Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Yates, James A. Fellows; Valtueña, Aida Andrades; Vågene‬, Åshild J.; Cribdon, Becky; Velsko, Irina M.; Borry, Maxime; Bravo-Lopez, Miriam; Fernàndez-Guerra, Antonio; Green, Eleanor Joan; Ramachandran, Shreya; Heintzman, Peter D.; Spyrou, Maria A.; Hübner, Alexander; Gancz, Abigail S.; Hider, Jessica; Allshouse, Aurora F.; Zaro, Valentina; Warinner, Christina

doi:10.1038/s41597-021-00816-y

Cited by 35 publications

(38 citation statements)

References 19 publications

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“…In total, more than twelve thousand papers were scanned. We supplemented our search results with relevant studies from AncientMetagenomeDir (Fellows Yates et al, 2021), which collates metagenomics datasets, plus three studies mentioned in the bibliography of our review (Adame & Reef, 2020; Cannon et al, 2016; Schabacker et al, 2020), and relevant studies from the last sed aDNA review (H. Li et al, 2023).…”

Section: Materials and Methodologymentioning

confidence: 99%

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

Revéret

Rijal

Heintzman

et al. 2023

Preprint

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Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.

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Section: Materials and Methodologymentioning

confidence: 99%

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

Revéret

Rijal

Heintzman

et al. 2023

Preprint

Self Cite

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“…This would allow for a more efficient use of economic resources, saving time for the researchers and preserving samples with a great scientific or cultural value. In that regard, it is worth mentioning the work carried out by the SPAAM community in its AncientMetagenomeDir database ( Fellows Yates et al 2021 ).…”

Section: Challenges Of Ancient Virus Detectionmentioning

confidence: 99%

An Adagio for Viruses, Played Out on Ancient DNA

de-Dios

Scheib

Houldcroft

2023

Genome Biology and Evolution

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Studies of ancient DNA have transformed our understanding of human evolution. Palaeogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic and pandemic pathogens. Viruses – and in particular those with single or double-stranded DNA genomes – are an important part of the palaeogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly-evolving viruses which cause disease. In this review, we will revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We will look at how palaeogenomics works for viral pathogens, such as the need for careful precautions against modern contamination, and robust computational pipelines to identify and analyse authenticated viral sequences. We will discuss the insights into virus evolution which have been gained through palaeogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.

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“…The de novo assembly methods [ 125 , 126 ] can be used for both modern and ancient metagenomes without using the reference databases, and this makes it possible to obtain more accurate sequence of the genome. Moreover, new studies have been conducted regularly: at present, over a thousand of ancient metagenomes have been published [ 127 ]. This would allow to perform a broader systematic analysis and not only spot studies of individual specimens in future.…”

Section: Near-future Perspectivesmentioning

confidence: 99%

Genomics of Ancient Pathogens: First Advances and Prospects

Malyarchuk

Andreeva

Kuznetsova

et al. 2022

Biochemistry Moscow

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Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today’s world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.

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Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Cited by 35 publications

References 19 publications

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

An Adagio for Viruses, Played Out on Ancient DNA

Genomics of Ancient Pathogens: First Advances and Prospects

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