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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 byBatrachochytrium dendrobatidis(Bd), has led to global amphibian declines. Yet, some populations now show signs of recovery, even thoughBdis 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 experiencedBd‐related declines followed by apparent recoveries:Colostethus panamansis,Lithobates warszewitschiiandSachatamia 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.
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This content will become publicly available on January 1, 2027
Using Serially Collected Specimens to Investigate the Potential Population Genetic Consequences of Reported Declines in Eastern Woodland Salamanders
ABSTRACT Biodiversity is facing global change at an unprecedented rate. Understanding how populations have responded to accelerated change over the last century is key to informing effective conservation policies. Serially collected specimens from natural history repositories can provide a window into how populations change over time and highlight further vulnerabilities in remaining populations. Changes in observed population abundance during field surveys suggest that somePlethodonsalamander populations experienced declines since the 1960s, but the potential population genetic consequences of these declines remain unstudied. Thanks to decades of sustained collection‐based efforts,Plethodonsalamanders serve as a model to test the utility of historical DNA to identify shifts in genetic diversity at recent time scales. Here, we investigate demographic change in sixPlethodonspecies through time using DNA from formalin‐fixed museum specimens (1960s–1970s), historic frozen blood (1980s–1990s), and contemporary sampling. We generated several reduced representation SNP datasets using a target‐capture approach to investigate two sites in the Appalachian Range: one with documented declines (Indian Grave Gap) and one without (Skull's Gap). We quantify the impact of bioinformatic choices on estimates of genetic diversity, quantify demographic shifts, and trace changes in allele frequencies in immune‐related loci to explore the potential impact of pathogens on putative declines. We found consistent patterns of genetic diversity change across datasets and filtering regimes. At Skull's Gap, our results suggest that populations were stable or expanding, while at Indian Grave Gap, our results suggest contraction in one species and mixed signals of contraction and expansion in the others. Analyses of immune loci suggest that balancing selection is maintaining shared polymorphism through time in all but one species. Our study outlines important considerations for leveraging historical DNA in time series collections to quantify the genomic effects of localized population declines.
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- Award ID(s):
- 2131060
- PAR ID:
- 10664281
- Publisher / Repository:
- Wiley
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 16
- Issue:
- 1
- ISSN:
- 2045-7758
- Subject(s) / Keyword(s):
- genetic diversity historical DNA museum genomics Plethodon salamanders population declines time series analysis
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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