Document Type
Article
Publication Date
2026
DOI
10.1086/738468
Publication Title
American Naturalist
Volume
207 (Advance online publication)
Issue
1
Pages
18 pp.
Abstract
Evaluating the evolutionary impacts of anthropogenic activity on populations is key to understanding species resiliency and to designing effective conservation strategies. Sequencing DNA from historical specimens provides the opportunity to establish a historical baseline and empirically assess changes in genetic diversity, changes in effective population size, and selection over time. Here, we sequenced historical and contemporary samples of the cardinalfish Taeniamia zosterophora collected in 1908 and in 2021–2022 across two sites with differing human impact in the Philippines. At both sites, genetic diversity increased over time, with contemporary samples having significantly higher Watterson’s θ than historical samples. This diversity increase was primarily attributable to positive selection on low-frequency alleles such that they increased toward intermediate frequencies through time. For the putatively neutral fraction of the genome, in contrast, there was a slight but significant decline in Watterson’s θ at both low and high human impact sites, suggesting that drift strengthened and effective population sizes declined through time. There was more evidence for selection and greater loss of neutral diversity at the site with higher human impact. Our results provide empirical evidence for the surprising preservation of genetic diversity through the action of natural selection in the face of anthropogenic impacts.
Rights
© 2025 The University of Chicago. All rights reserved, including rights for text and data mining and training of artificial intelligence technologies or similar technologies.
Submitted for publication to American Naturalist on October 22, 2024.
Included with a 12-month embargo in accordance with publisher policy.
Data Availability
Article states: "Sequence data have been archived in the National Center for Biotechnology Information Sequence Read Archive. The BioProject numbers and links to data are as follows: PRJNA1185294 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1185294), PRJNA1185280 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1185280), PRJNA1185271 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1185271), and PRJNA1185264 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1185264). Scripts for bioinformatics and population genomics analysis are available in Zenodo (https://doi.org/10.5281/zenodo.15384658; Fitz 2025)."
Original Publication Citation
Fitz, K. S., Abesamis, R. A., Baldisimo, J. G. P., Bucol, A. A., Clark, R. D., Garcia, E., Lopez, I. R., Magnuson, S. F., Malabag, M. J., Muallil, R. N., Parenti, L. R., Reid, B. R., Santos, M. D., Bird, C. E., Carpenter, K. E., & Pinsky, M. L. (2026). Preservation of genetic diversity and selection over a century in a coral reef fish (Taeniamia zosterophora) in the Philippines. American Naturalist. Advance online publication. https://doi.org/10.1086/738468
Repository Citation
Fitz, Kyra S.; Abesamis, Rene A.; Baldisimo, Jemelyn Grace P.; Bucol, Abner A.; Clark, René D.; Garcia, Eric; Lopez, Ivan R.; Magnuson, Sharon F.; Malabag, Marial J.; Muallil, Richard N.; Parenti, Lynne R.; Reid, Brendan R.; Santos, Mudjekeewis D.; Bird, Christopher E.; Carpenter, Kent E.; and Pinsky, Malin L., "Preservation of Genetic Diversity and Selection Over a Century in a Coral Reef Fish (Taeniamia zosterophora) in the Philippines" (2026). Biological Sciences Faculty Publications. 672.
https://digitalcommons.odu.edu/biology_fac_pubs/672
ORCID
0000-0002-3615-025X (Baldisimo), 0000-0002-1334-3753 (Garcia), 0000-0003-3618-1811 (Carpenter)
Supplemental Material
Included in
Aquaculture and Fisheries Commons, Ecology and Evolutionary Biology Commons, Genetics and Genomics Commons