scholarly journals Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core

2021 ◽  
Vol 9 ◽  
Author(s):  
Johanna Krueger ◽  
Verena Foerster ◽  
Martin H. Trauth ◽  
Michael Hofreiter ◽  
Ralph Tiedemann

Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.

Author(s):  
Rob Marchant

The climatology of East Africa results from the complex interaction between major global convergence zones with more localized regional feedbacks to the climate system; these in turn are moderated by a diverse land surface characterized by coastal to land transitions, high mountains, and large lakes. The main climatic character of East Africa, and how this varies across the region, takes the form of seasonal variations in rainfall that can fall as one, two, or three rainy seasons, the times and duration of which will be determined by the interplay between major convergence zones with more localized regional feedbacks. One of the key characteristics of East Africa are climatic variations with altitude as climates change along an altitudinal gradient that can extend from hot, dry, “tropical” conditions to cool, wet, temperate conditions and on the highest mountains “polar” climates with permanent ice caps. With this complex and variable climate landscape of the present, as scientists move through time to explore past climatic variability, it is apparent there have been a series of relatively rapid and high-magnitude environmental shifts throughout East Africa, particularly characterized by changing hydrological budgets. How climate change has impacted on ecosystems, and how those ecosystems have responded and interacted with human populations, can be unearthed by drawing on evidence from the sedimentary and archaeological record of the past six thousand years. As East African economies, and the livelihoods of millions of people in the region, have been clearly heavily affected by climate variability in the past, so it is expected that future climate variability will impact on ecosystem functioning and the preparedness of communities for future climate change.


2019 ◽  
pp. 451-458
Author(s):  
Peter W. Rein

Developments in the technology of production of sugar from sugarcane tend to be incremental improvements in an effort to reduce costs and boost revenue. Nonetheless the developments are significant and contribute to sustainable sugarcane enterprises. Some technologies have adapted to changing environmental conditions, and more attention is being given to boosting revenue through associated activities, particularly in enhancing the potential for sugarcane operations to exploit the energy value of sugarcane. This paper outlines recent developments of interest in processing sugarcane.


2021 ◽  
pp. 146960532199394
Author(s):  
Venla Oikkonen

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.


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

Author(s):  
Wilmar Salo ◽  
William C. Auferheide ◽  
Michael Madden ◽  
John Streitz ◽  
Jane Buikstra ◽  
...  

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.


2021 ◽  
Author(s):  
Stefano Meucci ◽  
Luise Schulte ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Konstantin Krutovsky ◽  
...  

<p>Siberian larch forests dominate large areas of northern Russia and contribute important roles for the world´s ecosystem. In order to understand the past dynamics of larches and their adaptive genetic variation, sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores is a crucial source of genetic material. The difficulty of retrieving extremely rare DNA sequences from samples reaching back up to 25000 years in age, is challenging. Previous studies (Schulte et al.) showed that the hybridization capture allowed an enrichment of targeted sequences by several orders of magnitude in comparison to shotgun sequencing method. Therefore, we established for the first time, a hybridization capture method targeting 65 candidate adaptive genes laying on the Larix nuclear genome. Our preliminary results showed the ability of our newly established method to enrich extremely rare DNA sequences of the targeted Larix candidate adaptive genes, which were not retrieved by shotgun sequencing method applied on the same samples. Furthermore, the results allowed to detect and compare specific nucleotide polymorphism of adaptive candidate genes among sedaDNA samples distributed in space and time. The establishment of this new method is laying the basis to investigate possible adaptive variation of larch species acquired across the dry and cold conditions of the Last Glacial Maximum (LGM); as well as their possible advantages or disadvantages in relation to the current environmental changes toward dry and warm conditions.</p>


Koedoe ◽  
1989 ◽  
Vol 32 (1) ◽  
Author(s):  
Ina Plug

Faunal remains obtained from archaeological sites in the Kruger National Park, provide valuable information on the distributions of animal species in the past. The relative abundances of some species are compared with animal population statistics of the present. The study of the faunal samples, which date from nearly 7 000 years before present until the nineteenth century, also provides insight into climatic conditions during prehistoric times.


Africa ◽  
1928 ◽  
Vol 1 (1) ◽  
pp. 63-72 ◽  
Author(s):  
J. H. Driberg

Generalizations based on insufficient or inaccurate data have in the past contributed to many anthropological fallacies. Instances of such hasty generalizations will come to mind readily enough, and it will be recollected that whole theories have been so formulated and, after leading anthropological enquiry down sterile labyrinths of thought to dogmatical culs-de-sac, have had to be jettisoned with all their accumulated impedimenta of false inferences and falser conclusions. There is no room as yet for broad generalizations in cultural anthropology: our reliable information is still too fragmentary and unrelated.


2016 ◽  
Vol 17 (2) ◽  
pp. 300-313 ◽  
Author(s):  
Elmira Mohandesan ◽  
Camilla F. Speller ◽  
Joris Peters ◽  
Hans-Peter Uerpmann ◽  
Margarethe Uerpmann ◽  
...  

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