| Abstract | | The endangered annual endemic Butte County meadowfoam (BCM, Limnanthes floccosa ssp. californica) is restricted to vernal pools along the eastern flank of the Sacramento Valley from central Butte County to the northern portion of the City of Chico. Within the last 30 years known BCM populations were subject to urban development, airport maintenance activities, conversion of agricultural lands to other uses, and road widening or realignment. The relatively small number of remaining extant sites, and results from this and a previous isozyme study on a subset of sites suggest that the loss of any populations may represent a significant deficit of the total amount of genetic variability for the species, making BCM extremely vulnerable to chance catastrophes. BCM recovery will require conservation and restoration of existing populations and protection of their habitat. Knowledge of the extant genetic composition is essential to more appropriately design reintroduction efforts during establishment of new and restoration of declining populations, and to identify populations with particularly unique genetic resources. Analysis of the genetic diversity (within population allelic variation) and regional genetic structure (among population allelic variation) of BCM populations will inform our conservation decisions with respect to possible translocation of individuals (i.e., seeds or plants) from one area to another to recover critically declining populations, and to guide the design of possible seed collection scenarios for long-term ex situ seed storage. To examine fine scale and range-wide genetic structure we genetically surveyed 457 individuals from 21 known geographically separate (> 0.25 kilometers apart) extant BCM occurrences using 9 polymorphic microsatellite markers adapted from a suite of markers developed for Limnanthes alba. Despite utilizing a highly polymorphic marker system our data confirmed earlier accounts of low within population genetic diversity: average allelic diversity = 1.9 (0.06 SE) alleles per locus; average H obs = 0.10 ± 0.018, average H exp = 0.19 ± 0.015, mean Shannon’s information index 0.317 ± 0.025, mean fixation index 0.556 ± 0.044. The number of polymorphic loci ranged between 11% and 89%, with an average of 55% among populations. Bayesian ordination determined 20 distinct population clusters, and we confirmed high genetic structure among these populations (Fst = 0.65, P < 0.000). We identified notable barriers to gene flow across genetically distinct BCM populations and confirmed evidence for regional structuring between three previously defined centers of population density and two outlying populations (Fst = 0.21, P < 0.000). Population size estimates for all collection sites ranged between ~50 and >5000 extant plants per site. All four Chico airport occurrences showed extremely low population numbers and had notably declined from population levels reported in 1992. We recommend close examination of the microhabitats of these and other declining sites and potential genetically similar seed source sites to determine the potential for human assisted gene flow via seed movement.
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