical standards in scientific research is the reporting of a verifiable declaration of ethical approval and, when human subjects are involved - informed consent, in published works. The level of reporting of ethical permission for research published in forensic and investigative sciences journals has not been explored to date. Hence, we examined the reporting of ethical approval and informed consent in original research utilising human or animal subjects published in six forensic science journals from 2010 to 2019. We identified 10,192 articles and retained 3010 that satisfied the inclusion criteria of utilising human (91.2%), or animal (7.0%) or both (1.8%) subjects or tissues in experiments. Just over a third (1079/3010) of all studies declared obtaining ethical approval, with 927 (85.9%) of those indicating the name of the ethical committee, but only 392 (36%) provided an approval code. Furthermore, while consent was said to have been sought in 527 (17.5%) of studies, only 155 of those reported that written informed consent was obtained, eleven stated oral (verbal) consent, while the remaining 357 studies (67.7%) did not report the process used to gain consent. Ethical approval reporting rates differed between different research types, availability of financial support and whether authors were affiliated to academia or industry. The results demonstrate a low level of declaration of ethical approval and informed consent in forensic science research and publication, requiring urgent rectification. We support the adoption of the model proposed by Forensic Science International: Genetics as baseline recommendations to facilitate consistent nomenclature, transparency, and standard of ethical reporting in forensic science.Item Open Access Biocultural Drivers of Salivary Microbiota in Australian Aboriginal and Torres Strait Islander Children(Frontiers, 2021) Handsley-Davis, M.; Skelly, E.; Johnson, N.W.; Kapellas, K.; Lalloo, R.; Kroon, J.; Weyrich, L.S.Australian Aboriginal and Torres Strait Islander children experience unacceptably high rates of dental caries compared to their non-Indigenous Australian counterparts. Dental caries significantly impacts the quality of life of children and their families, particularly in remote communities. While many socioeconomic and lifestyle factors impact caries risk, the central role of the oral microbiota in mediating dental caries has not been extensively investigated in these communities. Here, we examine factors that shape diversity and composition of the salivary microbiota in Aboriginal and Torres Strait Islander children and adolescents living in the remote Northern Peninsula Area (NPA) of Far North Queensland. We employed 16S ribosomal RNA amplicon sequencing to profile bacteria present in saliva collected from 205 individuals aged 4–17 years from the NPA. Higher average microbial diversity was generally linked to increased age and salivary pH, less frequent toothbrushing, and proxies for lower socioeconomic status (SES). Differences inmicrobial composition were significantly related to age, salivary pH, SES proxies, and active dental caries. Notably, a feature classified as Streptococcus sobrinus increased in abundance in children who reported less frequent tooth brushing. A specific Veillonella feature was associated with caries presence, while features classified as Actinobacillus/Haemophilus and Leptotrichia were associated with absence of caries; a Lactobacillus gasseri feature increased in abundance in severe caries. Finally, we statistically assessed the interplay between dental caries and caries risk factors in shaping the oral microbiota. These data provide a detailed understanding of biological, behavioral, and socioeconomic factors that shape the oral microbiota and may underpin caries development in this group. This information can be used in the future to improve tailored caries prevention and management optionsItem Open Access Morphological variation in skull shape and size across extinct and extant populations of the greater stick-nest rat (Leporillus conditor): implications for translocation(CSIRO Publishing, 2022) Onley, I.; Moseby, K.; Austin, J.; Sherratt, E.; Richardson, B.Within-species morphological variation is often observed across spatial and climatic gradients. Understanding this variation is important to conservation planning, as specialised adaptations may influence a population’s persistence following translocation. However, knowing whether local adaptations are prevalent within a species can be challenging when the species has undergone range contractions. Here, we used museum specimens to study size and shape variation of the greater stick-nest rat (Leporillus conditor). We aimed to determine whether intraspecific size and shape variation previously existed within the species across its historical range, and inform on possible implications for translocations of the remaining extant population. We found significantly larger skull size in the Franklin Islands and arid populations, possibly indicating a historically continuous population experiencing similar selection pressures such as high predation pressure, competition with other large arid zone rodents or climatic extremes. Conversely, skull shape variation within the species adheres to an allometric trajectory, indicating no specific local adaptations of skull shape. This absence of local skull shape adaptation suggests that the Franklin Islands population is likely suitable for mainland translocations. However, further research into the historical phylogeography of the species is recommended to identify whether large size resulted from shared ancestry or convergent evolution.Item Open Access Late Holocene climate anomaly concurrent with fire activity and ecosystem shifts in the eastern Australian Highlands(Elsevier, 2022) Thomas, Z.A.; Mooney, S.; Cadd, H.; Baker, A.; Turney, C.; Schneider, L.; Hogg, A.; Haberle, S.; Green, K.; Weyrich, L.S.; Pérez, V.; Moore, N.E.; Zawadzki, A.; Kelloway, S.J.; Khan, S.J.The alpine area of the Australian mainland is highly sensitive to climate and environmental change, and potentially vulnerable to ecosystem tipping points. Over the next two decades the Australian alpine region is predicted to experience temperature increases of at least 1 °C, coupled with a substantial decrease in snow cover. Extending the short instrumental record in these regions is imperative to put future change into context, and potentially provide analogues of warming. We reconstructed past temperatures, using a lipid biomarker palaeothermometer technique and mercury flux changes for the past 3500 years from the sediments of Club Lake, a high-altitude alpine tarn in the Snowy Mountains, southeastern Australia. Using a multi-proxy framework, including pollen and charcoal analyses, high-resolution geochemistry, and ancient microbial community composition, supported by high-resolution 210Pb and AMS 14C dating, we investigated local and regional ecological and environmental changes occurring in response to changes in temperature. We find the region experienced a general warming trend over the last 3500 years, with a pronounced climate anomaly occurring between 1000 and 1600 cal yrs. BP. Shifts in vegetation took place during this warm period, characterised by a decline in alpine species and an increase in open woodland taxa which co-occurred with an increase in regional fire activity. Given the narrow altitudinal band of Australian alpine vegetation, any future warming has the potential to result in the extinction of alpine species, including several endemic to the area, as treelines are driven to higher elevations. These findings suggest ongoing conservation efforts will be needed to protect the vulnerable alpine environments from the combined threats of climate changes, fire and invasive species.Item Open Access Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus(Springer Nature, 2021) Farrer, A.G.; Wright, S.L.; Skelly, E.; Eisenhofer, R.; Dobney, K.; Weyrich, L.S.Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.Item Open Access Genomic Approaches for Conservation Management in Australia under Climate Change(MDPI AG, 2021) Onley, I.; Moseby, K.; Austin, J.Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.Item Metadata only Investigating the demographic history of Japan using ancient oral microbiota(The Royal Society Publishing, 2020) Eisenhofer Philipona, R.; Kanzawa-Kiriyama, H.; Shinoda, K.I.; Weyrich, L.S.While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species—Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.Item Open Access Signatures of landscape and captivity in the gut microbiota of Southern Hairy-nosed Wombats (Lasiorhinus latifrons)(Springer Science and Business Media LLC, 2021) Eisenhofer Philipona, R.; Helgen, K.M.; Taggart, D.Background: Herbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes. Recent research has found that captive management—an important conservation tool for many species—can alter the gut microbiota of mammals. Such changes could negatively impact the ability of herbivorous mammals to derive energy from their native diets, and ultimately reduce host fitness. To date, nothing is known of how captivity influences the gut microbiota of the Southern Hairy-nosed Wombat (SHNW), a large herbivorous marsupial that inhabits South Australia. Here, using 16S rRNA gene sequencing, we characterized the faecal microbiota of SHNWs in captivity and from three wild populations, two from degraded habitats and one from an intact native grass habitat. Results: We found that captive SHNWs had gut microbiota that were compositionally different and less diverse compared to wild SHNWs. There were major differences in gut microbiota community membership between captive and wild animals, both in statistically significant changes in relative abundance of microbes, and in the presence/absence of microbes. We also observed differences in microbial composition between wild populations, with the largest difference associated with native vs. degraded habitat. Conclusions: These results suggest that captivity has a major impact on the gut microbiota of SHNWs, and that different wild populations harbour distinct microbial compositions. Such findings warrant further work to determine what impacts these changes have on the fitness of SHNWs, and whether they could be manipulated to improve future management of the species.Item Open Access Sex assignment in a non-model organism in the absence of field records using Diversity Arrays Technology (DArT) data(Springer (part of Springer Nature), 2021) Onley, I.R.; Austin, J.J.; Mitchell, K.J.Conservation genomics research often relies on accurate sex information to make inferences about species demography, dispersal, and population structure. However, field determined sex data are not always available and can be subject to human error, while laboratory sex assignment methods such as PCR assays can often be costly and challenging for non-model species. Conservation genomics programs increasingly use reduced-representation genome sequencing to assess neutral and functional genetic diversity, population structure, gene flow and pedigrees in threatened species. Here we demonstrate that sex can be determined from reduced-representation sequencing data produced by the increasingly popular Diversity Arrays Technology sequencing workflow (DArT-seq) using a program originally designed for application to shotgun data. This program—sexassign—compares the “dosage” of sequencing reads mapping to autosomes versus the X chromosome. In the present study, sexassign was used to identify the sex of 60 field-collected Greater Stick-Nest Rat (Leporillus conditor) samples, despite the absence of an annotated reference genome for the species. This “read-dosage” approach is not only more accurate and affordable than traditional sex assignment methods, but can be applied to any diploid organism with a heterogametic sex determination system—including non-model and understudied species of conservation importance—by using FASTQs generated by DArT.Item Open Access Counterfeit formulations: analytical perspective on anorectics(Springer-Verlag, 2021) Bonsu, D.O.M.; Afoakwah, C.; Aguilar-Caballos, M.D.L.P.Purpose: This paper examines the scope of anorectics in counterfeit weight-reducing formulations and provides insight into the present state of research in determining such adulterants. Analytical techniques utilised in profiling adulterants found in slimming products, including limitations and mitigation steps of these conventional methods are also discussed. The current legal status of the anorectics and analogues routinely encountered in non-prescription slimming formulations is also explored. Methods: All reviewed literature was extracted from Scopus, Web of Science, PubMed, and Google Scholar databases using relevant search terms, such as, ‘counterfeit drugs’, ‘weight loss drugs’, ‘weight-reducing drugs’, ‘slimming drugs’, ‘anorectic agents’, and ‘counterfeit anorexics’. Legislation related to anorectics was obtained from the portals of various government and international agencies. Results: Anorectics frequently profiled in counterfeit slimming formulations are mostly amphetamine derivatives or its analogues. Five routinely reported pharmacological classes of adulterants, namely anxiolytics, diuretics, antidepressants, laxatives, and stimulants, are mainly utilised as coadjuvants in fake weigh-reducing formulations to increase bioavailability or to minimise anticipated side effects. Liquid and gas chromatography coupled with mass spectrometric detectors are predominantly used techniques for anorectic analysis due to the possibility of obtaining detailed information of adulterants. However, interference from the complex sample matrices of these fake products limits the accuracy of these methods and requires robust sample preparation methods for enhanced sensitivity and selectivity. The most common anorectics found in counterfeit slimming medicines are either completely banned or available by prescription only, in many countries. Conclusions: Slimming formulations doped with anorectic cocktails to boost their weight-reducing efficacy are not uncommon. Liquid chromatography combined with mass spectrometry remains the gold standard for counterfeit drug analysis, and requires improved preconcentration methods for rapid and quantitative identification of specific chemical constituents. Extensive method development and validation, targeted at refining existing techniques while developing new ones, is expected to improve the analytical profiling of counterfeit anorectics significantly.