Abstract
Infectious diseases can cause severe population declines, reducing genetic diversity, ecological function, and prospects for long‐term survival. Such declines often result in genetic bottlenecks, with small, isolated populations that are especially vulnerable to extinction due to genetic drift and inbreeding. Chytridiomycosis, caused by Batrachochytrium dendrobatidis ( Bd ), has led to global amphibian declines. Yet, some populations now show signs of recovery, even though Bd is present and pathogenic. In this study, we use a genomic approach to investigate the genetic patterns underlying recoveries in three amphibian species from Panama that experienced Bd ‐related declines followed by apparent recoveries: Colostethus panamansis , Lithobates warszewitschii and Sachatamia albomaculata . These species differ in life history traits and dispersal capacities, allowing us to examine how such differences influence genetic signatures of recovery. Here, we employed a frog‐specific genomic capture assay to analyse the effective population sizes, population structures, and both genome‐wide and immune‐specific genetic diversity. Our results reveal recent genetic bottlenecks and low effective population sizes across all three species, consistent with evidence of past disease‐driven declines. However, we found distinct patterns of gene flow and immune genetic diversity among species. These findings suggest that gene flow may serve as a key demographic and adaptive contributor of recovery in some species by introducing novel genetic variation. Understanding how populations recover from infectious disease impacts is critical for informing conservation efforts. Our study provides insights into the genetic signatures associated with recovery and highlights the importance of species‐specific traits in shaping evolutionary responses to emerging diseases.