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 Now an official says DNA tests have solved the mystery by identifying bone shards found in a forest as those of Alexei and his sister, Grand Duchess Maria.
The remains of their parents -- Nicholas II and Empress Alexandra -- and three siblings, including the czar's youngest daughter, Anastasia, were unearthed in 1991 and reburied in the imperial resting place in St. Petersburg. The Russian Orthodox Church made all seven of them saints in 2000.
Despite the earlier discoveries and ceremonies, the absence of Alexei's and Maria's remains gnawed at descendants of the Romanov dynasty, history buffs and royalists. Even if Wednesday's announcement is confirmed and widely accepted, many descendants of the royal family are unlikely to be fully assuaged; they seek formal "rehabilitation" by the government.
"The tragedy of the czar's family will only end when the family is declared victims of political repression," said German Lukyanov, a lawyer for royal descendants.
Nicholas abdicated in 1917 as revolutionary fervor swept Russia, and he and his family were detained. They were shot by a firing squad on July 17, 1918, in the basement of the Yekaterinburg house where they were being held.
Rumors persisted that some of the family had survived and escaped. Claims by women to be Anastasia were particularly prominent, although there were also pretenders to Alexei's and Maria's identities.
"It was 99.9 percent clear they had all been killed; now with these shards, it's 100 percent," said Nadia Kizenko, a Russian scholar at the University at Albany, State University of New York. "Those who regret this news will be those who liked the royal pretender myth."
Alexei was one of the more compelling of the victims, drawing sympathy because of his hemophilia. His mother's terror of the disease and fear that he would not live to gain the throne were key to her falling under the thrall of the hypnotic and sexually ravenous self-declared holy man Rasputin, who exerted vast influence on the royal family.
Researchers unearthed the bone shards last summer in a forest near Yekaterinburg, where the royal family was killed, and enlisted Russian and U.S. laboratories to conduct DNA tests.
Eduard Rossel, governor of the region 900 miles east of Moscow, said tests done by a U.S. laboratory had identified the shards as those of Alexei and Maria.
"This has confirmed that indeed it is the children," he said. "We have now found the entire family."
"The main genetic laboratory in the United States has concluded its work with a full confirmation of our own laboratories' work," Rossel said.
He did not specify the laboratory, but a genetic research team working at the University of Massachusetts Medical School has been involved in the process. Evgeny Rogaev, who headed the team that tested the remains in Moscow and at the medical school in Worcester, Mass., was called into the case by the Russian Federation Prosecutor's Office.
He told The Associated Press on Wednesday that he delivered the results to Russian authorities, but said it was up to the prosecutor's office
-- not him or his team -- to disclose the findings.
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 "The most difficult work is done and we have delivered to them our expert analysis, but we are still working," he said. "Scientifically, we want to make the most complete investigation possible."
The test results were based on analysis of mitochondrial DNA, the genetic material passed down only from mothers to children. That DNA is more stable than nuclear DNA
-- the material inherited from the father's side -- especially when remains are badly damaged.
In this case, the bone fragments were so shattered and burned that Rogaev's team first had to determine whether enough uncontaminated genetic material still existed for testing.
The delicate work proved that, indeed, useful DNA could be extracted from a very small amount of the material
-- a critical fact, since they wanted to preserve as much of the bone fragments as possible out of respect for the victims.
The researchers also compared DNA from the remains with those of Empress Alexandra, who was a granddaughter of Britain's Queen Victoria and a distant relative of Prince Philip, the husband of Queen Elizabeth II.
With the mitochondrial analysis completed, the team is working on the nuclear DNA analysis and comparing the samples to paternal relatives of the czar's family.
That information, along with conclusions already delivered to the Russian prosecutors, eventually will be submitted to a professional journal for peer review and publication.
It was unclear if the Russian Orthodox Church will recognize them as genuine. The church's press service said no one could comment on Wednesday's announcement.
It was also unclear whether the descendents of the royal family would accept the identification. Lukyanov said neither he nor his clients had received confirmation.
Lukyanov's efforts to get the government to declare the royal family victims of political repression have been repeatedly rejected by Russian courts, which have said the family's killing was premeditated murder, not a political reprisal.
He said Russia had much to do to overcome its tortured past.
"They say that as long as the last soldier remains unburied, the war continues," Lukyanov told AP. "So long as the last victim of Bolshevik terror and the Communist regime remains
unrehabilitated, the repression will continue."
[Associated
Press; By MIKE ECKEL]
Associated Press writers Carley Petesch in New York and Stephanie Reitz in Hartford, Conn., contributed to this report.
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