Background

Anthropogenic forces have resulted in staggering losses of biodiversity and population declines in many species over the past two centuries. Associated with these declines are potential adverse effects linked to small population sizes, including loss of genetic diversity and increased levels of inbreeding. Here, we leverage DNA sequencing from museum specimens to examine genetic variation between historic and contemporary populations of four species of warblers (Aves, Setophaga) that vary with respect to degree of population changes over this period. To explore the genetic impacts of varying population declines, we gathered polymorphism data at 157 PCR-amplified loci in 341 individuals sampled in two time periods—historic (1789–1955) vs contemporary (2001–2020).

Results

For all four species, we observed decreases in nucleotide diversity and heterozygosity in contemporary data sets compared to historic data sets. In three species, this loss was accompanied by a corresponding increase in inbreeding coefficient FIS. We find that these genetic diversity declines correspond to declining contemporary effective population sizes (Ne) over deeper time scales, as well as fluctuations in contemporary estimates of Ne.

Conclusion

Our findings suggest that loss of genetic diversity resulting from historic population declines persists over time (50–100 years), even when population trajectories later stabilize. Our results highlight the utility of long-term genetic temporal comparisons to reveal hidden genetic diversity loss and reveal important considerations for managing genetic diversity loss.