Howellia aquatilis A.Gray (water howellia) is a federally-listed threatened aquatic plant species with limited distribution in four states: California, Idaho, Montana, and Washington. Previous studies have shown a lack of genetic variation within the species; these studies, however, have excluded samples from one or more states. There have been no published studies on the population biology or genetics of the six known California populations or their evolutionary relationship to the other Pacific Northwest populations. We used Amplified Fragment Length Polymorphisms to identify genetic variation within and among the California populations, and to compare the California populations to the Idaho, Montana, and Washington populations. Analysis of molecular variance of 92 individuals from the six California populations show that 83.8% of genetic variation is found within populations and 16.2% among populations (P < 0.001). All sampled populations from all states provide 83.7% variation within and 16.3% variation among populations (P < 0.001). A UPGMA analysis confirms there is no clear clustering of Howellia aquatilis populations within California, that the Montana populations cluster within the California populations, and, although with limited population sample sizes, the Idaho and Washington populations are distantly related to all other populations. Waterfowl migration patterns support a hypothesis for avian dispersal as a primary factor in gene flow in Howellia aquatilis.
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