Pricing is primarily based on what an airline feels the value is of travel between your starting point and your final destination. How you get there is a secondary consideration.
If there is a large supply of unsold seats on the nonstop flights, then those tickets will likely be cheaper than flights with connections.
If there is a small supply of unsold seats on the nonstop flights, then those few remaining tickets will likely be more expensive than flights with connections.
These prices will change up or down based on how many tickets are sold as you get closer to departure time.
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