Julie MacDonald resigned April 30 as deputy assistant secretary of the Department of Interior, a month after the department's office of inspector general issued a scathing report that accused her of altering scientific reports in the U.S. Fish and Wildlife Service's endangered species programs and improperly leaking internal reports to industry groups and friends.
The report said nothing about MacDonald's participation in the decision to remove the Sacramento splittail from protection under the Endangered Species Act.
But documents show she edited the decision on the fish, at one point softening scientists' conclusion that the species "is likely" experiencing a population decline to say it "may be" in such a decline.
The Sacramento splittail, which was classified as a threatened species from 1999 to 2003, appears to be the only fish -- other than those that have gone extinct -- ever removed from the list of threatened and endangered species.
Documents show MacDonald was deeply involved in crafting the language used to justify the final decision.
The decision to withdraw the protective status of the fish was first made in the Fish and Wildlife Service's Sacramento office, leaving the extent of MacDonald's involvement in those earlier stages unclear.
But her participation in the decisionmaking at any stage of the process may have violated conflict of interest rules because MacDonald owns an 80-acre farm in the Yolo Bypass, a floodplain of wetlands, pastures and row crops north of the Delta that is key habitat for the fish.
In almost all circumstances, federal law prohibits federal employees from participating in decisions in which they have a personal interest.
MacDonald did not return repeated phone calls seeking comment to her Washington and Dixon homes. Her husband, who answered the door at the Dixon farm this week, said she was in Washington.
In response to Times inquiries, the Department of Interior issued a written statement.
"To our knowledge, senior departmental officials were unaware of these issues," the statement read. "The Department of the Interior Inspector General investigated former Deputy Assistant Secretary MacDonald's role in administering the Endangered Species Act and issued a report. We rely upon the Inspector General's investigation and counsel. If it turns out that former Deputy Assistant Secretary MacDonald acted inappropriately regarding the Sacramento splittail, we will conduct an appropriate review of the regulatory process that led to the final decision."
The splittail is more dependent on floodplains than any other fish in the Delta. And the Yolo Bypass is the last big floodplain in the Central Valley.
That's why landowners in the bypass have been concerned about the splittail's status: A mandate to boost the splittail's population could lead to more flooding in the bypass, which could inundate crops and equipment. Farmers also worry that measures to enhance splittail populations could force them to install costly fish screens at water intakes and submit to stricter regulations on their use of pesticides.
"In the Sacramento drainage, the most important spawning areas appear to be the Yolo and Sutter bypasses, which are extensively flooded during wet years," according to a 2004 white paper on splittail biology.
According to financial disclosure reports, MacDonald's farm is worth more than $1 million, and she receives $100,000 to $1 million a year in income from it.
"At the very least, this certainly has the appearance of a conflict of interest," said Mary Boyles, spokeswoman for Common Cause in Washington.
"The government ethics rules clearly state that you're not supposed to participate" in decisions that affect you personally, Boyles said. "We need enforcement of these rules that are on the books."
In addition to influencing the agency's decision on the splittail, MacDonald has come under fire for meddling with scientific reports on other endangered species, including the California tiger salamander.
The March 23 inspector general's report concluded that MacDonald, an engineer with no background in biology, "has been heavily involved with editing, commenting on, and reshaping the Endangered Species Program's scientific reports from the field."
The wildlife agency's deputy director, Marshall Jones, described MacDonald to the inspector general's investigator as a Bush administration "attack dog."
Though the report found no evidence of a crime, it said she broke rules against granting preferential treatment and distributing internal agency information.
The report said MacDonald:
The report noted that the director of the Fish and Wildlife Service, Dale Hall, said MacDonald was particularly interested in endangered species issues in her home state of California. But the report did not draw direct connections between endangered species and her farm.
Before MacDonald went to work in Washington, she participated in development of a "Yolo Bypass Management Strategy." She is listed as a "landowner" in the report's list of participants.
Several of the other participants were contacted for this story, but none could recall much, if anything, about her involvement.
But the strategy document, completed in 2001, reflects a number of concerns that landowners in the bypass had regarding ecosystem restoration projects to benefit fish, including splittail.
The fish is also of deep concern to water users elsewhere in the state because it could add a new layer of complexity to the increasingly difficult task of maintaining the state's water supply for farms and cities, and protecting its ecosystems.
That is because splittail's dependence on floodplains is unique in the Delta, and that opens up a new set of potential impacts on water supply.
Splittail are large minnows that can grow to more than 12 inches long and live five to seven years. Their populations tend to drop substantially during long droughts and rebound dramatically in response to wet weather.
There is an honest disagreement among scientists about whether the fish belongs on the list of protected species, with some arguing that splittail are well-suited to bounce back from depressed population numbers and others contending the population is on a worrisome downward trend.
In response to concerns that splittail were in decline, the wildlife service added it to the list of threatened species in 1999.
Central Valley farmers sued to overturn the listing and, in June 2000, they won a court order that required government scientists to review their decision in light of new data.
When the court ordered the listing decision redone, it set off a highly unusual series of reports in which biologists in the wildlife service's Sacramento field office concluded repeatedly that splittail should be kept on the list of threatened species.
But none of those reports was sent to Washington for final approval.
Then, in January 2003, the head of the Sacramento office, Steve Thompson, called a meeting to hear the latest presentation from the splittail team. After hearing a report from Jason Douglas, the lead biologist, every scientist in the room except Thompson agreed that splittail should remain on the list, according to notes from that meeting.
Shortly thereafter, Douglas was replaced as the lead biologist.
"I thought it was clear we weren't going to be able to list it. In the face of uncertainty, you err on the side of the species," said Douglas, who now works in the agency's Tucson, Ariz., office.
The splittail report -- concluding that the fish be taken off the list of threatened species -- was then sent to the agency's Washington headquarters.
The rest of the roughly 100-page report, however, was largely intact, and that inconsistency angered MacDonald, according to a participant on a conference call with MacDonald at the time.
"She's hopping mad and saying this thing reads like a listing package," said the participant, a wildlife service official in Washington who requested anonymity out of fear of retaliation. "She said something to the effect that she would just have to do this herself."
The official added that although the recommendation to take the fish off the list was made in Sacramento, "without a doubt the decision was made the way it was because of pressure from Julie MacDonald. She was the one that forced the decision."
Thompson, the head of the Sacramento office who made the recommendation, said he did not specifically recall speaking with MacDonald about the splittail listing but added that he was sure the issue came up.
"Certainly, Julie MacDonald called me on a regular basis, and I'm sure she talked to me about it," Thompson said.
On Sept. 15, 2003, eight days before the decision to take splittail off the threatened species list was made final, the Washington office faxed to Sacramento six marked-up pages of the new rule with the cover page notation, "re: Julie MacD's latest comments/edits."
In it, MacDonald made numerous changes and comments, most of which appear to have been aimed at softening the language of the rule. In addition to changing the conclusion that splittail "are likely" declining to "may be" declining, she wrote that, "At this point, none of the threats individually or collectively rise to a level of concern that warrants listing."
That sentence does not appear in the final report.
MacDonald also took issue with the statistical methods employed by her agency's biologists.
At the time of the decision, there was a debate about how to perform statistical calculations to determine whether the splittail population was declining. The stricter method favored by some scientists, including biologists working for the state of California, did not offer a clear picture of a fish in decline.
But the relaxed method preferred by federal biologists did.
That dispute might have been rendered moot by a third statistical method that appeared to conclusively show that splittail was in decline.
The wildlife agency ignored the third method in its final rule, however.
In a memo filed in June 2003, former agency field supervisor Wayne White wrote that the new statistics reinforced what agency biologists had been saying since 1994: that the fish was in decline.
But, he noted, the new statistics had not been subject to public comment, and the officials who made the decision to take splittail off the list of threatened species were aware of the new data.
In the end, the agency concluded that even if the fish were in decline, new programs were in place to improve the fish's habitat.
Rep. George Miller, D-Martinez, a senior member of the House Committee on Natural Resources, said MacDonald's actions regarding the splittail listing were very serious and cast doubt on every endangered species decision she touched.
"This is like a police department where they tamper with evidence. You have to go back" and re-examine decisions that might be compromised, he said.
"It's clearly worthy of a criminal investigation," said Miller. "This was not an accident. She knowingly did this. She aggressively did this."
Mike Taugher covers natural resources. Reach him at 925-943-8257 or email@example.com.