Alker posted his second 3-under 67 in as many rounds for a 6-under-par 134 total. Shane Bertsch carded a 5-under 65 and is tied for third place with first-round leader Ryan Hietala (71) and Jon Mills (67). The trio is knotted at minus-5.
Villegas started on the back nine Friday and broke into red figures with a birdie at the par-5 12th. He parred his next five until a birdie at the 18th pushed him to 5 under par for the championship.
The 23-year-old made it two birdies in a row at the first, then birdied the fifth. Villegas parred his remaining holes for a bogey-free round, one of only three on Friday.
'I didn't make any bogeys, which is really saying something on a golf course as tough as this one,' said Villegas. 'I played really good golf today. I hit some solid shots and made my share of putts. I had so much fun out there.'
Villegas does not have any status on the Nationwide Tour in 2005, so a big finish this week would help. He got into the tournament this week on a sponsor's exemption and due to Panama's proximity to Colombia, was a huge fan favorite.
'The crowds were awesome today. They treated me just like I was home,' said Villegas, a three-time All-American at the University of Florida. 'I have to thank Tournament Director Roberto Duran for giving me the opportunity to play this week. It has been a pretty special week so far.'
Alker began on the second nine and parred his first nine holes. He birdied 18 and one, then added a birdie at the par-5 fourth. Alker dropped a shot at the par-3 sixth, but got within one of Villegas' lead with a birdie at nine.
'Obviously I like where I'm at through two rounds,' said Alker, who captured the 2002 Louisiana Open. 'I'd much rather be where I'm at than in the other half.'
Scott Sterling shot a 3-under 67 and is tied for sixth place with Vance Veazey, who carded a one-over 71 on Friday. The duo is knotted at 4-under-par 136.
Kevin Gessino-Kraft and Kris Cox each posted rounds of 3-under 67 in the second round. They share eighth place with 2002 U.S. Amateur champion Ricky Barnes, who carded a 69, at minus-3.