Thursday, March 02, 2023

Largest-ever genetic analysis of grapevine varieties reveals how glacial cycles shaped grape domestication and the rise of wine

Peer-Reviewed Publication

AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE (AAAS)

In the largest ever genetic analysis of grapevine varieties, including samples from previously undocumented specimens in private collections, researchers provide new insights into how, when, and where wine and table grapevines were domesticated, which has been a longstanding question. “This work represents a major international collaborative effort, challenging to do in any circumstances but especially so given that we conducted it during the COVID-19 pandemic and associated lockdowns,” said author Wei Chen, who will also participate in an embargoed briefing on this study this week.

Even though wine and grapes are very important culturally, when wine and table grapevines were domesticated, and where, has been difficult to confirm. This is largely because there haven’t been sufficiently wide genetic sequencing analyses on grapevine varieties. As a result, there are several standing hypotheses in the literature that remain uncertain. For example, researchers have thought the cultivated wine grapevine (Vitis vinifera) had a single domestication in Western Asia, from which all wine varieties stemmed, and that it happened before the advent of agriculture. They’ve also thought wine grapevines were cultivated before table grape grapevines. Now, a study by Yang Dong and colleagues pushes back on both ideas. Based on vast grapevine genetic data studied, their report shows there were two domestication events for the cultivated wine grapevine in two distinct places – Western Asia and the Caucasus region – separated during the last glacial advance. “Despite being separated by over 1000 [kilometers], the two domestication processes appear to have occurred contemporaneously with a high degree of shared signatures of selection on the same genes,” writes Robin Allaby in a related Perspective. What’s more, they showed that these domestication events took place 11,000 years ago – in line with the advent of farming, and about 4,000 years later than some studies have shown. The genetic data also suggest that wine and table grapes were cultivated at the same time – not the wine grapevine first. The authors also identify some genes involved in domesticating grapes – improving flavor and color and texture – that could help winemakers improve wine today and make varieties more resilient to climate change and other stresses. Among their findings, they uncover more about the genetics underlying white grape color, and the ancient muscat flavor; at least one allele underlying muscat flavor may be detrimental to plant health, they say.

To do this work, Dong and colleagues generated a high-quality chromosome level reference genome of wild grapevine progenitor Vitis sylvestris. They then re-sequenced more than 3,000 individual grapevine plant samples collected from wide geographic locations – including from wild locations and from private collections. “Our collaborators reached out to their connections and looked for old and local varieties,” said Chen. “For instance, a lot of the Armenia [samples] from old vineyards turned out to be undocumented varieties.” The multimedia related to this paper includes videos from several international collaborators reflecting on the study’s process and significance.

**This paper is related to an Annual Meeting Briefing for Science, titled “Largest-ever genetic analysis of grapevine varieties reveals how glacial cycles shaped grape domestication and the rise of wine,” to be held on March 2nd at 11:00 am US ET. You can access the briefing virtually here if you are registered for the AAAS Annual Meeting (Please add briefing link to your calendars).

NOTE: If you’d like to attend this and other briefings at the 2023 Annual Meeting and have not yet registered, please do so by March 1st [Register Here. At the Registration Access Code step, please enter PRESS.]**

Ecological improvement of freshwater ecosystems benefits fish and people

Peer-Reviewed Publication

LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES

Ecosystem-based habitat enhancement through creation of shallow water zones. 

IMAGE: ECOSYSTEM-BASED HABITAT ENHANCEMENT THROUGH CREATION OF SHALLOW WATER ZONES. PHOTO: THOMAS KLEFOTH view more 

CREDIT: THOMAS KLEFOTH

Biodiversity is declining rapidly. Many conservation actions focus on single species. An alternative approach is to comprehensively improve ecological processes and habitats, thereby supporting entire species communities. This so-called ecosystem-based management is however rarely implemented because it is costly. There is also a lack of evidence that ecosystem-based habitat management is more effective than obvious alternatives, such as releasing animals to enhance stocks.

Important lesson for fish conservation 

A research team based in Berlin, in close cooperation with numerous angling clubs organized in the Angler Association of Lower Saxony, has presented a groundbreaking study. Scientists and practitioners worked together to conduct a set of whole-lake experiments and assess the outcomes of ecosystem-based habitat enhancement versus fish stocking in 20 gravel pit lakes over a period of six years. In some of the lakes, additional shallow water zones were created. In other lakes, coarse wood bundles were added to enhance structural diversity. Other study lakes were stocked with five fish species of interest to fisheries; unmanipulated lakes served as controls. The study was based on a sample of more than 150,000 fish.

The key result: The creation of shallow water zones was the most effective method to enhance fish populations. These zones are ecologically important for many fish species, especially as spawning grounds and nursery areas for young fish. The introduction of coarse wood had only positive effects in selected lakes; fish stocking completely failed. "Restoring central ecological processes and habitats – ecosystem-based management – is likely to have stronger long-term effects for rebuilding fish species and populations than narrow, species-focused conservation actions," explained Johannes Radinger of the IGB, lead author of the study.

From the laboratory to jointly executed whole-lake experiments

Never before have fish communities been studied on such a large-scale set of whole-lake experiments involving numerous angling clubs and other practitioners. "In contrast to studies in the laboratory, field experiments that consider natural ecosystem variation as well as ecological and social interactions allow to gain robust evidence about the effectiveness of management measures," explained Thomas Klefoth, professor at the Hochschule Bremen and co-initiator of the project. "To include multiple gravel pit lakes in the experiments was only possible through close cooperation between research and practice. The transdisciplinary approach contributed to a rethinking of fish stocking and fostered the acceptance of more sustainable, ecosystem-based management alternatives," summarized study leader Robert Arlinghaus, Professor of Integrative Fisheries Management at the HU and the IGB.

Two key messages for freshwater conservation and fisheries management

The study highlights two central messages that are relevant beyond gravel pit lakes to other aquatic ecosystems as well: restoring ecological processes has a more sustainable impact on communities and species than narrow, species-focused conservation actions. Additionally, freshwater biodiversity conservation is most effective when user groups, such as angling clubs, take responsibility and are supported in their efforts by authorities, associations, and science. This approach allows for the reconciliation of conservation and use, as both species and fisheries benefit from ecosystem-based management.

******

About the project:

BAGGERSEE (www.baggersee-forschung.de) is a joint project of the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), the Angler Association of Lower Saxony (AVN), and the Technical University of Berlin (TU), in cooperation with the Hochschule Bremen (HSB). The research and implementation project was funded until the end of 2022 as part of the joint funding initiative "Research for the implementation of the National Biodiversity Strategy" by the Federal Ministry of Education and Research (BMBF) and the Federal Agency for Nature Conservation (BfN) with funds from the Federal Ministry for the Environment, Nature Conservation, Nuclear Safety and Consumer Protection (BMUV). The project has been coordinated by Prof. Dr. Robert Arlinghaus, who is affiliated with the IGB and the Humboldt Universität zu Berlin (HU). Further details about the working group can be found at www.ifishman.de.

 

About the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB):

“Research for the future of our freshwaters” is the mission of the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB). IGB is Germany’s largest and one of the leading international centres for freshwater research. It integrates basic and preventive research, and studies freshwater ecosystems and their biotic communities in all their complexity. With more than 350 employees at five locations, the Institute conducts research on how water bodies develop over very long periods of time, how they react to natural and human-caused environmental changes or how new forms of use, restoration or conservation affect rivers, lakes, wetlands and various species. In close collaboration with partners from research, politics, authorities, practice and civil society, IGB also deals with current ecological and societal challenges, such as how adaptation to climate change can succeed, how we protect and conserve aquatic biodiversity and how we use land and water bodies more sustainably. IGB is a member of the Leibniz Association and part of the Forschungsverbund Berlin e.V. www.igb-berlin.de.

European perch (Perca fluviatilis) - one of the study species - is a key predator in temperate lakes. 


Photo: Florian Möllers

Most detailed geological model reveals Earth’s past 100 million years

Sophisticated digital tool can help us understand the past and predict the evolution of the Earth’s surface

Peer-Reviewed Publication

UNIVERSITY OF SYDNEY

Animation of landscape dynamics model over past 100 million years 

VIDEO: ANIMATION OF LANDSCAPE DYNAMICS MODEL OVER PAST 100 MILLION YEARS SHOWING LANDSCAPE EROSION AND SEDIMENT DEPOSITION. view more 

CREDIT: DR TRISTAN SALLES, THE UNIVERSITY OF SYDNEY

Climate, tectonics and time combine to create powerful forces that craft the face of our planet. Add the gradual sculpting of the Earth’s surface by rivers and what to us seems solid as rock is constantly changing.

However, our understanding of this dynamic process has at best been patchy.

Scientists today have published new research revealing a detailed and dynamic model of the Earth’s surface over the past 100 million years.

Working with scientists in France, University of Sydney geoscientists have published this new model in the prestigious journal Science.

For the first time, it provides a high-resolution understanding of how today’s geophysical landscapes were created and how millions of tonnes of sediment have flowed to the oceans.

Lead author Dr Tristan Salles from the University of Sydney School of Geosciences, said: “To predict the future, we must understand the past. But our geological models have only provided a fragmented understanding of how our planet’s recent physical features formed.

“If you look for a continuous model of the interplay between river basins, global-scale erosion and sediment deposition at high resolution for the past 100 million years, it just doesn’t exist.

“So, this is a big advance. It’s not only a tool to help us investigate the past but will help scientists understand and predict the future, as well.”

Using a framework incorporating geodynamics, tectonic and climatic forces with surface processes, the scientific team has presented a new dynamic model of the past 100 million years at high resolution (down to 10 kilometres), broken into frames of a million years.

Second author Dr Laurent Husson from Institut des Sciences de la Terre in Grenoble, France, said: “This unprecedented high-resolution model of Earth’s recent past will equip geoscientists with a more complete and dynamic understanding of the Earth’s surface.

“Critically, it captures the dynamics of sediment transfer from the land to oceans in a way we have not previously been able to.”

Dr Salles said that understanding the flow of terrestrial sediment to marine environments is vital to comprehend present-day ocean chemistry.

“Given that ocean chemistry is changing rapidly due to human-induced climate change, having a more complete picture can assist our understanding of marine environments,” he said.

The model will allow scientists to test different theories as to how the Earth’s surface will respond to changing climate and tectonic forces.

Further, the research provides an improved model to understand how the transportation of Earth sediment regulates the planet’s carbon cycle over millions of years.

“Our findings will provide a dynamic and detailed background for scientists in other fields to prepare and test hypotheses, such as in biochemical cycles or in biological evolution.”

Authors Dr Salles, Dr Claire Mallard and PhD student Beatriz Hadler Boggiani are members of the EarthColab Group and Associate Professor Patrice Rey and Dr Sabin Zahirovic are part of the EarthByte Group. Both groups are in the School of Geosciences at the University of Sydney.

The research was undertaken in collaboration with French geoscientists from CNRS, France, Université Lyon and ENS Paris.

DOWNLOAD animated models of landscape dynamics and photos at this link.

AVAILABLE FOR INTERVIEW

Dr Tristan Salles | School of Geosciences | tristan.salles@sydney.edu.au |
(Speaks English and French)

CAPTION

Lead author Dr Tristan Salles from the School of Geosciences at the University of Sydney.

CREDIT

Stefanie Zingsheim, The University of Sydney

World map animation of landscape evolution over past 100 million years (VIDEO)  https://www.eurekalert.org/multimedia/976138

Animals best to supress personalities for group efficiency

Peer-Reviewed Publication

UNIVERSITY OF BRISTOL

Social animals should limit individuality to conform with the behaviour of the group, a University of Bristol study has found.

Scientists at Bristol’s School of Biological Sciences observed that group safety was improved when animals paid attention to the behaviours of each other.

Their findings, published today in PLoS Computational Biology, reveal that simple social behavioural rules can drive conformity behaviour in groups, eroding consistent behavioural differences shown by individual animals.

Lead author Dr Sean Rands said: “Personality suppression may be a common strategy in group-living animals, and in particular, we should tend to see the behaviours of the most adventurous or shy individuals shifting towards what the majority of the group are doing.”

The team modelled the behaviour of a small group of animals with differing tendencies while performing risky behaviours when travelling away from a safe home site towards a foraging site. They then compared this to their behaviour while completing the same activity in a group.

The group-aware individuals spent longer in the safe space and moved more quickly to the foraging spot, making the mission less dangerous.

Co-author Professor Christos Ioannou, explained: “Groups are usually made up of individuals who are different to each other in the way that they normally behave – these consistent individual differences are what determines the personality of the individual.

“Experimental evidence for this comes from animals like the stickleback fish that we study in our lab. We can measure the personality of individual fish when they are given a food-finding task on their own, and compare it to what happens when they are put in a group of mixed personalities and given the same task.

“When faced with a social task, we find that the fish tend to suppress their own behaviour, and instead conform with what other fish in the group are doing.”

Dr Rands concluded: “We find that if individuals pay attention to other group members, this has an overall impact on the efficiency of the group, and demonstrates that simple social behaviours can result in the suppression of individual personalities.

“This suggests that compromise may lie at the heart of many social behaviours across the animal kingdom.”

 

Paper:

‘Personality variation is eroded by simple social behaviours in collective foragers’ by Sean Rands and Christos Ioannnou in PLoS Computational Biology.

 

“You throw up, then you cough, then you feel better or die”

Children’s drawings during the COVID-19 pandemic - a Swedish study

Peer-Reviewed Publication

UPPSALA UNIVERSITY

Two children fighting Corona 

IMAGE: CHILD, AGED 5: "CORONA. TWO CHILDREN FIGHTING CORONA". A NEW STUDY ABOUT CHILDREN'S DRAWING ABOUT COVID-19 PANDEMIC view more 

CREDIT: SWEDISH ARCHIVE OF CHILDREN’S ART

Detailed images of illness, death and cancelled activities; these were some of the common themes of children’s drawings during the COVID-19 pandemic. A new study from Uppsala University, in which researchers studied 91 drawings made by children aged between 4 and 6, shows that the pandemic affected the children significantly and that they had extensive knowledge about the disease.

It is not every day that children’s drawings become the focus of a scholarly article. In the new study published in the journal Acta Paediatrica, however, the research was entirely based on drawings about the pandemic. The researchers collected all of the drawings produced by children between the ages of 4 and 6 that had been submitted to the Swedish Archive of Children’s Drawings between April 2020 and February 2021.

“It was a very fun study to carry out. I was actually quite uncertain as to whether a medical journal would publish the article, but they did, including the children’s drawings and everything,” explains Anna Sarkadi, Professor of Social Medicine and leader of the study.

Using a method of analysis whereby children’s own explanations of their image were combined with a visual analysis of the drawings, the researchers were able to show that even younger children were strongly affected by the pandemic. They drew detailed images of illness, death and cancelled activities. Fear, worry and missing grandparents were common themes. Some children described the coronavirus as a monster, while others described how to protect yourself. One drawing depicted two children in a fencing battle against a giant virus.

“The drawings were often covered in a lot of snot. On one drawing, a child wrote: ‘You throw up, then you cough, then you feel better or die,’ with extremely clear illustrations,” explains Maria Thell, doctoral student in the CHAP research team and one of the authors behind the study.

The children also had a high level of health literacy related to COVID-19, i.e. knowledge of the virus’s characteristics, how it spread and what symptoms the disease could cause. The project was part of investigations into children’s voices in the public space during the pandemic.

“As a researcher with a background in child and youth science, I would love to develop this method further,” adds Thell.

The team will continue the research at the request of the Public Health Agency of Sweden, which has tasked them with analysing drawings made by 7­­–11-year-olds during or just after the pandemic.

Sarkadi, A, Thell, M, Jirblom, K. Perceptions of the COVID-19 pandemic as demonstrated in drawings of Swedish children aged 4–6 years. Acta Paediatr. 2023; 00: 1– 9. https://doi.org/10.1111/apa.16706

 

Child, aged 6: “Closed for playing” (Lekstängt)

CAPTION

Child, aged 5: “A boy coughed and put his hands over there (on the house) and someone came and touched it, then they got sick. X means that you shouldn't go outside and catch bacteria. The bacteria are underground. Blue faces mean you feel sick.”

CREDIT

Swedish Archive of Children’s Art

Small differences in mom’s behavior may show up in child’s epigenome

Peer-Reviewed Publication

WASHINGTON STATE UNIVERSITY

PULLMAN, Wash. – Adding evidence to the importance of early development, a new study links neutral maternal behavior toward infants with an epigenetic change in children related to stress response. 

Epigenetics are molecular processes independent of DNA that influence gene behavior. In this study, researchers found that neutral or awkward behavior of mothers with their babies at 12 months correlated with an epigenetic change called methylation, or the addition of methane and carbon molecules, on a gene called NR3C1 when the children were 7 years old. This gene has been associated with regulating the body’s response to stress. 

“There is evidence of a relationship between the quality of maternal-infant interaction and methylation of this gene though these are small effects in response to a relatively small variation in interaction,” said Elizabeth Holdsworth, a Washington State University biological anthropologist and lead author of the study published in the American Journal of Human Biology

Other studies have connected extreme stress in early life, like neglect and abuse, to more dramatic methylation on this particular gene in adults. However, Holdsworth emphasized that the small difference indicated by this study may be an indication of normal human variation and it’s hard to determine if there are any long-term effects. 

For this study, Holdsworth and her co-authors analyzed a subsample of 114 mother-infant pairs from the Avon Longitudinal Study of Parents and Children, a project that tracks a cohort of children born in 1991 and 1992 in Avon, UK. 

The researchers first analyzed data from an observational study of the mothers sharing a picture book with their children at 12 months, in which their interactions were coded on warmth. The study focused on mothers because they are often infants’ primary caregivers. The vast majority of the women in this sample were white, college-educated and from middle-income households. The range of warmth they displayed only varied slightly with the “coldest” behavior classified as awkward or neutral, but this is exactly what the researchers hoped to test: that if even small differences in social interaction could be linked to an epigenetic change.  

The observed behavior was then compared against data from an epigenetic analysis of the children’s blood samples taken at age seven. The researchers found that the mothers showing awkward or neutral behavior toward their infant correlated with a small increase of methylation on the NR3C1 gene. This gene encodes a receptor involved in the regulation of the HPA axis -- the interaction between the body’s hypothalamus, pituitary and adrenal glands. This axis plays a role in stress response, including production of the body’s primary “stress” hormone, cortisol.

The HPA axis can be activated by almost anything that requires a quick release of energy from reacting to a real threat to watching a scary movie to simply exercising. The NR3C1 gene is known to be involved in activating this axis, but more research is needed to understand how methylation of that gene is associated with stress response, Holdsworth said, as some studies have shown increased methylation linked to hypo-reactivity, or blunted response while others have shown hyper-reactivity.

Researchers are working to uncover how these changes happen, particularly during infancy when the body is developing rapidly – as well as what they might mean. 

“Within developmental biology, we know humans grow to fit the environment that they’re in, which contributes to normal human biological variation. It’s not necessarily good or bad,” she said. 

In addition to Holdsworth, co-authors on this study include Lawrence Schell and Allison Appleton from University at Albany, State University of New York. This research received support from the Biotechnology and Biological Sciences Research Council, the National Institutes of Health, the National Science Foundation and the Wellcome Trust.

Biopesticides should be preferred over chemical pesticides for fall armyworm control, study suggests

Safer-to-use and more environmentally-friendly biopesticides should be preferred to fight the fall armyworm (Spodoptera frugiperda) pest instead of more harmful chemical pesticides, a new CABI-led study published in the Journal of Pest Science suggests.

Peer-Reviewed Publication

CABI

Fall armyworm 

IMAGE: THE OUTBREAK OF THE FALL ARMYWORM HAS LED TO SEVERAL RECOMMENDATIONS ON INSECTICIDES, INCLUDING BIOPESTICIDES, BUT THE EFFECTS OF THESE PRODUCTS ON THE ENVIRONMENT – ESPECIALLY PARASITOIDS – HAS NOT PREVIOUSLY BEEN ASSESSED UNDER FIELD CONDITIONS view more 

CREDIT: CABI

Safer-to-use and more environmentally-friendly biopesticides should be preferred to fight the fall armyworm (Spodoptera frugiperda) pest instead of more harmful chemical pesticides, a new CABI-led study published in the Journal of Pest Science suggests.

CABI scientists teamed up with colleagues from Ghana’s CSIR-Savanna Agricultural Research Institute (SARI), the University for Development Studies (UDS) and the Plant Protection and Regulatory Services Directorate (PPRSD) to investigate the effects of insecticides – including biopesticides – on the environment.

Specifically, the researchers conducted experiments both on-station in Wa and Nyankpala and on-farm in Wa during the 2020 rainy season to test the effect of commonly used biopesticides on fall armyworm in northern Ghana.

The fall armyworm is a highly destructive pest of cereals and has invaded Africa, parts of Asia and Australia over the past six years – threatening the food security and income of millions of smallholder farmers many of whom rely on maize as their staple crop.

While the outbreak of the pest in Africa has led to several recommendations of insecticides, including biopesticides, the effects of these products on the environment – especially parasitoids – have not been assessed under field conditions.

Active ingredients tested included neem oil (3% Azadirachtin), maltodextrin (282g/l), 55% Bacillus thuringienis (Bt) combined with 45% Monosultap, and a Pieris rapae granulosis virus combined with 5% Bt.

A chemical insecticide based on emamectin benzoate and acetamiprid was used as positive control while non-treated maize plots were considered as untreated control.

The two most abundant parasitoids in Wa were Coccygidium luteum and Chelonus bifoveolatus, while in Nyankpala they were C. luteum and Meteorus sp. Total larval parasitism rates on-station were 18.7% and 17.6% in Wa and Nyankpala, respectively, and 8.8% in Wa on-farm.

Dr Lakpo Koku Agboyi, Project Manager – Invasive Species Management at CABI and lead author on the paper, said, “Untreated maize plots showed the highest larval density and plant damage, the highest cob damage, and generated the lowest yields. The other treatments showed hardly any difference in cob damage and yields, suggesting that biopesticides should be preferred over chemical pesticides for fall armyworm control.”

The researchers found that, in general, parasitism was lower in the maize fields treated with Ema Star and Bypel 1 as compared to untreated plots and those treated with other biopesticides, although the tendency was not consistently significant throughout the sites and dates.

This may be due the fact, the scientists suggest, that parasitoid complex varied with sites and dates and it is well known that different parasitoid species may react differently to pesticide and biopesticide treatments.

Another possible reason for the relatively low impact of pesticides and biopesticides on parasitism is the size of the plots and the ability of parasitoids to quickly move from adjacent, untreated fields or vegetation to the previously treated plots, they believe.

Dr Jerry Nboyine, of the CSIR-SARI, said, “There was no consistent difference in cob damage and yields among the chemical pesticide and the biopesticides. In such situations, biopesticides should be preferred to minimize negative effects on human health, natural control and the environment in general.”

 

Additional information

Main image: The outbreak of the fall armyworm has led to several recommendations on insecticides, including biopesticides, but the effects of these products on the environment – especially parasitoids – has not previously been assessed under field conditions (Credit: CABI).

Full paper reference

Agboyi, L.K., Nboyine, J.A., Asamani, E. et al. ‘Comparative effects of biopesticides on fall armyworm management and larval parasitism rates in northern Ghana,’ Journal of Pest Science (2023) DOI: 10.1007/s10340-023-01590-z

You can read the paper in full open access here: https://rdcu.be/c5ZJO

Funding acknowledgement

The research was financially supported by the Foreign, Commonwealth and Development Office (FCDO), UK, the Directorate-General for International Cooperation (DGIS), the Netherlands, the European Commission Directorate-General for International Cooperation and Development (DEVCO) and the Swiss Agency for Development and Cooperation (SDC) through CABI’s Action on Invasives and Plantwise Plus Programmes. CABI is an international intergovernmental organisation and we gratefully acknowledge the core financial support from our member countries and lead agencies. See https://www.cabi.org/aboutcabi/who-we-work-with/key-donors/ for details.