Population genomics of European gull-billed terns

Many migratory species have experienced severe population declines, but the genetic consequences of such declines are still rarely assessed. The last Central European population of gull-billed terns (Gelochelidon nilotica) has declined from 500 breeding pairs in the 1940s to 55 in 2024, whereas Mediterranean populations of this migratory waterbird still thrive. Here, we compare whole-genome sequencing (WGS) data from the declining population to those of two thriving populations, as well as to WGS data from its ancestors using museum specimens. We found comparable nucleotide diversity, but lower observed heterozygosity, in the Central European population compared to the Mediterranean populations. Some population structure was also observed, although admixture analyses, low genetic differentiation (FST) and low inbreeding coefficients (FROH) still suggested potential population connectivity, too. Data from the historical population revealed a comparable level of genetic diversity as the contemporary population, but effective population size estimates suggested two past population declines. While FROH values in the extant Central European population were significantly higher than in the historical population, they were not elevated compared to those in the thriving contemporary populations. These results suggest that population structure may be emerging, and although inbreeding is not yet at worrisome levels in the last and small Central European population of gull-billed terns, the possibility that this population is at the early stages of inbreeding depression cannot be ruled out. If the population remains small and isolation manifests, the effects of inbreeding depression could become more pronounced over time, potentially reducing fitness and increasing the risk of extinction.