Here's an interesting review of the subject - Treaty rights vs ESA. Turns out that so far, what few cases have been edudicated, it comes down to whether there is evidence that Congress, when creating and passing the law, intended the law to abrogate the treaties or not.

Warning, it's a direct pdf download...

https://www.google.com/url?sa=t&source=web&rct=j&url=http://scholarship.law.umt.edu/cgi/viewcontent.cgi%3Farticle%3D1240%26context%3Dplrlr&ved=0ahUKEwiBi8ON4PvMAhVBwWMKHVE0DjwQFggeMAE&usg=AFQjCNHPaXkqehuYuSkNwIh_agTqQ4DoFw