Benjamin et al. (2018) research about detecting hybrids and backcrosses between Wakasagi, Delta Smelt, and Longfin Smelt featured in UC Davis news!
Shannon Kieran, a PhD student in the GVL won the Jastro Shields award for her proposal to look at Branchiopod cysts in the soil bank to further understand Branchiopod population genetics and ecology. Congratulations Shannon!
Welcome Shannon Joslin and Ensieh Habibi to the Genomic Variation Lab! Shannon comes from the world of humans to work on the assembly and annotation of the Delta Smelt genome, as well as examining Ne in historical samples and searching for a sex marker. Ensie comes to us from Berlin and Iran, and will be studying domestication in the hatchery population of Delta Smelt.
GVL members Andrea Schreier, Mandi Finger, and Daphne Gille (in collaboration with Cramer Fish Sciences) were awarded a grant by California Department of Water Resources to bring stakeholders to the table to develop a reintroduction plan for Delta Smelt. The is the first step in coming to terms with the fact that we may need to use hatchery fish to supplement/reinforce the wild population while restoration projects are underway.
One of my favorite projects over the years is the very first project I worked on – the reintroduction of the Paiute cutthroat trout (PCT) to its native habitat in Lower Silver King Creek (SKC), California.
The PCT has the narrowest range of any native trout subspecies in the world. It is endemic to a ~10 mile stretch of stream above a fish barrier in SKC. Lower SKC’s upstream barrier is a waterfall called Llewellyn Falls. SKC is a headwater tributary to the East Fork Carson River. PCT are notable for their near complete lack of spots:
I decided it would be a good time to provide an update about the project, as I just visited SKC to help out with electrofishing sampling.
First some history: if we go back to 1912, some PCT were moved above a fish barrier (Llewellyn Falls) by a Basque sheepherder. This is fortunate, because subsequently multiple stockings of various trout species occurred in Lower SKC during what can be considered the fish stocking heydey of the 20th century. Being an isolated subspecies with no natural competitors, the PCT was quickly outcompeted in Lower SKC, leaving a few refuge populations of genetically pure PCT above Llewellyn Falls. Without this inadvertent “rescue” the PCT might be extinct.
I’m going to leave out a lot of history of chemical treatments and restocking efforts here. Please see this page for some sources of more information.
Fast forward to the early 2000s. Having long recognized that the PCT was threatened yet has high potential for recovery and restoration, the Department of Fish and Wildlife, US Forest Service, and US Fish and Wildlife Service planned on chemically treating Lower SKC to remove nonnative fish. After a number of legal battles that fought to stop the chemical treatment, in 2005 everybody was all set to go and begin the treatment the following morning. However at the very last minute a judge blocked the treatment, sending hikers out with headlamps in the middle of the night to ensure that agency biologists knew that they could not proceed. This was a bit rude given that the biologists had already received word of the judge’s orders via radio. It was not a happy night.
2006 is when I began working on the project. First designing assays to detect hybridization so that we could assess the Lower SKC population. Second I wrote a paper in collaboration with Eric Anderson at NOAA that examined this population further, and showed variability in hybridization amongst the various markers. In 2013 I wrote a Genetic Management Plan for the reintroduction efforts. In the meantime CDFW and the rest of the project team had finally gotten the green light to begin the chemical treatment in 2013. Treatment was conducted in 2013, 2014, and 2015. Lower SKC is now fishless, save PCT getting washed downstream.
At present we are waiting on eDNA results, snorkel surveys, and the lower fish barrier assessment to make 100% sure that the lower fish barrier is intact and there are no rainbow trout in Lower SKC. This is critically important – if any rainbow trout are left behind in Lower SKC, the monumental efforts to chemically treat are likely to have been wasted. We would be back at square one.
Enter the historic California drought from 2012-present, and the latest surveys of the extant refuge populations. The refuge populations in Upper SKC have been regularly surveyed every few years for decades using electrofishing. The first year I worked on the project (2006) I visited SKC and watch the Wild Trout Crew shock Upper and Lower SKC. It was incredible how many fish we found. The populations were healthy and thriving.
Over the past few years coinciding with the drought, the census numbers have dropped precipitously in Upper Silver King, Four Mile Canyon Creek, and Corral Valley Creek. As there is plenty of water in the basin (it’s largely decomposed granite, which acts as a sponge), the prevailing theory is that the drought has resulted in an absence of insulating snowpack, causing the formation of anchor ice, further resulting in winter fish kills. Whatever the cause, the outlook is not good, and we are now left with two known healthy populations in-basin (Coyote Creek and Fly Valley Creek), four populations known to be struggling (Upper SKC, Four Mile Canyon Creek, North Fork Cottonwood Creek (an out of basin population in the White Mountains), and Corral Valley Creek), and at least three whose the status is unknown due to access difficulties.
The whole situation is sadly ironic; it was environmental groups that fought the chemical treatment back in 2005 (pushing back against the use of rotenone, the use of gas-powered equipment in a wilderness area, and what they thought was an insufficient EIS), and now we are worried about the extinction of an iconic trout subspecies. If the PCT had been reintroduced in 2006, their habitat are would have been significantly expanded, and we might not be so worried. At this point we are concerned about whether or not there are enough fish to take from the refuge populations to introduce in lower SKC. It would be a mistake to take so many fish from depleted refuge populations.
What we can do now is wait for the final confirmation that lower SKC no longer has rainbow trout. PCT will be washing downstream into Lower SKC either way. Ideally we would reintroduce a number of fish from the various refuge populations to ensure maximum genetic diversity. Conservation is rarely so straightforward. We must work with what we’ve got, and remember that doing nothing is also a choice.
This is a unique project. Very few areas are able to utilize chemical treatments safely and successfully to remove fish. The PCT is native to a small area, we still have genetically pure individuals, and the reason for their decline is removed when the nonnative fish are removed. We still have hope that the restoration will be successful.
Below are some movies from the latest trip.