The existence of red-legged frogs along the route of the bypass could require Caltrans to obtain a special permit from the Army Corps of Engineers. Caltrans is hoping to receive a nationwide permit, which is basically a rubber stamp, but the existence of a threatened species could force Caltrans to pursue a much stricter "individual" permit.
Army Corps regulations state, "No activity is authorized by any nationwide permit if that activity is likely to jeopardize the continued existence of a threatened or endangered species as listed or proposed for listing under the Federal Endangered Species Act, or to destroy or adversely modify the critical habitat of such species."
The regulations go on to say, "Except as provided under Section 404(b)(2), no discharge of dredged or fill material shall be permitted if there is a practicable alternative to the proposed discharge which would have less adverse impact on the aquatic ecosystem, so long as the alternative does not have other significant adverse environmental consequences...In addition, where a discharge is proposed for a special aquatic site, all practicable alternatives to the proposed discharge which do not involve a discharge into a special aquatic site are presumed to have less impact on the aquatic ecosystem, unless clearly demonstrated otherwise."
In other words, if Caltrans were required to obtain an Individual Permit, they would have to prove that the practicable alternative (i.e. the tunnel) would have a greater impact on the frog's habitat than the bypass. As we've learned, Caltrans is great at manipulating facts and figures, but this one could pose quite a challenge.