Wednesday, November 03, 2021

History of insect invasions offers insight into the future

History of insect invasions offer insight into the future
Spotted lanternfly is a destructive insect that feeds on a wide range of fruit, ornamental, 
and hardwood trees, including grapes, apples, walnut, and oak; a serious threat to the 
United States' agriculture and natural resources. Credit: USDA / Lance Cheung.

Over the past two centuries, thousands of non-native insects have hitchhiked to the United States in packing material, on live plants, and in passenger baggage. Scientists with two U.S. Department of Agriculture (USDA) agencies and their partners used the history of live plant imports and invasion by a common group of insects to estimate the rate at which new insects are arriving and how many new insect species may yet be in store for U.S. forests and agricultural fields.

Findings suggest that efforts to reduce biological hitchhiking on live plant imports, often referred to as "biosecurity," are working. However, more than a century of invasion by Hemiptera insects also suggests that increased trade might offset the effects of improved biosecurity. As many as 25 percent of invading Hemiptera insects may have yet to be detected in the nation's forests and agricultural fields.

The study, "Hidden patterns of insect establishment risk revealed from two centuries of alien species discoveries," was published recently in the journal Science Advances. The study's lead author, Matthew MacLachlan, a research economist with the USDA Economic Research Service, and co-author Andrew Liebhold, a research entomologist with the USDA Forest Service, examined records from 1854 to 2012; they found that 930 non-native species of plant-feeding insects in the Hemipter order have invaded the United States. The research team was able to identify the origins of 770 of those species.

"Our work quantifying the establishment risk posed by imports from distinct regions and how these risks have changed with the accumulation of trade history and time gives policy-makers a better picture of the risks of insect invasion per unit of  and region," MacLachlan said.

Hemiptera are small, plant-feeding insects (the order includes true bugs, aphids, and scales), and many of these species cause considerable damage to agricultural and forest . The Hemiptera order includes more than 80,000 insect species, and accidental transport of live plants or plant products is the main pathway by which most Hemiptera move among continents.

"Data on historical discoveries of non-native Hemiptera in the United States helped us estimate rates of new  establishments that may occur as a result of plant imports from various world regions today," Liebhold said.

Co-authors include Takehiko Yamanaka of the Institute for Agro-Environmental Sciences, NARO (NIAES) in Japan and Michael R. Springborn of the University of California, DavisPlants can prepare for insect attack sequence

More information: Matthew J. MacLachlan et al, Hidden patterns of insect establishment risk revealed from two centuries of alien species discoveries, Science Advances (2021). DOI: 10.1126/sciadv.abj1012

Journal information: Science Advances 

Provided by USDA Forest Service 

As-needed pesticide use brings wild bees, increases watermelon yield without reducing corn profits

As-needed pesticide use brings wild bees, increases watermelon yield without reducing corn profits
A team of researchers at Purdue University found as-needed pesticide use increased 
pollination from wild bees and increased watermelon yield. 
Credit: Purdue University / Tom Campbell

Many farmers rent bee hives to pollinate crops, but they could tap into the free labor of wild bees by adopting an as-needed approach to pesticides, a new proof-of-concept study shows.

A multiyear study of commercial-scale fields in the Midwest found this approach led to a 95% reduction in pesticide applications, while maintaining or increasing crop yield for corn and watermelon. The findings are detailed in a paper published in the Proceedings of the National Academy of Sciences.

"An as-needed approach to pesticide treatment can benefit ," said Ian Kaplan, professor of entomology at Purdue University, who led the project. "With reduced pesticide use, we saw within the first year wild bees returned to the fields, and our findings showed an average 26% increase in watermelon yield."

The team of researchers from Purdue's College of Agriculture studied fields at five different locations in Indiana and the Midwest over a period of four years to compare conventional pest management with an , or IPM, approach. The IPM approach relied on scouting the fields and applying  only when pest levels reached previously established thresholds for damage that would lead to economic losses.

In the last few decades, pesticides have been used preemptively, beginning with treated seed and followed by applications on a set schedule, said Christian Krupke, professor of entomology and member of the research team.

"Using these potent insecticides, more often, increases the potential for unintended consequences and harm to insects, animals and human health. This study shows that we may not need such powerful weapons to control pests, and at a minimum, we don't need to use them as frequently as we do," Krupke said.

Agricultural sustainability and the benefits of IPM are gaining attention. Walmart recently announced a policy requiring all global fresh produce and floral providers to adopt IPM practices by 2025.

"It is important for people to know that there is another option between conventionally grown produce and organic produce," said Kaplan who leads Purdue's Insect Ecology Lab. "IPM can greatly reduce the amount of pesticides used to grow food without taking the tool entirely away from farmers or putting the food supply at risk."

Midwest growers also are attuned to the issue and want solutions to protect their crops and their pollinators, said Laura Ingwell, assistant professor of entomology. Indiana is one of the major watermelon production states in the U.S. and the pollinator-dependent crop accounts for an average of 7,000 acres of land annually.

"Unfortunately, it is hard to find untreated corn or soybean seed," she said. "Across the Midwest watermelon fields are like islands in a sea of corn and soybeans. We need to understand how the management of one impacts the other because many Indiana farmers have all of these crops in rotation."

The team worked with farm staff at the Purdue research fields to grow both corn, which is wind pollinated, and watermelon, which is insect pollinated, to replicate a real agricultural ecosystem in Indiana. Each site had a pair of 15-acre fields, one with untreated seed and using IPM, and the other using treated seed and conventional pest management practices like calendar-based insecticide sprays. The crops were rotated over the course of the study, and the different locations allowed the team to examine the impact of different soil types and environmental conditions, said Jacob Pecenka, a graduate student who performed much of the study.

"We used weekly scouting to monitor pests at the IPM fields, which means we would go into the field, look for pests and take a sample count of the numbers of different pests present," he said. "It was surprising that the pests rarely reached the established threshold for economic risk to the crops. Only four times during the course of the study did pests reach a threshold that triggered pesticide application. That is a huge reduction from the 97 treatments of the conventionally managed fields."

Pecenka and his team also monitored the flowers and counted the number of visits by bees in the watermelon fields.

"The IPM fields had a 130% increase in the number of flower visits over the conventional fields," he said. "The biggest players in pollination were native, wild bees. They are efficient pollinators and serious foragers."

Due to watermelon crops being grown in the middle of the cornfields, any wild pollinators had to travel at least 100 feet to get to the watermelon flowers. Despite this challenge, wild  made up 80% of the flower visits while honeybees were only 20%, even though their colonies were placed within a few feet of the watermelon , Pecenka said.

"We don't have a great understanding of the biology of many wild bee species, but this study suggests they are important and resilient," he said. "Within the first year these bees were a significant presence in the fields with low levels of pesticide, which can kill the , confuse their navigation and repel them."

The team also observed an increase in the number of beneficial insects in the IPM fields, Ingwell said.

"Wasps, ladybugs and other natural predators of watermelon pests step in when the pest levels rise," she said. "It is tempting to pretreat with pesticides as an insurance policy for your crop, but this study shows we can trust the natural system most of the time. Weekly scouting in the watermelon crop is enough to maintain the yield and benefit the insect community in terms of pest suppression and pollination."

Resources for pollinator protection, and fruit and vegetable growers are available through the Purdue Extension offices.

The team, which also included professor emeritus Rick Foster, next plans to scale up the study using 50-acre commercial fields.More support needed for pollination services in agriculture

More information: Jacob R. Pecenka et al, IPM reduces insecticide applications by 95% while maintaining or enhancing crop yields through wild pollinator conservation, Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2108429118

Journal information: Proceedings of the National Academy of Sciences 

Provided by Purdue University 

Study reveals 'extensive network' of industry ties with healthcare

healthcare
Credit: CC0 Public Domain

The medical product industry maintains an extensive network of financial and non-financial ties with all major healthcare parties and activities, reveals a study published by The BMJ today.

This network seems to be mostly unregulated and opaque, and the researchers call for enhanced oversight and transparency "to shield  from commercial influence and to preserve public trust in healthcare."

Although the medical product industry is a critical partner in advancing healthcare, particularly in developing new tests and treatments, their main objective is to ensure  to shareholders.

In an influential 2009 report, the Institute of Medicine described a multifaceted healthcare ecosystem rife with industry influence.

Yet most studies of conflict of interests related to pharmaceutical, medical device, and  have focused on a single party (eg. , hospitals, or journals) or a single activity (eg. research, education, or clinical care). The full extent of industry ties across the healthcare ecosystem is therefore still uncertain.

To address this gap, a team of US researchers set out to identify all known ties between the medical product industry and the healthcare ecosystem.

They searched the medical literature for evidence of ties between pharmaceutical, , and biotechnology companies and parties (including hospitals, prescribers and professional societies) and activities (including research, health professional education and guideline development) in the healthcare ecosystem.

Data in 538 articles from 37 countries, along with expert input, was used to create a map depicting these ties. These ties were then verified, cataloged, and characterized to ascertain types of industry ties (financial, non-financial), applicable policies on conflict of interests, and publicly available data sources.

The results show an extensive network of medical product industry ties—often unregulated and non-transparent—to all major activities and parties in the healthcare ecosystem.

Key activities include research, healthcare education, guideline development, formulary selection (prescription drugs that are covered by a health plan or stocked by a healthcare facility), and clinical care.

Parties include non-profit entities (eg. foundations and advocacy groups), the healthcare profession, the market supply chain (eg. payers, purchasing and distribution agents), and government.

For example, the researchers describe how opioid manufacturers provided funding and other assets to prescribers, patients, public officials, advocacy organizations, and other healthcare parties, who, in turn, pressured regulators and public health agencies to quash or undermine opioid related guidelines and regulations.

And they warn that many other examples of harm from industry promoted products remain unexplored.

The results show that all party types have financial ties to medical product companies, with only payers and distribution agents lacking additional, non-financial ties.

They also show that policies for conflict of interests exist for some financial and a few non-financial ties, but publicly available data sources seldom describe or quantify these ties.

The researchers acknowledge that their findings are limited to known or documented industry ties, and that some data might have been missed. However, they say their strategy of systematic, duplicative searching and feedback from an international panel of experts is unlikely to have missed common or important ties.

As such, they conclude: "An extensive network of medical product industry ties to activities and parties exists in the  ecosystem. Policies for conflict of interests and publicly available data are lacking, suggesting that enhanced oversight and transparency are needed to protect patients from commercial influence and to ensure ."

Financial ties between researchers and drug industry linked to positive trial results
More information: Mapping conflict of interests: scoping review, BMJ (2021). DOI: 10.1136/bmj-2021-066576
Journal information: British Medical Journal (BMJ) 
Provided by British Medical Journal 

CRIMINAL CAPITALI$M WAGE THEFT

More than 140,000 Amazon drivers to be repaid nearly $60 million in alleged withheld tips

Amazon
Credit: Unsplash/CC0 Public Domain

Over 140,000 Amazon drivers are being repaid nearly $60 million in tips that the company allegedly withheld from them, the Federal Trade Commission announced Tuesday.

The FTC and Amazon reached a settlement in February, with the company agreeing to pay more than $61.7 million, the full amount the tech giant allegedly withheld which will be used by the FTC to compensate Amazon Flex .

The FTC said in February that Amazon Flex Drivers were told they would be paid $18 to $25 an hour, with many statements saying things such as "you will receive 100% of the tips you earn while delivering with Amazon Flex."

"Rather than passing along 100% of customers' tips to drivers, as it had promised to do, Amazon used the money itself," Daniel Kaufman, acting director of the FTC's Bureau of Consumer Protection, said in February.

The FTC is sending out 139,507 checks and 1,621 PayPal payments to drivers. The average check for Amazon Flex drivers included in the settlement will be $422, but 19,980 drivers will receive checks for more than $600. The highest amount going to a single Amazon Flex driver is $28,000.

Amazon Flex is different from the regular Amazon delivery drivers. Flex drivers are  who can download an app that will allow them to select different orders they want to deliver, and they need a personal vehicle like a 4-door, mid-sized sedan or larger vehicle, such as a truck, to make the deliveries.

Flex drivers deliver goods and groceries ordered through Amazon Prime Now and AmazonFresh programs, according to the FTC. These allow for customers to tip their drivers.

Affected drivers should deposit or cash their checks before Jan. 7, 2022.

2021 USA Today. Distributed by Tribune Content Agency, LLC.

Study casts doubt on theory that women aren't as competitive as men


Peer-Reviewed Publication

UNIVERSITY OF ARIZONA

As researchers investigate reasons for America's persistent gender wage gap, one possible explanation that has emerged in roughly the last decade is that women may be less competitive than men, and are therefore passed over for higher-ranking roles with larger salaries.

But a new study suggests that it's likely not that simple. Researchers found that women enter competitions at the same rate as men – when they have the option to share their winnings with the losers.

The study, conducted by Mary L. Rigdon, associate director of the UArizona Center for the Philosophy of Freedom, and Alessandra Cassar, professor of economics at the University of San Francisco, is published in the journal Proceedings of the National Academy of Sciences.

Rigdon's research involves studying how market structure, information and incentives impact behavior. Her work over the last 20 years has explored questions about trust, reciprocity, competition, altruism, cheating and more, with a particular focus on gender differences, especially the gender wage gap.

"If we're finally going to close the gender pay gap, then we have to understand the sources of it – and also solutions and remedies for it," said Rigdon, who is also a faculty affiliate in the Department of Political Economy and Moral Science in the College of Social and Behavioral Sciences.

In 2021, women will earn 82 cents for every dollar earned by men, Rigdon said, meaning women work nearly three months extra to receive the same amount of pay. This statistic does not account for certain characteristics, such as an employee's age, experience or level of education.

But even when considering those characteristics, women are still paid about 98 cents for every dollar earned by men, Rigdon said. In other words, a woman is paid 2% less than a man with the same qualifications.

Economists have considered a few possible explanations for this, Rigdon said. One theory, known as the "human capital explanation," suggests that there are gender differences in certain skills, leading women to careers that pay less. Another theory – perhaps the most widely considered – is patent discrimination.

Rigdon and Cassar zeroed in on the relatively new theory that women are less competitive and less willing to take risks than men.

But if women were more reluctant to compete, then they would occupy fewer high-ranking positions at the tops of major companies, and that's not the trend that's taken shape over the last several years, Rigdon said. Women make up about 8% of the CEOs leading Fortune 500 companies. While that number is low overall, it's a record high.

"We thought it must be the case that women are as competitive as men, but they just exhibit it differently, so we wanted to try to get at that story and demonstrate that that is the case," Rigdon said. "Because that's then a very different story about the gender wage gap."

Rigdon and Cassar randomly assigned 238 participants – split nearly evenly by gender – to two different groups for the study. Participants in each of those two groups were then randomly assigned to four-person subgroups.

For all participants, the first round of the study was the same: Each was asked to look at tables of 12 three-digit numbers with two decimal places and find the two numbers that add to 10. Participants were asked to solve as many tables as possible – up to 20 – in two minutes. Each participant was paid $2 for every table they solved in the first round.

In round two, participants were asked to do the same task, but the two groups were incentivized differently. In the first group, the two participants in each four-person team who solved the most tables earned $4 per table solved, while their other two team members were given nothing. In the other group, the top two performers of each four-person team also earned $4 per table, but they had the right to decide how much of the prize money to share with one of the lower performing participants.

In the third round, all participants were allowed to choose which payment scheme they preferred from the two previous rounds. For half the study participants, this meant a choice between a guaranteed $2 per correct table, or potentially $4 per correct table if they became one of the top-two performers in their four-person subgroup. For the other half of the participants, the choice was $2 per correct table, or $4 per correct table for the top-two performers with the option to share the winnings with one of the losing participants.

The number of women who chose the competitive option nearly doubled when given the option to share their winnings; about 60% chose to compete under that option, while only about 35% chose to compete in the winner-take-all version of the tournament.

About 51% of men in the study chose the winner-take-all option, and 52.5% chose the format that allowed for sharing with the losers.

Rigdon said she and Cassar have a few theories about why women are more inclined to compete when they can share the winnings. One suggests female participants are simply interested in controlling the way the winnings are divvied up among the other participants.

Another theory that has emerged among evolutionary psychologists, Rigdon said, suggests that female participants may be inclined to smooth over bad feelings with losers of the competition.

"We really have to ask what it is about this social incentive that drives women to compete. We think it's recognizing the different costs and benefits that come from your different biological and cultural constraints," she said. "But at the end of the day, I think we still have this question."

Rigdon and Cassar are now developing an experiment that gets to the heart of that question, Rigdon said.

The researchers are careful to not propose policies for corporate America based on a line of research that still has many questions. But, Rigdon said, the latest finding suggests that corporations might do well to engage in more socially responsible activity.

"Maybe you'll attract a different set of applicants to your CEO positions or your board of director positions," she said. "Women might be more attracted to positions where there is this social component that isn't there in more traditional, incentive-based firms where it's all about CEO bonuses."

The research was funded by a grant from the National Science Foundation.

TGen case study documents first reported US transmission of COVID from a pet owner to pets

Using precision genomic sequencing, TGen matched the exact strain of coronavirus shared among a Phoenix-area owner, his cat and his dog

Peer-Reviewed Publication

THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTE

FLAGSTAFF, Ariz. — Nov. 1, 2021 — For the first time in the U.S., the transmission of COVID-19 from pet parent to pet is documented genetically as part of a study by the Translational Genomics Research Institute (TGen), an affiliate of City of Hope.

The published findings from the ongoing study appear in the journal One Health. This is one of five pilot studies nationwide examining COVID in animals. The TGen study, however, is the only one to include genomic sequencing of the virus from both pet and human samples. This level of testing resulted from TGen’s overall efforts to monitor the virus and its potentially more-dangerous variants by sequencing as many positive human samples of the virus as possible.

TGen’s COVID animal study is conducted under a grant from the Arizona Department of Health Services (ADHS). As with the other pilot studies, the funds come from the U.S. Centers for Disease Control and Prevention (CDC) in coordination with the Council of State and Territorial Epidemiologists (CSTE).

In the Arizona case study, the pet owner, cat and dog all were infected with the identical strain of coronavirus: B.1.575, an early and unremarkable version of SARS-CoV-2, the virus that causes COVID. Fewer than 25 documented cases exist of Arizonans infected with this strain, according to information drawn from the COVID variant tracking dashboard that TGen maintains for the CDC and ADHS. To date, more than 46,000 positive samples of Arizonans with COVID have been sequenced.

“This case study was the first example we had from the project that demonstrated the likelihood of virus transmission from a pet owner to animals in the household,” said Hayley Yaglom, a TGen Epidemiologist and lead author of the study.

Researchers deduced that the virus spread from the pet parent to either the dog or cat, or both. The animals were confined to an apartment and therefore had little-to-no opportunity to be exposed to the virus, and so it was highly unlikely that the pets infected their owner. Plus, in each case examined in the study, it was the pet parent who exhibited COVID first. Worldwide, there is no documented case of COVID transmission from a pet to its pet parent.

Researchers were unable to tell if the dog or cat were infected first, or if one infected the other, though that is a possibility. This particular dog and cat were buddies who had close contact with each other, researchers said.

Steps owners should take to protect pets

Yaglom said pet owners should protect their pets by getting vaccinated. If they do get COVID, they should wear masks when they are around their pets. As difficult as it might be for many pet owners, they should avoid cuddling, kissing, allowing pets to lick their faces, or sleeping with them.

Owners don’t have to completely isolate from their pets, Yaglom said, but they should minimize contact “as best they can” while they exhibit COVID symptoms.

In the case study, the pet parent was not yet vaccinated, took little precaution to protect his cat and dog, and entertained guests who were not vaccinated. The owner recovered from COVID, and both his pets were asymptomatic.

Including this case study, Arizona researchers tested 61 pets — 39 dogs and 22 cats — living in 24 households. There were 14 positive cases of COVID in pets among six of the households.

The study will continue through the rest of 2021, and would continue into 2022 if researchers obtain additional funding, which would allow them to continue education and outreach efforts, bolstering active surveillance of the virus.

More study subjects needed

Dog and cat owners who have tested positive for COVID-19 within the past two weeks are eligible to participate in the study. The tests are free. Owners must be at least 18, provide consent and fill out a questionnaire. The pet must be vaccinated against rabies, mainly housed indoors, and tolerant of the handling and restraint necessary for routine veterinary care. A veterinarian is present when samples are taken. No animals are harmed in the course of this study.

Pet owners must wear masks during sample collection, and project staff will wear masks and gloves. Spanish-speaking staff will be available, as needed. Pet owners will be notified of test results within 3-4 weeks. For pets that test positive, owners may be asked to enable collection of additional samples. Positive tests will be reported to the Arizona State Veterinarian and ADHS.

For more information about testing pet dogs or cats for COVID, or to participate in the study, please send questions to: covidpetprojectaz@tgen.org.

The study — Genomic investigation of a household SARS-CoV-2 disease cluster in Arizona involving a cat, dog, and pet owner — was published in the journal One Health.

“This is a great example of using genomics to gain intelligence about pathogens,” said David Engelthaler, Ph.D., director of TGen’s Pathogen and Microbiome Division, the branch of TGen studying infectious diseases. “This study shows that we can not only use genomics to help track COVID variants across the globe, but we can also use this technology to track exact transmissions, and in this case transmission from pet owners to pets.”

# # #

About TGen, an affiliate of City of Hope
Translational Genomics Research Institute (TGen) is a Phoenix, Arizona-based nonprofit organization dedicated to conducting groundbreaking research with life-changing results. TGen is affiliated with City of Hope, a world-renowned independent research and treatment center for cancer, diabetes and other life-threatening diseases: CityofHope.org.  This precision medicine affiliation enables both institutes to complement each other in research and patient care, with City of Hope providing a significant clinical setting to advance scientific discoveries made by TGen. TGen is focused on helping patients with neurological disorders, cancer, diabetes and infectious diseases through cutting-edge translational research (the process of rapidly moving research toward patient benefit). TGen physicians and scientists work to unravel the genetic components of both common and complex rare diseases in adults and children. Working with collaborators in the scientific and medical communities worldwide, TGen makes a substantial contribution to help our patients through efficiency and effectiveness of the translational process. For more information, visit: tgen.org. Follow TGen on FacebookLinkedIn and Twitter @TGen.

Media Contacts:

Steve Yozwiak
TGen Senior Science Writer
602-343-8704
syozwiak@tgen.org

For ADHS media inquiries, please email pio@azdhs.gov.

Researchers uncover “genetic goldmine” underlying plant resilience in extreme desert environment


Evolutionary genomics approach identifies genes that enable plants to live in the Atacama Desert, offering clues for engineering more resilient crops to face climate change

Peer-Reviewed Publication

NEW YORK UNIVERSITY

Atacama Desert 

IMAGE: THE CHILEAN RESEARCH TEAM ESTABLISHED AN UNPARALLELED “NATURAL LABORATORY” IN THE ATACAMA DESERT IN NORTHERN CHILE, ONE OF THE DRIEST AND HARSHEST ENVIRONMENTS ON EARTH. view more 

CREDIT: MELISSA AGUILAR

An international team of researchers has identified genes associated with plant survival in one of the harshest environments on Earth: the Atacama Desert in Chile. Their findings, published in Proceedings of the National Academy of Sciences (PNAS), may help scientists breed resilient crops that can thrive in increasingly drier climates.

 

“In an era of accelerated climate change, it is critical to uncover the genetic basis to improve crop production and resilience under dry and nutrient-poor conditions,” said Gloria Coruzzi, Carroll & Milton Petrie Professor in the New York University (NYU) Department of Biology and Center for Genomics and Systems Biology, who co-led the study with Rodrigo Gutiérrez.  

 

The study was an international collaboration among botanists, microbiologists, ecologists, evolutionary and genomic scientists. This unique combination of expertise enabled the team to identify the plants, associated microbes, and genes that enable the Atacama plants to adapt to and flourish in extreme desert conditions, which could ultimately help to enhance crop growth and reduce food insecurity.

 

“Our study of plants in the Atacama Desert is directly relevant to regions around the world that are becoming increasingly arid, with factors such as drought, extreme temperatures, and salt in water and soil posing a significant threat to global food production,” said Gutiérrez, professor in the Department of Molecular Genetics and Microbiology at Pontificia Universidad Católica de Chile.

 

Establishing a “natural laboratory” in one of Earth’s driest places

 

The Atacama Desert in northern Chile, sandwiched between the Pacific Ocean and Andes Mountains, is the driest place on the planet (excluding the poles). Yet dozens of plants grow there, including grasses, annuals, and perennial shrubs. In addition to limited water, plants in the Atacama must cope with high altitude, low availability of nutrients in the soil, and extremely high radiation from sunlight.

 

The Chilean research team established an unparalleled “natural laboratory” in the Atacama Desert over a 10-year period, in which they collected and characterized the climate, soil, and plants at 22 sites in different vegetational areas and elevations (every 100 meters of altitude) along the Talabre-Lejía Transect. Measuring a variety of factors, they recorded temperatures that fluctuated more than 50 degrees from day to night, very high radiation levels, soil that was largely sand and lacked nutrients, and minimal rain, with most annual rain falling over a few days.

 

Using genomics to explore the evolution of resilient plants

 

The Chilean researchers brought the plant and soil samples—preserved in liquid nitrogen—1,000 miles back to the lab to sequence the genes expressed in the 32 dominant plant species in the Atacama and assess the plant-associated soil microbes based on DNA sequences. They found that some plant species developed growth-promoting bacteria near their roots, an adaptive strategy to optimize the intake of nitrogen—a nutrient critical for plant growth—in the nitrogen-poor soils of the Atacama.

 

To identify the genes whose protein sequences were adapted in the Atacama species, the researchers at NYU next conducted an analysis using an approach called phylogenomics, which aims to reconstruct evolutionary history using genomic data. In consultation with colleagues at the New York Botanical Garden, they compared the genomes of the 32 Atacama plants with 32 non-adapted but genetically similar “sister” species, as well as several model species.

 

“The goal was to use this evolutionary tree based on genome sequences to identify the changes in amino acid sequences encoded in the genes that support the evolution of the Atacama plant adaptation to desert conditions,” said Coruzzi.

 

“This computationally intense genomic analysis involved comparing 1,686,950 protein sequences across more than 70 species. We used the resulting super-matrix of 8,599,764 amino acids for phylogenomic reconstruction of the evolutionary history of the Atacama species,” said Gil Eshel, who conducted this analysis using the High Performance Computing Cluster at NYU.

 

The study identified 265 candidate genes whose protein sequence changes were selected by evolutionary forces across multiple Atacama species. These adaptive mutations occurred in genes that could underlie plant adaptation to the desert conditions, including genes involved in response to light and photosynthesis, which may enable plants to adapt to the extreme high-light radiation in the Atacama. Similarly, the researchers uncovered genes involved in the regulation of stress response, salt, detoxification, and metal ions, which could be related to the adaptation of these Atacama plants to their stressful, nutrient-poor environment.

CAPTION

Gabriela Carrasco, an undergraduate researcher at the time, is identifying, labeling, collecting, and freezing plant samples in the Atacama Desert. These samples then traveled 1,000 miles, kept under dry ice to be processed for RNA extractions in Rodrigo Gutiérrez’s lab in Santiago de Chile. The species Carrasco is collecting here are Jarava frigida and Lupinus oreophilus.

CREDIT

Melissa Aguilar

What we can learn from this “genetic goldmine”

 

The majority of scientific knowledge of plant stress responses and tolerance has been generated through traditional lab-based studies using a few model species. While beneficial, such molecular studies likely miss the ecological context in which plants have evolved.

 

“By studying an ecosystem in its natural environment, we were able to identify adaptive genes and molecular processes among species facing a common harsh environment,” said Viviana Araus of the Pontificia Universidad Católica de Chile in Gutierrez’ lab and a former postdoctoral associate at NYU’s Center for Genomics and Systems Biology.

 

“Most of the plant species we characterized in this research have not been studied before. As some Atacama plants are closely related to staple crops, including grains, legumes, and potatoes, the candidate genes we identified represent a genetic goldmine to engineer more resilient crops, a necessity given the increased desertification of our planet,” said Gutiérrez.

 

In addition to Gutiérrez and Araus, their collaborators in Chile included Claudio Latorre of the Pontificia Universidad Católica de Chile and Mauricio González of the Universidad de Chile. Coruzzi and Eshel at NYU worked on the phylogenomic pipeline and analysis with collaborators in the U.S., including Kranthi Varala of Purdue University, Dennis Stevenson of the New York Botanical Garden, Rob DeSalle of the American Museum of Natural History, as well as members of their research teams.

 

This work was supported by Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007) in Chile, and in the U.S. by the Zegar Family Foundation (A160051), and by a Department of Energy Biological and Environmental Research grant (DE-SC0014377).