The Bonneville cisco (Prosopium gemmiferum), a small planktivorous whitefish, is an important part of the distinctive fish community of Bear Lake, Utah-Idaho. The Bonneville cisco plays a key role in the trophic structure by converting zooplankton to fish biomass and providing a major forage sour ce for cutthroat and lake trout. Aspects of cisco feeding ecology studied include characterization of the zooplankton community composition and dynamics and cisco feeding habits and prey select ion.

The mountain whitefish (Prosopium williamsoni) has been largely overlooked in population genetic analyses despite its wide distribution in discrete drainage basins in western North America for over four million years. Its closest sister taxa the Bear Lake whitefish (P. abyssicola), Bonneville cisco (P. gemmifer), and Bonneville whitefish (P. spilonotus) are found only in Bear Lake Idaho-Utah and were also included in the analyses. A total of 1,334 cytochrome b and 1,371 NADH dehydrogenase subunit 2 sequences from the Bonneville Basin, the Columbia River Sub-basin, the lower Snake River Sub-basin, the upper Snake River Sub-basin, the Green River Basin, the Lahontan Basin, and the Missouri Basin were examined to test for geographically based genetic differentiation between drainage basins and sub-basins and phylogeographic relationships to determine the invasion route of Prosopium into western North America and to aid in understanding current relationships. Prosopium entered the region via the Missouri River connection to Hudson Bay and moved in two waves: one colonized the lower Snake River Sub-basin, Columbia River Sub-basin, and the Lahontan Basin; the second wave colonized the upper Snake River Sub-basin, Bonneville Basin, Green River Basin, and established the Bear Lake Prosopium. Mountain whitefish exhibit a large amount of geographical genetic differentiation based on drainage basin except between the upper Snake River and the Bonneville Basin while the Bear Lake Prosopium show large amounts of gene flow between the three species. The apparent paraphyly of the mountain whitefish and the limited genetic structure of the Bear Lake Prosopium warrant recognition in the management of Prosopium and raise questions regarding species definitions in the group.