Supplementary material to "Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30,000 years"

2019 ◽  
Author(s):  
Heike H. Zimmermann ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Juliane Müller ◽  
Rüdiger Stein ◽  
...  
Keyword(s):  
Sea Ice ◽  
Ancient Dna ◽  
Fram Strait ◽  
The Past ◽  
Supplementary Material

scholarly journals Sedimentary ancient DNA from Kronotsky Peninsula: how sea ice, salinity and insolation dynamics have shaped diatom composition and richness over the past 20,000 years

2020 ◽  
Author(s):  
Heike H. Zimmermann ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Dirk Nürnberg ◽  
Ralf Tiedemann ◽  
...  
Keyword(s):  
Sea Ice ◽  
Ancient Dna ◽  
The Past

scholarly journals Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30 000 years

Ocean Science ◽  
2020 ◽  
Vol 16 (5) ◽  
pp. 1017-1032
Author(s):  
Heike H. Zimmermann ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Juliane Müller ◽  
Ruediger Stein ◽  
...  
Keyword(s):  
Sea Ice ◽  
Ancient Dna ◽  
Cold Water ◽  
Taxonomic Composition ◽  
Fram Strait ◽  
Pcr Products ◽  
Ideal Study ◽  
Late Weichselian ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Abstract. The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are scarce, rarely exceed the Holocene, and contain sparse information about past richness and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. Amplifying a short, partial rbcL marker from samples of sediment core MSM05/5-712-2 resulted in 95.7 % of our sequences being assigned to diatoms across 18 different families, with 38.6 % of them being resolved to species and 25.8 % to genus level. Independent replicates show a high similarity of PCR products, especially in the oldest samples. Diatom sedaDNA richness is highest in the Late Weichselian and lowest in Mid- and Late Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice-associated diatoms and suggests several reorganisations – after the Last Glacial Maximum, after the Younger Dryas, and after the Early and after the Mid-Holocene. Different sequences assigned to, amongst others, Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2 % of the assemblage point towards past sea-ice presence.

scholarly journals Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30,000 years

2019 ◽  
Author(s):  
Heike H. Zimmermann ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Juliane Müller ◽  
Rüdiger Stein ◽  
...  
Keyword(s):  
Sea Ice ◽  
Ancient Dna ◽  
Cold Water ◽  
Taxonomic Composition ◽  
Fram Strait ◽  
Pcr Products ◽  
Ideal Study ◽  
Late Weichselian ◽  
The Last Glacial Maximum ◽  
The Last Glacial

Abstract. The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are underrepresented, rarely exceed the Holocene and contain sparse information about past diversity and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. By amplifying a short, partial rbcL marker, 95.7 % of our sequences are assigned to diatoms across 18 different families with 38.6 % of them being resolved to species and 25.8 % to genus level. Independent replicates show high similarity of PCR products, especially in the oldest samples. Diatom richness is highest in the Late Weichselian and lowest in Mid- and Late-Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice associated diatoms and shows two re-organizations – one after the Last Glacial Maximum and another after the Younger Dryas. Different sequences assigned, amongst others, to Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2 % of the assemblage point towards past sea-ice presence.

scholarly journals Variability of sea-ice conditions in the Fram Strait over the past 30,000 years

2009 ◽  
Vol 2 (11) ◽  
pp. 772-776 ◽  
Author(s):  
Juliane Müller ◽  
Guillaume Massé ◽  
Rüdiger Stein ◽  
Simon T. Belt
Keyword(s):  
Sea Ice ◽  
Fram Strait ◽  
The Past ◽  
Ice Conditions

scholarly journals Conceptualizing histories of multispecies entanglements: Ancient pathogen genomics and the case of Borrelia recurrentis

2021 ◽  
pp. 146960532199394
Author(s):  
Venla Oikkonen
Keyword(s):  
East Africa ◽  
Ancient Dna ◽  
Relapsing Fever ◽  
Borrelia Recurrentis ◽  
The Past ◽  
Cultural Implications ◽  
Past Millennium

This article explores the conceptual and cultural implications of using pathogen ancient DNA (aDNA) collected in archaeological contexts to understand the past. More specifically, it examines ancient pathogen genomics as a way of conceptualizing multispecies entanglements. The analysis focuses on the 2018 sequencing of Borrelia recurrentis bacteria retrieved from a medieval graveyard in Oslo, Norway. B. recurrentis is associated with louse-borne relapsing fever (LBRF), known to have killed several million people in Europe during the past millennium, and it is still encountered in parts of East Africa. The article demonstrates that while aDNA research often foregrounds multispecies entanglements, its epistemic tools cannot easily address the ontological blurriness of pathogens and their embeddedness in vibrant material processes. The article draws on feminist posthumanities work on microbes and materiality to highlight conceptual openings that a theorization of ancient pathogens could engender.

Hierarchical Reinforcement Learning

2021 ◽  
Vol 54 (5) ◽  
pp. 1-35
Author(s):  
Shubham Pateria ◽  
Budhitama Subagdja ◽  
Ah-hwee Tan ◽  
Chai Quek
Keyword(s):  
Reinforcement Learning ◽  
Future Research ◽  
Comprehensive Overview ◽  
Open Problems ◽  
Practical Applications ◽  
Hierarchical Reinforcement Learning ◽  
The Past ◽  
Agent Learning ◽  
Multi Agent ◽  
Supplementary Material

Hierarchical Reinforcement Learning (HRL) enables autonomous decomposition of challenging long-horizon decision-making tasks into simpler subtasks. During the past years, the landscape of HRL research has grown profoundly, resulting in copious approaches. A comprehensive overview of this vast landscape is necessary to study HRL in an organized manner. We provide a survey of the diverse HRL approaches concerning the challenges of learning hierarchical policies, subtask discovery, transfer learning, and multi-agent learning using HRL. The survey is presented according to a novel taxonomy of the approaches. Based on the survey, a set of important open problems is proposed to motivate the future research in HRL. Furthermore, we outline a few suitable task domains for evaluating the HRL approaches and a few interesting examples of the practical applications of HRL in the Supplementary Material.

Sea ice protists in arctic marine sedaDNA records: origins, diversity, and vertical export of DNA from the sea surface to the seafloor 

2021 ◽  
Author(s):  
Sara Harðardóttir ◽  
Connie Lovejoy ◽  
Marit-Solveig Seidenkrantz ◽  
Sofia Ribeiro
Keyword(s):  
Sea Ice ◽  
Ocean Circulation ◽  
Ancient Dna ◽  
Genetic Material ◽  
Amplicon Sequencing ◽  
Arctic Sea Ice ◽  
The Arctic ◽  
Gene Copy ◽  
Marine Biodiversity ◽  
Vertical Export

<p>Arctic sea ice is declining at an unprecedented pace as the Arctic Ocean heads towards ice-free summers within the next few decades. Because of the role of sea ice in the Earth System such as ocean circulation and ecosystem functioning, reconstructing its past variability is of great importance providing insight into past climate patterns and future climate scenarios. Today, much of our knowledge of past sea-ice variability derives from a relatively few microfossil and biogeochemical tracers, which have limitations, such as preservation biases and low taxonomic resolution. Marine sedimentary ancient DNA (marine <em>seda</em>DNA) has the potential to capture more of the arctic marine biodiversity compared to other approaches. However, little is known about how well past communities are represented in marine <em>seda</em>DNA. The transport and fate of DNA derived from sea-ice associated organisms, from surface waters to the seafloor and its eventual incorporation into marine sediment records is poorly understood.  Here, we present results from a study applying a combination of methods to examine modern and ancient DNA to material collected along the Northeast Greenland Shelf. We characterized the vertical export of genetic material by amplicon sequencing the hyper-variable V4 region of the 18S rDNA at three water depths, in surface sediments, and in a dated sediment core.  The amplicon sequencing approach, as currently applied, includes some limitations for quantitative reconstructions of past changes such as primer competition, PCR errors, and variation of gene copy numbers across different taxa. For these reasons we quantified amplicons from a single species, the circum-polar sea ice dinoflagellate <em>Polarella glacialis</em> in the marine <em>seda</em>DNA, using digital droplet PCR. The results will increase our understanding on the taphonomy of DNA in sea ice environments, how sedimentation differs among taxonomic groups, and provide indications to potentially useful marine <em>seda</em>DNA-based proxies for climate and environmental reconstructions.</p>

The Paleoepidemiology of American Trypasonomiasis (Chagas disease)

1970 ◽  
Vol 80 (1) ◽  
Author(s):  
Wilmar Salo ◽  
William C. Auferheide ◽  
Michael Madden ◽  
John Streitz ◽  
Jane Buikstra ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Ancient Dna ◽  
Academic Discipline ◽  
Atacama Desert ◽  
Geographic Area ◽  
Northern Chile ◽  
Kinetoplast Dna ◽  
Testing Hypotheses ◽  
The Past ◽  
Tissue Specimens

Ancient DNA methodology was applied to extract and amplify a segment of kinetoplast DNA of Trypanosoma cruzi in soft tissue specimens from about 300 spontaneously mummified human bodies from the Atacama Desert in northern Chile and southern Peru. A DNA probe was then employed to hybridize with the amplicon. Results indicate that about 41% of the population in that geographic area were infected with the trypanosome over the past 9000 years. The epidemiological implications of these findings are discussed. It is also emphasized that this and several other paleoepidemiological studies in progress have established that population-study cohorts of mummies now can generate statistically valid paleoepidemiological investigations capable of testing hypotheses. These reflect the maturation of the academic discipline of the scientific study of mummies.

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