Background:Our ability to monitor populations or species that were once threatened or endangered and in the process of recovery is enhanced by using genetic methods to assess overall population stability and size over time. This can be accomplished most directly by obtaining genetic measures from temporally-spaced samples that reflect the overall stability of the population as given by changes in genetic diversity levels (allelic richness and heterozygosity), degree of population differentiation (F_ST and D_EST), and effective population size (N_e). The primary goal of any recovery effort is to produce a long-term self-sustaining population, and these measures provide a metric by which we can gauge our progress and help make important management decisions.

Methodology/Principal Findings:The peregrine falcon in North America (Falco peregrinus tundrius and anatum) was delisted in 1994 and 1999, respectively, and its abundance will be monitored by the species Recovery Team every three years until 2015. Although the United States Fish and Wildlife Service makes a distinction between tundrius and anatum subspecies, our genetic results based on eleven microsatellite loci, including those from Brown et al. (2007), suggest no differentiation and warrant delineation of a subspecies in its northern latitudinal distribution from Alaska through Canada into Greenland. Using temporal samples collected at Padre Island, Texas during migration (seven temporal time periods between 1985-2007), no significant differences in genetic diversity or significant population differentiation in allele frequencies between time periods were observed and were indistinguishable from those obtained from tundrius/anatum breeding locations throughout their northern distribution. Estimates of harmonic mean N_e were variable and imprecise, but always greater than 500 when employing multiple temporal genetic methods.

These results, including those from simulations to assess the power of each method to estimate Ne, suggest a stable population consistent with data from field-based monitoring indicating that this species is stable or continuing to increase in abundance. Therefore, historic and continuing efforts to prevent the extinction of the peregrine falcon in North America appear successful, further highlighting the importance of archiving samples for continual assessment of population recovery and long-term viability.