Lag in Effective Population Size Decline Amid Demographic Collapse: A Case Study of the Delta Smelt (Hypomesus...

Effective population size (N_e), census size (N_c) and their ratio (N_e/N_c) are widely used indicators in conservation genetics, yet long-term empirical data tracking of all three metrics over long time scales in wild populations remains rare. Using monitoring data from 1995 to 2020, we examined temporal dynamics of N_e, N_c and their relationship during the demographic collapse of Delta Smelt (Hypomesus transpacificus), an endangered fish endemic to the San Francisco Estuary, California, USA. We estimated N_e for 21 annual cohorts using restriction site-associated DNA sequencing data, applying the linkage disequilibrium method, temporal method and a recently developed combined method. Abundance was represented by model-based survey indices (N_c*). N_e varied substantially through time (145-1928), declining in recent years but remaining above commonly cited conservation thresholds for long-term persistence (e.g., N_e > 500) until the final years of collapse. N_e was positively correlated with N_c* (r = 0.58), but the shallow slope (β = 0.25) indicates that demographic decline outpaced genetic decline. N_e/N_c* was consistently low (0.0001-0.056), but it increased significantly through time. Our results show that genetic erosion may lag behind demographic collapse and that N_e/N_c* is not constant and therefore cannot be easily inferred from either variable alone. This study demonstrates the need for additional empirical data sets to facilitate interpretation of N_e, N_c* and N_e/N_c* for the conservation of global biodiversity.