Sampling through space and time: multi-year analysis reveals dynamic population genetic patterns for an amphibian metapopulation

Metapopulations are dynamic, and population genetics can reveal both spatial and temporal metapopulation variation. Yet, population genetic studies often focus on samples collected within a single time period or combine samples taken across time periods due to limited resources and the assumption that these approaches capture patterns and processes occurring over decadal and longer temporal scales. However, this may leave important fine-scale temporal variation in genetic composition undetected, particularly for metapopulations in which dynamic populations are expected. We investigated temporal patterns of population genetic diversity, effective population size, and differentiation across three sample periods for a dryland amphibian metapopulation. We sampled nine distinct Arizona treefrog (Hyla (Dryophytes) wrightorum) breeding ponds in 2014, 2018/2019, and 2021 and genotyped 17 microsatellite loci to quantify spatial and temporal population genetic dynamics. Genetic diversity within and between populations varied significantly among years. Most notably, we identified a concerning decline in allelic richness across populations, with an average − 26.11% difference between a population’s first and last sample period. Effective population sizes were generally small (N_e < 100) and variable within and among populations over time, with many populations falling below common conservation thresholds by the final sample period. Trends in global genetic diversity, as measured by heterozygosity, and population differentiation were relatively consistent across all sampling periods. Overall, we found that “snapshot” or single-time sampling approaches may miss temporal variability in genetic composition that has important conservation implications, including early warning signs of decline in genetic diversity.