JetBlue Airways (JBLU) said Wednesday it will end its Northeast Alliance (NEA) partnership with American Airlines (AAL) in an effort to focus on its proposed combination with low-cost carrier Spirit Airlines (SAVE).

JetBlue shares were down about 3.7% in early trading Thursday and American Airline's shares fell roughly 2%. Spirit Airlines stock was up about a percent.

The NEA is a series of agreements between American Airlines and JetBlue through which they consolidated their operations in Boston and New York City. The court ruled that the agreement effectively stopped competition in Boston and New York, increasing fares for travelers and reducing choices.

While JetBlue said it strongly disagreed with the court's ruling, the carrier decided against appealing to the court and has initiated a wind-down process that will terminate the NEA over the coming months.

American Airlines said it will move forward with the appeal since the carrier considers the judicial decision as erroneous and the NEA as competitive.

In ending the agreement with American Airlines, JetBlue hopes to salvage its acquisition of Spirit Airlines. Earlier this year, the Justice Department filed a suit to prevent JetBlue from buying its low-cost rival for $3.8 billion, citing concerns about higher prices if the two airlines stopped competing.

The DOJ has concerns about consolidation across the airline industry. A series of mergers has left travelers with few choices outside of the Big Four airlines. That includes three “legacy” carriers—Delta (DAL), United (UAL), and American Airlines—and low-cost Southwest (LUV). Those four carriers control close to 80% of the domestic airline industry, with alliances extending their reach even further.