A top federal bee scientist from South Dakota says he's being punished for publicizing work on pesticides and pollinators.

Jonathan Lundgren's research found bees and monarch butterflies can be harmed by a widely used class of insecticides. In a whistleblower case filed Wednesday, the United States Department of Agriculture entomologist alleges he faced retaliation because of his research.

"Once he started publishing this work, he went from golden boy to pariah, and that's what this case is about," said Jeff Ruch, executive director of the Washington, D.C.-based group Public Employees for Environmental Responsibility, which is representing Lundgren in his complaint to a federal whistleblower protection board.

Lundgren's 11-year career at USDA appeared stellar. He had excellent performance reviews. USDA even named him its Outstanding Early Career Research Scientist in 2011.

The complaint says that all changed when Lundgren began to study how neonicotinoid insecticides affect bees and other beneficial insects. His research and work travel fell under intense scrutiny and he was suspended for violating agency protocols.

Ruch contends that pressure from the pesticide industry has led USDA to stifle scientists like Lundgren. He had no evidence, but said the complaint will let attorneys seek information and interview USDA officials about the Lundgren case. He believes that work will prove USDA targeted Lundgren because of his neonicotinoid research.

Those pesticides are among the most widely used in the world and are used heavily on farm fields and in backyards.

But they're under fire for contributing to an international decline in bee populations. Neonicotinoid insecticides are systemic. Plants take up the chemical along with nutrients. It's in the leaves, flowers and pollen.

Lundgren claims his trouble started in early 2014 when he began to talk publicly about negative effects of neonicotinoids. He reviewed a study by the Center for Food Safety. The study was critical of overuse of neonicotinoids on crops. He also did media interviews about the topic.

Lundgren declined an on-the-record interview, saying he fears additional retaliation. He alleges a USDA official asked him to stop talking publicly about the pesticide.

A USDA spokesperson said that while the agency can't discuss individual cases it takes scientific integrity seriously. "We fully review allegations of wrong-doing and make the results of those reviews available to the public online. USDA, he added, has "procedures for staff to report any perceived interference with their work, seek resolution, and receive protection from recourse for doing so."

In September 2014, Lundgren filed an internal complaint alleging USDA was violating its scientific integrity policy by retaliating because of the content of his research.

"Within one week of these late-March press interviews and the release of the CFS study, improper reprisal, interference and hindrance of my research and career began in earnest," according to the internal complaint.

He said "national program staff" removed his research objective examining pesticide risk. Instead, the goals focused on "strategies to improve diversity and health of beneﬁcial insects," a change he said makes examining pesticide risk risky since it would "no longer be officially supported by USDA."

USDA found his scientific integrity complaint was without merit. Lundgren appealed. The appeal is awaiting a USDA response.

Lundgren was suspended in October 2014 for three days after USDA investigators found emails among his research staff which included off-color jokes.

Entomologist Jonathan Lundgren examined a pollinator food plot with colleague Christina Mogren, a postdoctoral researcher, near Brookings, S.D., in July. Dan Gunderson | MPR News file

Ruch says no employees had complained about the emails and employees in Lundgren's lab wrote letters of support for their boss.

"This is a scientist who has many prestigious journals publishing his work. He is invited to make presentations both nationally and internationally," Ruch said. "If it was not the sensitive nature of his research this would be somebody they would be promoting, not on the verge of terminating."

Earlier this year Lundgren again ran afoul of USDA supervisors.

He wrote a paper on research that showed neonicotinoid insecticides killed or stunted growth of monarch butterfly larvae. Monarch populations have plummeted in recent years because of habitat loss. Lundgren's research showed milkweed plants growing near farm fields treated with the insecticide could harm monarch larvae.

He believed he had permission from USDA to publish the paper.

Lundgren was interviewed about his research for an MPR News story in February. The whistleblower complaint says that interview prompted a sharp response two weeks later from his supervisor in Brookings, S.D.

Lundgren says he was told USDA considered his research "sensitive" and requiring additional layers of approval. The paper was published in March.

In early March, Lundgren traveled to speak at a National Academy of Sciences gathering and to an agricultural group in Pennsylvania.

While he was traveling to the meetings, he received a message saying his travel was not approved because he failed to get a required supervisor's signature.

He was considered absent without leave and ordered to return immediately to South Dakota.

Ruch said the travel paperwork mistake is one often overlooked at USDA.

In early August USDA area supervisor John McMurtry wrote to Lundgren imposing a 14-day unpaid suspension for "blatant disregard of Agency rules and regulations."

McMurtry said Lundgren's behavior "suggests a low potential for rehabilitation."

According to an internal USDA document, Lundgren was told that "additional misconduct will not be tolerated and may result in disciplinary action up to and including your removal from the Federal service."

Ruch says that that threat led to the whistleblower complaint to the Federal Merit Systems Protection Board.

Ruch's group says the charges are "patently exaggerated, and the punishment is disproportionate to the alleged wrongdoing." Ruch also believes the case will show the conflicts were about the research, not rule violations.

"There were repeated expressions about the sensitivity of the subject matter that made it clear there was concern that went much higher than (USDA's) Agricultural Research Service office in South Dakota," he said. "We believe that there was communication among high level managers of USDA that predetermined what they were going to do."