Gannett Co.'s (GCI) USA Today remained the top newspaper by total average daily circulation, which includes digital readers, while News Corp's (NWSA, NWS) The Wall Street Journal continued to have the largest print circulation, according to a data tracker Thursday.

The continued shift by readers to electronic devices and away from print is not only forcing newspapers to change how they present the news but also prompting auditors to alter how they calculate a paper's audience.

The Alliance for Audited Media said changes to how it tabulates readers make its figures for the six months ended March 31, released Thursday, not comparable with its past data. More changes are on the way, the alliance said, as the September report would be the last of its kind, with more frequent reports expected in the future.

Through March, the top three U.S. newspapers remained USA Today, The Wall Street Journal and the New York Times.

USA Today had a total daily average circulation of 3.3 million, the alliance said. The print edition count comprised roughly 1.2 million, or about 36% of the total circulation. USA Today--which doesn't charge for access to its website or mobile applications--began including digital readers for the first time last year, giving the paper's overall tally a significant boost.

The Wall Street Journal reported a total average circulation of 2.3 million. The print edition comprised 1.4 million, or 59% of the total. In addition to The Journal, News Corp also owns this newswire.

New York Times' total circulation was 2.2 million with print circulation of 680,905, or 32% of the total.

Both The Wall Street Journal and New York Times have "paywalls" that limit non-subscribers' access to their digital editions. The alliance has said that newspapers may include digital editions, tablet or smartphone apps, PDF replicas and e-reader editions in their total circulation.

The alliance's latest report included 610 U.S. newspapers, with nearly half of them reporting a Monday-to-Friday average, and 531 of them reporting digital editions. The group stopped requiring daily newspapers with circulations of more than 50,000 to provide five-day-average figures last year.

Write to Tess Stynes at tess.stynes@wsj.com

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