Ancient plant DNA in lake sediments Parducci, Laura; Bennett, Keith D.; Ficetola, Gentile Francesco ...
New phytologist,
20/May , Letnik:
214, Številka:
3
Journal Article
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Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of ...palaeofloras.Hitherto, ancient frozen soils have proved excellent in preservingDNAmolecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a fewmetres fromthe sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNAfromlake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here,we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progressmade up to the present.Weargue that aDNAanalyses add newand additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
A theoretical analysis of taxonomic binning accuracy Sanctis, Bianca; Money, Daniel; Pedersen, Mikkel Winther ...
Molecular ecology resources,
August 2022, 2022-Aug, 2022-08-00, 20220801, Letnik:
22, Številka:
6
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Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read ...aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species–query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k‐mer‐based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning‐accuracy.
Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleo-ecological analyses of this archive ...have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including non-fossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.
Ancient and modern environmental DNA Pedersen, Mikkel Winther; Overballe-Petersen, Søren; Ermini, Luca ...
Philosophical transactions - Royal Society. Biological sciences,
01/2015, Letnik:
370, Številka:
1660
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DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ...ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught ...with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
Metagenomic data generated from environmental samples is increasingly common in the analysis of modern and ancient biological communities. To obtain taxonomic profiles from this type of data, DNA ...sequences are aligned against large genomic reference databases and the lowest common ancestor (LCA) needs to be inferred for each sequence with multiple alignments. To date, efforts have mainly focused on improving the speed, sensitivity and specificity of alignment tools, and little effort has been applied to the LCA algorithm that generates the taxonomic profiles from alignments.
We present ngsLCA, a command‐line toolkit with two separate modules: the main program (in C/C++) performing LCA inference, and an R package for generating tables and visualisations of the taxonomic profiles.
ngsLCA processed large datasets in BAM/SAM alignment format 4–11 times faster and used less memory compared to other available programs. It is compatible with the NCBI taxonomy and has flexible parameter settings. Furthermore, the toolkit offers functions for filtering, contamination removal, taxonomic clustering, and multiple ways of visualising the generated taxonomic profiles.
ngsLCA bridges a gap in current metagenomic analyses by supplying a computationally light, easy‐to‐use, accurate, fast and flexible LCA algorithm with R functions for processing and illustrating the taxonomic profiles
We use 2nd generation sequencing technology on sedimentary ancient DNA (sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the ...results with those previously obtained from pollen and macrofossils in the same lake. Thirty-eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g–h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (Scrophulariaceae and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650 cal yr BP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less detailed than pollen and macrofossil analyses can be a complementary tool for establishing the composition of both terrestrial and aquatic local plant communities and a method for identifying additional taxa.
Comparing table of plant families found with three different methods in lake sediments, highlights the potential of DNA for finding additional taxa. Display omitted
•We successfully extracted terrestrial deposited DNA from ancient lake sediments.•The DNA show a relative large overlap with pollen and macrofossils.•We found two plant families not found by neither Pollen nor Macrofossils.
Abstract
Ancient environmental DNA (aeDNA) is a crucial source of information for past environmental reconstruction. However, the computational analysis of aeDNA involves the inherited challenges of ...ancient DNA (aDNA) and the typical difficulties of eDNA samples, such as taxonomic identification and abundance estimation of identified taxonomic groups. Current methods for aeDNA fall into those that only perform mapping followed by taxonomic identification and those that purport to do abundance estimation. The former leaves abundance estimates to users, while methods for the latter are not designed for large metagenomic datasets and are often imprecise and challenging to use.
Here, we introduce
euka
, a tool designed for rapid and accurate characterisation of aeDNA samples. We use a taxonomy‐based pangenome graph of reference genomes for robustly assigning DNA sequences and use a maximum‐likelihood framework for abundance estimation. At the present time, our database is restricted to mitochondrial genomes of tetrapods and arthropods but can be expanded in future versions.
We find
euka
to outperform current taxonomic profiling tools and their abundance estimates. Crucially, we show that regardless of the filtering threshold set by existing methods,
euka
demonstrates higher accuracy. Furthermore, our approach is robust to sparse data, which is idiosyncratic of aeDNA, detecting a taxon with an average of 50 reads aligning. We also show that
euka
is consistent with competing tools on empirical samples.
euka
's features are fine‐tuned to deal with the challenges of aeDNA, making it a simple‐to‐use, all‐in‐one tool. It is available on GitHub:
https://github.com/grenaud/vgan
.
euka
enables researchers to quickly assess and characterise their sample, thus allowing it to be used as a routine screening tool for aeDNA.
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago
had climates resembling those forecasted under future warming
. Palaeoclimatic records show strong polar amplification with ...mean annual temperatures of 11-19 °C above contemporary values
. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare
. Here we report an ancient environmental DNA
(eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
The demographic history of Greenland is characterized by recurrent migrations and extinctions since the first humans arrived 4,500 years ago. Our current understanding of these extinct cultures ...relies primarily on preserved fossils found in their archaeological deposits, which hold valuable information on past subsistence practices. However, some exploited taxa, though economically important, comprise only a small fraction of these sub-fossil assemblages. Here we reconstruct a comprehensive record of past subsistence economies in Greenland by sequencing ancient DNA from four well-described midden deposits. Our results confirm that the species found in the fossil record, like harp seal and ringed seal, were a vital part of Inuit subsistence, but also add a new dimension with evidence that caribou, walrus and whale species played a more prominent role for the survival of Paleo-Inuit cultures than previously reported. Most notably, we report evidence of bowhead whale exploitation by the Saqqaq culture 4,000 years ago.
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