ANCHORAGE, Alaska (AP) – Republican Lisa Murkowski earned a term in the Senate in her own right Wednesday, defeating popular former Gov. Tony Knowles and overcoming the commotion that arose when her father, the governor, appointed her to fill his Senate term.

With all precincts reporting, Murkowski had 49 percent to Knowles’ 45 percent, a lead of more than 11,000 votes.

Knowles, a Democrat, called Murkowski to congratulate her but stopped short of formally conceding defeat Wednesday. He said he wanted to let the democratic process run its course to ensure that every vote is counted.

“But it’s improbable that we’ll make up the existing difference,” he said.

Elections officials said thousands of questioned ballots and absentee votes remain to be counted. The state sent out 58,559 absentee ballots, nearly double the number distributed in 2000. Under state law, the post-election deadline for absentee ballots is 10 days for those mailed domestically and 15 days for overseas voters.

“Right now we’re in the gathering stage,” said Carol Thompson, elections supervisor for Alaska’s south-central region. “We’ll be getting ballots in every single day, so we’ll constantly be changing our totals.”

The contest was one of the most competitive Senate campaigns in the country, featuring accusations of nepotism and charges that Knowles was too liberal for conservative Alaskans. Murkowski’s victory means Republicans will hold 55 Senate seats next year.

“What we see here, folks, is Alaskans speaking up and saying thank you for running a good campaign,” Murkowski said. “It’s been an honor working for you as Alaskans and it’s something I look forward to doing for six more years.”

The election was Murkowski’s first time before the voters, and she managed to overcome naysayers who remained convinced that she unfairly gained the job because of her family ties. Her most ardent foes placed bumper stickers on their vehicles that read: “Yo, Lisa! Who’s yer daddy?!”

Murkowski, a 47-year-old former state lawmaker, was appointed by Gov. Frank Murkowski to the Senate seat he vacated when he was elected governor in 2002. The appointment was made possible by a change in state law enacted by the Legislature that year.

Nepotism was such an issue this year that more than 50,000 voters signed petitions for an initiative on Tuesday’s ballot to require Senate vacancies be filled by special election. The measure was approved.

Despite the controversy, Murkowski had strong name recognition, the power of incumbency and history on her side – Alaska has not sent a Democrat to Washington in 30 years.

Murkowski had the high-profile endorsement of GOP Sen. Ted Stevens, who called her “a hell of a lot better senator than her dad ever was.” She also was endorsed by President Bush and Vice President Dick Cheney, who appeared in Alaska along with several other top Republicans.

Knowles, 61, a former mayor of Anchorage and a two-term governor, tried to distance himself from national Democrats, saying he would be an independent voice for Alaskans.