SEDIMENTARY ANCIENT DNA, FLORA AND FAUNA EVA CHOCHOLOVÁ LABORATORY OF BIOLOGICAL AND MOLECULAR ANTHROPOLOGY DEPARTMENT OF EXPERIMENTAL BIOLOGY SEDIMENTARY ANCIENT DNA • Abbreviated to sedaDNA • Proxies (indirect sources of information) – e.g., fossil assemblages, indicator species, geochemical proxies… • Before HTS mostly limited to fossil record (molluscs, diatoms, foraminifera…) • Often for study of palaeoenvironment, climate change, biodiversity • Greater resolutions compared to pollen analysis • Best preservation in anoxic and cold environment, high clay, borate and organic content • Organisms underrepresented in databases, missing references, unknown organisms SEDIMENTARY ANCIENT DNA Armbrecht et al., 2019 DOI: 10.1016/j.earscirev.2019.102887 SEDIMENTARY ANCIENT DNA Armbrecht et al., 2019 DOI: 10.1016/j.earscirev.2019.102887 Observed in cave sediments and non-frozen soil SOURCES • Lakes and other freshwater sources • Marine • Cave • Burials • Settlements • Permafrost • (Ice, glacier) • (Latrines) • (Extraterrestrial sources) Heintzman et al., 2023 DOI: 10.1007/978-3-031-43799-1_3 METHODOLOGICAL CONSIDERATIONS Heintzman et al., 2023 DOI: 10.1007/978-3-031-43799-1_3 SEDIMENT CORING • Cold storage, subsampling ideally on board in case of marine sediments • Horizontal (accessible profiles – permafrost, soil, cave) • from bottom to top to prevent cross-contamination • Vertical (inaccessible profiles – marine, lake, ice) • Contamination monitoring by addition of exotic DNA or synthetic tracers • Archiving in specialized facilities, e.g., LacCore facility in Minnesota, Permafrost ArChives Science (PACS) Laboratory at the University of Alberta, International Ocean Discovery Program https://www.iodp.org/resources/core-repositories Armbrecht et al., 2019 DOI: 10.1016/j.earscirev.2019.102887 Fig. 2. Overview of IODP coring systems. A) Advanced piston coring system (APC), shown before and after stroking; only small volumes of drill fluid can enter the space between the core barrel and collar from above after stroking, greatly reducing the risk of contamination. B) Extended core barrel system (XCB) and C) Rotary core barrel system (RCB); both containing circulation jets at the bottom of the core barrel through which drill-fluid enters and removes coring debris by transporting it upwards within the drill hole to the surface. D) Comparison of rotary and piston cored sediments demonstrating the well-preserved lamination in Piston cored material. Figure adapted from Sun et al. (2018) and IODP (iodp.tamu.edu/tools/index.html) Armbrecht et al., 2019 DOI: 10.1016/j.earscirev.2019.102887 Heintzman et al., 2023 DOI: 10.1007/978-3-031-43799-1_3 Armbrecht et al., 2020 DOI: 10.5670/oceanog.2020.211 MARINE sedaDNA • Research always multidisciplinary – geology, organic and inorganic chemistry, geomorphology, palaeoceanography, micropaleontology… • More dynamic environment than freshwater systems Nguyen et al., 2023 DOI: 10.3389/fmars.2023.1185435 MARINE sedaDNA Nguyen et al., 2023 DOI: 10.3389/fmars.2023.1185435 MARINE sedaDNA Schepper et al., 2019 DOI: 10.1038/s41396-019-0457-1 LAKE sedaDNA Parducci et al., 2017 DOI: 10.1111/nph.14470 • Accumulation of both aquatic and terrestrial environmental components • Lower disturbance, temperature stability • Preferencial winter sampling Parducci et al., 2017 DOI: 10.1111/nph.14470 Jia et al., 2022 DOI: 10.1016/j.quascirev.2022.107703 Fig. 2. Conceptual model of the taphonomic processes of extracellular DNA from lake sediments. After having been released into the environment, extracellular DNA can be incorporated into soil or sediment particles by adsorbing to, for example, clay minerals and humic substances, which is the primary mechanism responsible for longterm DNA preservation. Adsorbed DNA can subsequently be transported into the lake through catchment runoff. Most large lakes on the Tibetan Plateau are expected to have high upstream DNA inputs because of diverse landscapes and well-developed hydrographical networks in their catchments. However, high-level ultraviolet (UV) radiation on the Tibetan Plateau might photochemically damage DNA over long transport distances. During the deposition stage, terrestrial adsorbed DNA is expected to be well preserved in deep lakes with neutral to slightly alkaline water pH (7–9), intermediate water conductivities (100–500 μS cm−1; suitable cation concentrations), and high clay sediment input. On the other hand, DNA from aquatic organisms (e.g., fish and macrophytes) might still be preserved in many Tibetan lakes characterized by high water pH (≥9) and conductivity (>1000 μS cm−1). After sediment particles are finally deposited and buried in the lake bottom, DNA is adsorbed within the sediment and stored in a cold and anoxic environment that limits bioturbation, sediment reworking, and microbial activity, which favors long-term DNA preservation. To conclude, we infer that some deep glacial lakes with freshwater and high clay sediment input, such as those from the southern and southeastern Tibetan Plateau, may have a high potential for sedimentary ancient DNA studies in the future. MORE ON sedaDNA • Burials • Contamination control (comparison of samples and sedaDNA) • Non-destructive for remains • Have to be sampled early • Potentially human DNA, pathogens, parasites, diet, … • Caves! Slon et al., 2017; DOI: 10.1126/science.aam9695 Fig. 1 Ancient taxa detected in Late Pleistocene (LP) and Middle Pleistocene (MP) sediment samples from seven sites. For each time period, the fraction of samples containing DNA fragments that could be assigned to a mammalian family and authenticated to be of ancient origin is indicated. The shaded symbols representing each family are not to scale. Slon et al., 2017; DOI: 10.1126/science.aam9695 MORE ON sedaDNA • Burials • Contamination control (comparison of samples and sedaDNA) • Non-destructive for remains • Have to be sampled early • Potentially human DNA, pathogens, parasites, diet, … • Caves! • Mostly megafauna and hominins MORE ON sedaDNA • Burials • Contamination control (comparison of samples and sedaDNA) • Non-destructive for remains • Have to be sampled early • Potentially human DNA, pathogens, parasites, diet, … • Caves! • Mostly megafauna and hominins • Microstratigraphy PLANTS • Domestication! • Greatest genome size, polyploidization allows subfunctionalization and neofunctionalization, transposable elements crucial • aDNA offers insight into timing, number and locality of domestication events, processes behind domestication (human behaviour, genome changes) • Research of wild and early-domesticated ancestors, adaptation to pathogens and environmental changes • Palaeoecology • Sources: seeds, herbarium specimens, wood, pollen, sediments, various plant fragments Pont et al., 2019 DOI: 10.1186/s13059-019-1627-1 FAUNA • Domestication!, introgression, loss of diversity, migrations and contact • Domestication – commensal, directed, prey • Wild animals, extinct species such as mammoth Irving-Pease et al., 2018; DOI: 10.1007/13836_2018_55, CONSERVATION AND aDNA • Biodiversity levels: • Diversity of ecosystems • Species diversity • Genetic diversity • Loss of biodiversity usually in presented in lost species, genetic diversity often unknown CONSERVATION AND aDNA • Biodiversity levels: • Diversity of ecosystems • Species diversity • Genetic diversity • Loss of biodiversity usually in presented in lost species, genetic diversity often unknown • Museum collections and sedaDNA Jensen et al., 2022 DOI: 10.1016/j.tree.2021.12.010 limit for shell DNA recovery to ≥100,000 years CONSERVATION AND aDNA • Biodiversity levels: • Diversity of ecosystems • Species diversity • Genetic diversity • Loss of biodiversity usually in presented in lost species, genetic diversity often unknown • Museum collections and sedaDNA • Ancient and historical DNA can help: • Set baselines for genetic diversity • Assess introgression, identify source populations • Assess evolutionary impacts of past events • Study effective population size, subpopulations and their distinctness • … Jensen et al., 2022 DOI: 10.1016/j.tree.2021.12.010 Jensen et al., 2022 DOI: 10.1016/j.tree.2021.12.010 DEEXTINCTION • Bringing extinct species back to life Jurassic Park (1993), Universal Pictures DEEXTINCTION • Bringing extinct species back to life • Similar phenotype by cross-breading https://www.quaggaproject.org/ DEEXTINCTION • Bringing extinct species back to life • Similar phenotype by cross-breading • Genome editing of close related species CRISPR/Cas • Goals more general, e.g.: • Elephant genome • Elephant tracking technologies • Artificial womb • Ecological restoration • Synthetic biology applications • Vaccine • Sustainable agriculture • … DEEXTINCTION • Bringing extinct species back to life • Similar phenotype by cross-breading • Genome editing of close related species • Cloning DEEXTINCTION • Bringing extinct species back to life • Similar phenotype by cross-breading • Genome editing of close related species • Cloning • Thylacine, Dodo, Quagga, Mammoth, Passenger pidgeon Extinct birds (1907), Frederick William Frohawk Birds of New York (1910), Louis Agassiz Fuertes DEEXTINCTION • Bringing extinct species back to life • Similar phenotype by cross-breading • Genome editing of close related species • Cloning • Thylacine, Dodo, Quagga, Mammoth, Passenger pidgeon • Ecosystem, habitat – do extinct species have a place? • Efficiency of funding DEEXTINCTION • Bringing extinct species back to life • Similar phenotype by cross-breading • Genome editing of close related species • Cloning • Thylacine, Dodo, Quagga, Mammoth, Passenger pidgeon • Ecosystem, habitat – do extinct species have a place? • Efficiency of funding • Recently extinct species! DEEXTINCTION • Bringing extinct species back to life • Similar phenotype by cross-breading • Genome editing of close related species • Cloning • Thylacine, Dodo, Quagga, Mammoth, Passenger pidgeon • Ecosystem, habitat – do extinct species have a place? • Efficiency of funding • Recently extinct species! • At least about 200-2000 species every year https://wwf.panda.org/discover/our_focus/biodiversity/biodiversity/ ! • Rhino and recently extinct species for deextinction • Deextiction types • sedaDNA subsampling (on boats in marine sedaDNA) • Plant domestication • Extraterrestrial sediment • Climate change and sedaDNA • Sampling in winter (lake sedaDNA) • Domestication types • Reintroduction of genetic diversity from past populations to current ones