scholarly journals Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan

2018 ◽  
Author(s):  
Rikai Sawafuji ◽  
Aiko Saso ◽  
Wataru Suda ◽  
Masahira Hattori ◽  
Shintaroh Ueda
Keyword(s):  
Dna Analysis ◽  
Dietary Diversity ◽  
Isotope Analysis ◽  
Dental Calculus ◽  
Edo Period ◽  
The Past ◽  
Dna Metabarcoding ◽  
Food Species ◽  
Genus Oryza ◽  
Taxonomic Groups

Objectives: Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of Edo people for the taxonomic identification of food species. Materials and Methods: DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza, because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi was also carried out to investigate dietary diversity. Results: We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Discussion: Most of the plant taxonomic groups are present in Japan and include species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as starch analysis and stable isotope analysis.

scholarly journals Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan

PLoS ONE ◽  
2020 ◽  
Vol 15 (3) ◽  
pp. e0226654 ◽  
Author(s):  
Rikai Sawafuji ◽  
Aiko Saso ◽  
Wataru Suda ◽  
Masahira Hattori ◽  
Shintaroh Ueda
Keyword(s):  
Ancient Dna ◽  
Dna Analysis ◽  
Dental Calculus ◽  
Edo Period ◽  
Ancient Dna Analysis

scholarly journals Impact of the COVID-19 pandemic on agricultural production, livelihoods, and food security in India: baseline results of a phone survey

Food Security ◽  
2021 ◽  
Author(s):  
Lindsay M. Jaacks ◽  
Divya Veluguri ◽  
Rajesh Serupally ◽  
Aditi Roy ◽  
Poornima Prabhakaran ◽  
...  
Keyword(s):  
Food Security ◽  
Agricultural Production ◽  
Dietary Diversity ◽  
The Past ◽  
Phone Survey ◽  
Extra Food ◽  
The Government ◽  
Time Of Year ◽  
Livestock Products ◽  
The Impact

AbstractThe aim of this study was to evaluate the impact of the COVID-19 lockdown on agricultural production, livelihoods, food security, and dietary diversity in India. Phone interview surveys were conducted by trained enumerators across 12 states and 200 districts in India from 3 to 15 May 2020. A total of 1437 farmers completed the survey (94% male; 28% 30–39 years old; 38% with secondary schooling). About one in ten farmers (11%) did not harvest in the past month with primary reasons cited being unfavorable weather (37%) and lockdown-related reasons (24%). A total of 63% of farmers harvested in the past month (primarily wheat and vegetables), but only 44% had sold their crop; 12% were still trying to sell their crop, and 39% had stored their crop, with more than half (55%) reporting lockdown-related issues as the reason for storing. Seventy-nine percent of households with wage-workers witnessed a decline in wages in the past month and 49% of households with incomes from livestock witnessed a decline. Landless farmers were about 10 times more likely to skip a meal as compared to large farmers (18% versus 2%), but a majority reported receiving extra food rations from the government. Nearly all farmers reported consuming staple grains daily in the past week (97%), 63% consumed dairy daily, 40% vegetables daily, 26% pulses daily, and 7% fruit daily. These values are much lower than reported previously for farmers in India around this time of year before COVID-19: 94–95% dairy daily, 57–58% pulses daily, 64–65% vegetables daily, and 42–43% fruit daily. In conclusion, we found that the COVID-19 lockdown in India has primarily impacted farmers’ ability to sell their crops and livestock products and decreased daily wages and dietary diversity.

First wolves in Luxembourg since 1893, originating from the Alpine and Central European populations

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Laurent Schley ◽  
Marianne Jacobs ◽  
Sebastian Collet ◽  
Alexander Kristiansen ◽  
Jan Herr
Keyword(s):  
Canis Lupus ◽  
Dna Analysis ◽  
Carcass Characteristics ◽  
Management Plan ◽  
Apex Predator ◽  
Grey Wolf ◽  
Melting Pot ◽  
Central European ◽  
The Past ◽  
Hard Evidence

Abstract Considering the spread of the grey wolf (Canis lupus) in Europe over the past 30 years, Luxembourg took some measures to prepare for the return of this apex predator, including the establishment of a management plan that notably addresses the issue of wolf depredation on livestock. Here we present the results of genetic analyses of putative wolf saliva, hair and scat samples collected from or near prey carcasses between 2015 and 2020. In two cases, the wolf was confirmed via DNA analysis: in July 2017 near Garnich and in April 2020 near Niederanven, both assigned to category C1 (hard evidence). A third case was classified as C2 (confirmed observation) based on prey carcass characteristics, while genetic analysis yielded no result. These are the first confirmed records of wolves in Luxemburg since 1893. Moreover, the two C1-cases originated from the Alpine (Garnich) and Central European (Niederanven) populations. Given similar developments in the neighboring countries and regions, we conclude that the area including the Benelux countries as well as Rhineland-Palatinate, Saarland and Northern France may well become a melting pot for wolves of the two aforementioned populations in the coming years and decades.

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>

scholarly journals Ecology of the Anthropocene signals hope for consciously managing the planetary ecosystem

2021 ◽  
Vol 118 (28) ◽  
pp. e2024150118
Author(s):  
Clarence Lehman ◽  
Shelby Loberg ◽  
Michael Wilson ◽  
Eville Gorham
Keyword(s):  
Population Growth ◽  
Cultural Evolution ◽  
Human Population ◽  
Human Populations ◽  
Present Moment ◽  
Minimal Set ◽  
The Past ◽  
Food Species ◽  
Large Predators ◽  
Population Numbers

Human populations have grown to such an extent that our species has become a dominant force on the planet, prompting geologists to begin applying the term Anthropocene to recognize the present moment. Many approaches seek to explain the past and future of human population growth, in the form of narratives and models. Some of the most influential models have parameters that cannot be precisely known but are estimated by expert opinion. Here we apply a unified model of ecology to provide a macroscale summary of the net effects of many microscale processes, using a minimal set of parameters that can be known. Our models match estimates of historic and prehistoric global human population numbers and provide predictions that correspond to some of the more complicated current models. In addition to fitting the data well they reveal that, amidst enormous complexity in our human and prehuman past, three key ecological discontinuities have occurred in turn: 1) becoming dominant competitors of large predators rather than their prey, 2) becoming mutualists with food species rather than acting as predators upon them, and 3) changing from a regime of uncontrolled population growth to one of controlled fertility instead. All three processes have been interlinked with cultural evolution and all three ushered in developments of the Anthropocene. Understanding the trajectories that have delivered us to this stage can help guide prudent paths into the future.

scholarly journals Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks

2019 ◽  
Vol 3 ◽  
Author(s):  
Vasselon Valentin ◽  
Rimet Frédéric ◽  
Domaizon Isabelle ◽  
Monnier Olivier ◽  
Reyjol Yorick ◽  
...  
Keyword(s):  
Water Framework Directive ◽  
High Throughput Sequencing ◽  
Ecological Status ◽  
Aquatic Environments ◽  
Morphological Identification ◽  
The Past ◽  
Sequencing Technologies ◽  
Dna Metabarcoding ◽  
Morphological Approach ◽  
Status Assessment

Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.

Conclusion

2020 ◽  
pp. 363-372
Keyword(s):  
United States ◽  
Human Rights ◽  
United Kingdom ◽  
Dna Analysis ◽  
The United States ◽  
Forensic Dna ◽  
Criminal Cases ◽  
Forensic Dna Analysis ◽  
The Past ◽  
Dna Technology

The first applications of DNA technology in criminal cases took place in the United States and United Kingdom more than 30 years ago. What have we learned over the past three decades from the use of forensic DNA analysis in criminal and human rights investigations and humanitarian disasters? And what challenges, opportunities, and potential pitfalls lie ahead?...

Nutritional Status Among School-Age Children of Bangladeshi Tea Garden Workers

2020 ◽  
Vol 41 (4) ◽  
pp. 424-429
Author(s):  
Mohd Shamim Iqbal ◽  
Amanda C. Palmer ◽  
Jillian Waid ◽  
S. M. Mustafizur Rahman ◽  
Md. M. Islam Bulbul ◽  
...  
Keyword(s):  
Nutritional Status ◽  
Food Insecurity ◽  
Dietary Diversity ◽  
Underserved Populations ◽  
World Health ◽  
School Age Children ◽  
School Age ◽  
The Past ◽  
Household Food ◽  
Plasma Retinol

Background: While considerable progress has been made in reducing undernutrition in Bangladesh, regional disparities are known to exist, and certain population subgroups may lag behind. Objective: To characterize nutritional status among school-age children in a historically marginalized population of Bangladesh. Methods: We conducted a cross-sectional assessment of children attending 14 nongovernmental organization-operated schools serving the tea estate population in Kulaura Upazila, Sylhet Division. We randomly selected 168 children from a population of 418 whose parents attended school-organized Parent–Teacher Association meetings. Parents provided consent and data on household food consumption in the past week, foods consumed by children in the past 24 hours, and household food insecurity. We drew venous blood from assenting children for the analysis of hemoglobin and plasma retinol, C-reactive protein, and α1-acid glycoprotein. Children were classified as stunted, underweight, or thin based on comparisons with the World Health Organization standards for height-for-age, weight-for-age, or body mass index-for-age, respectively. Results: Food insecurity was highly prevalent, with ∼85% of households affected. Roughly half of children had low dietary diversity. Prevalence estimates for stunting, underweight, and thinness were 32%, 50%, and 49%, respectively. Approximately 60% of children had a hemoglobin concentration <11 g/dL. The mean (±SD) plasma retinol concentration was 0.79 μmol/L (±0.23 μmol/L), with 34% deficient using a 0.70 μmol/L cutoff. Conclusions: A heightened focus on tracking progress in underserved populations and appropriately targeted programming will be critical as Bangladesh seeks to accelerate progress toward global development goals for nutrition.

scholarly journals The Under-Appreciated Rodent: Harbingers of Plague From the Middle Ages to the Twenty-First Century

2019 ◽  
Vol 50 (2) ◽  
pp. 171-185 ◽  
Author(s):  
Anne Hardy
Keyword(s):  
Middle Ages ◽  
Dna Analysis ◽  
First Century ◽  
Bubonic Plague ◽  
The Past ◽  
Black Rat ◽  
History Of ◽  
Ancient Dna Analysis ◽  
Long Term Trends

The history of the rat and the wider rodent family in relation to bubonic plague suggests multiple ways in which different research disciplines can contribute to the understanding of mortality, morbidity, and epidemics in the past: For instance, demographic approaches can can clarify long-term trends in, and disruptions to, patterns of mortality; the study of psychological responses to disease since 1850 can lend insights into past disease behaviors; and archaeological discoveries and the still-developing technology of ancient dna analysis can help in the determination of causes and effects. As the link between the black rat and bubonic plague shows, without the collaboration of interdisciplinary methods, our understanding would surely suffer. The history of plague and the Black Death encompasses far more than the involvement of rats, but the enduring sylvatic reservoirs of plague infection that the rats and their many rodent cousins constituted in the past, and still constitute, should not be blithely discounted.

scholarly journals Behavioral and trophic segregations help the Tahiti petrel to cope with the abundance of wedge-tailed shearwater when foraging in oligotrophic tropical waters

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andreas Ravache ◽  
Karen Bourgeois ◽  
Henri Weimerskirch ◽  
Angélique Pagenaud ◽  
Sophie de Grissac ◽  
...  
Keyword(s):  
Trophic Ecology ◽  
Isotope Analysis ◽  
Foraging Strategy ◽  
Gps Tracking ◽  
Ecological Niches ◽  
Extensive Search ◽  
Tropical Area ◽  
Time Space ◽  
Dna Metabarcoding ◽  
Breeding Seasons

Abstract Two species breeding in sympatry are more likely to coexist if their ecological niches are segregated either in time, space or in trophic habits. Here, we combined GPS-tracking, stable isotope analysis and DNA metabarcoding analysis to understand how the rare Tahiti petrel Pseudobulweria rostrata (TP) copes with the very abundant (i.e. 500,000 breeding pairs) wedge-tailed shearwater Ardenna pacifica (WTS) when breeding in sympatry in a tropical area. WTS foraged in restricted areas along their path, while TP predominantly foraged using extensive search behavior, suggesting a more opportunistic foraging strategy. Interspecific overlap of foraging areas was higher than intraspecific overlap. Breeding seasons largely overlap between species during the study, but TP seems to be asynchronous breeders. TP fed upon prey with higher δ15N values than WTS, and their diet was mainly composed of deep-sea organisms. TP could feed upon dead prey floating at the surface while WTS preyed mainly upon fish species that generally move in schools. Our study highlights several segregating mechanisms (temporal, behavioral and trophic) that could facilitate the coexistence of the two species despite the predominant number of WTS, and provides the very first information on the foraging and trophic ecology of the poorly-known TP.

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