Abstract
Global climate change is apparent within the A rctic and the south‐western deserts of N orth A merica, with record drought in the latter reflected within 640 000 km 2 of the C olorado R iver B asin. To discern the manner by which natural and anthropogenic drivers have compressed B asin‐wide fish biodiversity, and to establish a baseline for future climate effects, the S tream H ierarchy M odel ( SHM ) was employed to juxtapose fluvial topography against molecular diversities of 1092 B luehead S ucker ( C atostomus discobolus ). M t DNA revealed three geomorphically defined evolutionarily significant units ( ESU s): B onneville B asin, upper L ittle C olorado R iver and the remaining C olorado R iver B asin. Microsatellite analyses (16 loci) reinforced distinctiveness of the B onneville Basin and upper L ittle C olorado River, but subdivided the C olorado R iver B asin into seven management units ( MU s). One represents a cline of three admixed gene pools comprising the mainstem and its lower‐gradient tributaries. Six others are not only distinct genetically but also demographically (i.e. migrants/generation G rand C anyon and C anyon de C helly) are defined by geomorphology, two others (i.e. F remont‐ M uddy and S an R aphael rivers) are isolated by sharp declivities as they drop precipitously from the west slope into the mainstem C olorado/ G reen rivers, another represents an isolated impoundment (i.e. R ingdahl R eservoir), while the last corresponds to a recognized subspecies (i.e. Z uni R iver, NM ). Historical legacies of endemic fishes ( ESU s) and their evolutionary potential ( MU s) are clearly represented in our data, yet their arbiter will be the unrelenting natural and anthropogenic water depletions that will precipitate yet another conservation conflict within this unique but arid region.