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SAN JOSE — Defensive end Ray McDonald was arrested for felony domestic abuse Sunday morning in San Jose, bringing more scrutiny to a 49ers team that spent the offseason tangled in legal matters.

Police arrived at 2:48 a.m. to McDonald’s home, where a party was being held in honor of McDonald’s birthday. He turns 30 Tuesday.

McDonald apparently was involved in an altercation with his fiancee, whom a police source said is 10 weeks pregnant. When she showed police minor bruises on her neck and arms, McDonald was arrested without incident.

McDonald was booked at 5:30 a.m. in Santa Clara County jail for “inflicting injury on a spouse or cohabitant,” according to the Santa Clara County Department of Corrections. Bail was set at $25,000 and McDonald was released at 11:30 a.m.

Other 49ers players, including tight end Vernon Davis and defensive end Demarcus Dobbs, attended the party.

“The 49ers organization is aware of the recent reports regarding Ray McDonald and we take such matters seriously,” general manager Trent Baalke said in a statement. “As we continue to gather the facts, we will reserve further comment.”

McDonald was arrested for DUI in Santa Clara County in 2010.

Last week, in the wake of uproar over Ravens running back Ray Rice’s suspension, NFL commissioner Roger Goodell instituted harsher penalties for league employees involved in assault, battery, domestic violence or sexual assault. First-time offenders will receive a six-game suspension. A second offense results in a lifetime ban.

Rice was given a two-game suspension after hitting his then-fiancee in February. Surveillance cameras showed Rice dragging her out of a casino elevator, apparently unconscious, after the incident.

Coach Jim Harbaugh has told 49ers players that domestic violence would not be tolerated on his team.

“He said that we can do anything in the world and we can come and talk to him and he’ll forgive us except put our hands on women,” former 49ers safety Donte Whitner said in 2012. “If you put your hand on a woman, then you’re done in his book.”

McDonald’s arrest marks the ninth time a 49ers player has been arrested since Aldon Smith was pulled over for DUI in Miami beach in January 2012. That includes a March hit-and-run incident involving cornerback Chris Culliver and Smith’s April arrest at Los Angeles International Airport. No charges were filed in the LAX incident.

Smith, who has been arrested three times since he was drafted in 2011, was suspended for nine games by the league on Friday.

Along with fellow defensive end Justin Smith and linebacker Patrick Willis, McDonald has been one of the veteran leaders on defense since he became a starter in 2011. He’s started all but three games in that span and last season played through a biceps tear.

His main backups this year are Quinton Dial and Tank Carradine.

RG BOONE AGREES TO DEAL

A person with direct knowledge of the contract says holdout right guard Alex Boone has agreed to terms on a new $6 million, two-year contract that replaces the two years remaining on his previous deal.

Boone, represented by the agency of Schwartz & Feinsod, is expected to join the 49ers as soon as today as they prepare for their Week 1 game at Dallas on Sunday.

The person spoke on condition of anonymity Sunday because the team had yet to announce Boone’s return. He missed the Niners’ offseason program and was subject to fines for his absences from the mandatory minicamp and training camp. Those fines will be waived, the source said.

Boone’s presence will be felt for an offensive line that has struggled to protect quarterback Colin Kaepernick in the preseason.

The Associated Press contributed to this report.