scholarly journals Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

2021 ◽  
Vol 288 (1957) ◽  
pp. 20211252
Author(s):  
Nicolas Dussex ◽  
Nora Bergfeldt ◽  
Violeta de Anca Prado ◽  
Marianne Dehasque ◽  
David Díez-del-Molino ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Ecosystem Dynamics ◽  
Integrative Approach ◽  
Comprehensive Understanding ◽  
The Past ◽  
Combining Data ◽  
Simultaneous Study ◽  
Taxonomic Groups ◽  
Analytical Approaches ◽  
Source Materials

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

Building cyberinfrastructure systems to support integrative, macroscale analyses of sedimentary ancient DNA records: current resources, needs, and opportunities

2021 ◽  
Author(s):  
John Williams ◽  
Keyword(s):  
Ancient Dna ◽  
Unmet Need ◽  
Taxonomic Resolution ◽  
Joint Analysis ◽  
Sequence Variant ◽  
Bioinformatics Pipeline ◽  
Widespread Application ◽  
Sedimentary Environments ◽  
Taxonomic Groups ◽  
Analytical Approaches

<p>The number and extent of ancient DNA records from sedimentary environments (sedaDNA) is rapidly increasing, which creates new opportunities for integrative and macroscale investigations into past population, community, and environmental dynamics at unprecedented taxonomic resolution and spatiotemporal extent.  However, fully achieving this potential requires a robust cyberinfrastructure that supports the joint analysis of many sedaDNA records with each other and with genomic reference libraries, the latest geochronological controls and age-depth models, complementary paleoecological and paleoenvironmental proxies, and the most recent and updated DNA reference library for taxonomic identifications.  Any cyberinfrastructure for macroscale data synthesis must address the variety of ancient DNA records (e.g. taxonomic groups, analytical approaches, depositional contexts) and leverage existing resources and standards such as the Neotoma Paleoecology Database, the MGnify and MG-RAST resources for environmental genomics, and the MixS standard for genetic sequences.  In response, a Cyberinfrastructure for Ancient Sedimentary DNA working group has been meeting regularly since summer 2020 to assess the current state of science and informatics, assess needs and gaps, and establish recommendations for next steps forward.  An initial survey found over 420  sites worldwide with published or in-development sedaDNA records, with greatest densities in Eurasia.  Metabarcoding records, including Amplicon Sequence Variant data and derived taxonomic inferences, are a top priority for trial uploads to Neotoma, with pilot uploads underway, because of the relatively small dataset volumes, the widespread application of metabarcoding assays, and potential of integrating these records with other paleoecological data holdings in Neotoma and linked paleodata resources such as Linked Earth and paleoclimatic data at NOAA’s National Centers for Environmental Informatics.  Because taxonomic inferences are heavily conditioned by choice of bioinformatics pipeline and reference databases, a major unmet need is a repository for minimally processed output from raw sequences.  In general, no existing genomics or paleoecological resource meets all needs of the sedaDNA community, although each covers key elements, so there is a good potential of advancing macroscale data syntheses by leveraging and linking existing resources.</p>

scholarly journals Security‑related Cooperation among the V4 States

2018 ◽  
Vol 14 (2) ◽  
pp. 39-56 ◽  
Author(s):  
Jaroslav Ušiak
Keyword(s):  
Social Protection ◽  
Comparative Method ◽  
The Past ◽  
Different Types ◽  
Analysis And Synthesis ◽  
Hybrid Threats ◽  
Defence Cooperation ◽  
Analytical Approaches ◽  
Source Materials ◽  
Visegrád Countries

Abstract The need for security and defence cooperation is a significant driver bringing together many nation‑state groupings. Today, the renewal and strengthening of this cooperation is a pressing concern for all such alliances around the world. This cooperation is rooted in the history that initially highlighted its potential, but it also encompasses contemporary relationships formed under the influence of enormous challenges and pressures. Finally it draws on the past successes and failures of the group in question. The aim of this study is to trace the beginnings of the security‑related cooperation of the Visegrad countries and locate the point of coordination of their respective security policies. My methodology is based on an analysis and synthesis of key source materials, making use of different types of analytical approaches. In order to identify the factors that connected the V4 states, I have applied a comparative method. My conclusion highlights important areas of security‑related cooperation ranging from the coordination of energy policies to military and defence matters and social protection including the fight against extremism, radicalism and hybrid threats.

scholarly journals Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial ‘2D Folding Structure’ Point of View

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 583
Author(s):  
Giulia Furfaro ◽  
Paolo Mariottini
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Integrative Taxonomy ◽  
Point Of View ◽  
Past Study ◽  
Mitochondrial Coi ◽  
The Past ◽  
Combining Data ◽  
Folding Structure ◽  
Comparison Of The Results

Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and chemical. Regarding molecular analysis, there is currently a search for new genetic markers that could be diagnostic at different taxonomic levels and that can be added to the canonical ones. In marine Heterobranchia, the most widely used mitochondrial markers, COI and 16S, are usually analysed by comparing the primary sequence. The 16S rRNA molecule can be folded into a 2D secondary structure that has been poorly exploited in the past study of heterobranchs, despite 2D molecular analyses being sources of possible diagnostic characters. Comparison of the results from the phylogenetic analyses of a concatenated (the nuclear H3 and the mitochondrial COI and 16S markers) dataset (including 30 species belonging to eight accepted genera) and from the 2D folding structure analyses of the 16S rRNA from the type species of the genera investigated demonstrated the diagnostic power of this RNA molecule to reveal the systematics of four genera belonging to the family Myrrhinidae (Gastropoda, Heterobranchia). The “molecular morphological” approach to the 16S rRNA revealed to be a powerful tool to delimit at both species and genus taxonomic levels and to be a useful way of recovering information that is usually lost in phylogenetic analyses. While the validity of the genera Godiva, Hermissenda and Phyllodesmium are confirmed, a new genus is necessary and introduced for Dondice banyulensis, Nemesis gen. nov. and the monospecific genus Nanuca is here synonymised with Dondice, with Nanuca sebastiani transferred into Dondice as Dondice sebastiani comb. nov.

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.

scholarly journals Characterizing Bilingual Effects on Cognition: The Search for Meaningful Individual Differences

2021 ◽  
Vol 11 (1) ◽  
pp. 81
Author(s):  
Kristina C. Backer ◽  
Heather Bortfeld
Keyword(s):  
Individual Differences ◽  
Cognitive Processes ◽  
Language Background ◽  
Bilingual Advantage ◽  
The Past ◽  
General Movement ◽  
And Performance ◽  
Task Irrelevant ◽  
Analytical Approaches ◽  
The Relationship

A debate over the past decade has focused on the so-called bilingual advantage—the idea that bilingual and multilingual individuals have enhanced domain-general executive functions, relative to monolinguals, due to competition-induced monitoring of both processing and representation from the task-irrelevant language(s). In this commentary, we consider a recent study by Pot, Keijzer, and de Bot (2018), which focused on the relationship between individual differences in language usage and performance on an executive function task among multilingual older adults. We discuss their approach and findings in light of a more general movement towards embracing complexity in this domain of research, including individuals’ sociocultural context and position in the lifespan. The field increasingly considers interactions between bilingualism/multilingualism and cognition, employing measures of language use well beyond the early dichotomous perspectives on language background. Moreover, new measures of bilingualism and analytical approaches are helping researchers interrogate the complexities of specific processing issues. Indeed, our review of the bilingualism/multilingualism literature confirms the increased appreciation researchers have for the range of factors—beyond whether someone speaks one, two, or more languages—that impact specific cognitive processes. Here, we highlight some of the most salient of these, and incorporate suggestions for a way forward that likewise encompasses neural perspectives on the topic.

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

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.

Past and recent biodiversity profiling in ancient Lake Chalco Mexico by a metagenomics analysis

2021 ◽  
Author(s):  
Bárbara Moguel ◽  
Liseth Pérez ◽  
Luis David Alcaraz ◽  
Socorro Lozano-García ◽  
Luis Herrera-Estrella ◽  
...  
Keyword(s):  
Volcanic Belt ◽  
Environmental Dna ◽  
Radiocarbon Dates ◽  
The Past ◽  
Mexican Volcanic Belt ◽  
History Of ◽  
High Throughput Dna Sequencing ◽  
High Altitude Lake ◽  
Taxonomic Groups ◽  
The Relationship

<p>For decades, paleoecological studies in lake sediments have focused on reconstructing the environments of the past and explaining phenomena linked to climatic variations. Recent advances in high-throughput DNA sequencing have allowed access to environmental DNA (eDNA) and ancient sedimentary DNA (sedaDNA) as a new and efficient proxy for past and present biodiversity. The basin of Mexico (BM) is located in the central part of the Trans-Mexican Volcanic Belt at 2,200 m a.s.l.; with the southern portion harboring the Chalco sub-basin. Lake Chalco is one of the last remaining natural aquatic ecosystems within the ever-expanding urban area surrounding Mexico City. The paleoenvironmental history of this lake has been previously characterized using sedimentological and geochemical proxies, as well as preserved microfossils (diatoms, pollen) with a temporal framework based on multiple radiocarbon dates. However, information for the remaining taxonomic groups and metabolic pathways remained unexplored. Here, we present the first metagenomics-based study for the Holocene in a high-altitude lake in Central Mexico –Lake Chalco. We explored the relationship between the lake’s paleoenvironmental condition and estimations of taxonomic and metabolic profiles across the sedimentary sequence (2.5 meters long). Multiple biological and abiotic variables revealed three main environmental phases: 1) a cool freshwater lake (FW1: 11,500-11,000 cal years BP), 2) a warm hyposaline lake (HS2: 11,000-6,000 cal years BP), and 3) a temperate, subsaline lake (SS3, <6,000 cal years BP). We describe the structure of the microbiota community and taxonomy richness turnover in the three Holocene paleoenvironmental phases. During the past 12 000 years BP the most abundant domains in Lake Chalco sediments were Bacteria, followed by Archaea, and Eukarya (36,722 genera). The analysis of functional proteins showed high biodiversity with a total of 27,636,243 proteins identified, but it was only possible to annotate 3,227,398 of them. Also, we identified several genes associated with some relevant pathways, such as methanogenesis. Altogether, this study allowed us to reconstruct the natural history of lake Chalco and its surroundings.</p>

Allegorie della libertŕ e tipologie del sacro nell'iconografia rivoluzionaria russa

2012 ◽  
pp. 57-80
Author(s):  
Dogo Dunja
Keyword(s):  
Cultural History ◽  
Russian Revolution ◽  
Symbolic System ◽  
The Past ◽  
History Of ◽  
Source Materials

Allegories of liberty and typologies of the sacred in the iconography of revolutionary Russia. Revolutionary iconography addresses a topic that crosses the field of studies of the Russian Revolution, whose scope in the past two decades has begun to investigate the cultural history of 1917, thanks to easier access to source materials that have re-emerged after the opening of the Russian archives. Above all, the essay attempts to reconstruct how three particular typologies (St. George, the Angel, Liberty) came into use in the Russian revolutionary symbolic system and underwent a metamorphosis, contributing to a phenomenon of syncretism. Such discourses can show how different political subjects – at times on opposing sides - employed a common imagery within a struggle for the conquest of the symbol.

Sign in / Sign up

Export Citation Format

Share Document