A little fish in a big city: conservation genetics of the Arroyo chub

By Alyssa Benjamin

The Arroyo chub (Gila orcuttii) is a small omnivorous fish native to Southern California coastal streams whose existence has been severely impacted by human development. Because their range overlaps with the densely populated greater Los Angeles area, many streams and rivers once rife with habitat have now been paved over, fragmented, or eliminated completely. The recent decline of Arroyo chub has prompted an urgent need to better understand the remaining populations.


The same location in 2009 (Photo by Mark Yashinsky / CC BY-NC-SA).


The Los Angeles River at the Seventh Street Viaduct in 1938 shortly before it was paved for flood control (Photo from LA Public Library Collection).







In our study, newly published in Transactions of the American Fisheries Society, we used genetic information as a way to understand the Arroyo chub populations and determine appropriate conservation strategies. Genetic data is especially valuable because it can provide important clues as to the current and historical relationships and status of populations that may not be apparent by simple outward inspection of fish.

For this study, we analyzed over 200 Arroyo chub collected at different sites from six native watersheds and genotyped them using microsatellites. Microsatellites are regions in the genome, generally in non-coding areas, that have a repeating sequence of nucleotides (e.g. ACTGACTGACTG…). The number of repeated units varies greatly between individuals which makes microsatellites useful for looking at population level differentiation.


Arroyo chub captured during collection efforts. Photo by California Department of Fish and Wildlife.

Our analysis of the genetic data revealed two main points. First, we found a high degree of fragmentation between populations. Essentially, every sampled watershed had a unique Arroyo chub population and some watersheds even had multiple unique populations within the same river. This genetic differentiation is consistent with the overall isolation of fish as a result of human development, habitat loss, the current drought, and flood control measures.

The second finding was that most of the Arroyo chub populations, despite fragmentation and isolation, have managed to retain a lot of genetic diversity thus far. When populations show higher levels of genetic diversity, they are generally better able to adapt to environmental changes and are considered “healthier” populations.  However, the fact that most of the Arroyo chub populations are small and fragmented means they have a higher risk of losing genetic diversity in the future. While we did recommend some possible strategies for conservation in the article, habitat restoration will ultimately be most essential to securing the future of the Arroyo chub.

Reference: Alyssa Benjamin, Bernie May, John O’Brien & Amanda J. Finger (2016) “Conservation Genetics of an Urban Desert Fish, the Arroyo Chub.” Transactions of the American Fisheries Society, 145:2, 277-286. DOI: 10.1080/00028487.2015.1121925