A retrenchment of the "benefit of the doubt to the species"?

Yesterday the Eleventh Circuit Court of Appeals ruled in Miccosukee Tribe v. USA, a case concerning Army Corps activities in the Florida Everglades.  The tribe contended that the Corps' flooding activities jeopardized the Cape Sable seaside sparrow.  The Eleventh Circuit's opinion largely upheld the Corps' actions, and the Fish and Wildlife Service's biological opinion, save for a small point regarding the opinion's use of a habitat proxy for a numerical take limit in the bi-op's incidental take statement.  But what really stands out is the decision's rejection of the tribe's somewhat broad interpretation of the "benefit of the doubt goes to the species" notion, which concept ultimately traces back to TVA v. Hill (strangely enough not cited in Miccosukee) but more recently to the Ninth Circuit's decision in Conner v. Burford.   The Eleventh Circuit noted that the benefit of the doubt language itself comes from a 1979 House Report.  The court went on to observe that "the context of the benefit of the doubt language in the conference report suggests only that agencies, including the Service, cannot hide behind uncertain scientific data to shirk their duties under the Act."  The court then distinguished Connor in the following manner:

The Conner opinion does not suggest that there is any presumption in favor of the species if, as in this case, there is abundant data. In Conner the Service violated the Act by issuing a biological opinion without using the best available data.  Because that is not the case here the Tribe's reliance on Conner is misplaced.

To be sure, Miccosukee is not a repudiation of the presumption in favor of species, but it certainly defines the outer limits of that interpretive tool.