Conservation Genetics (hosted by AFS)

Contributed Paper Session

8:00AM Meddling with Matches? Exploring the Diverse Influences of Fisheries and Their Management on Salmon Migratory and Reproductive Phenology
Michael Tillotson, Heidy Barnett, Mary Bhuthimethee, Michele Koehler, Thomas Quinn
The timing of migration and reproduction link generations and substantially influences individual fitness. In salmonid fishes, such events (seasonal return to freshwater and spawning) vary among populations but are consistent among years, indicating local adaptation in these traits to prevailing environmental conditions. Changing reproductive phenology has been observed in many populations of Atlantic and Pacific salmon and is frequently interpreted as an adaptive response to climate change. However, there are many other potential drivers of phenological change including impacts from fisheries, and their management which can induce evolutionary responses, shorten breeding seasons and reduce phenotypic diversity. These changes can in turn influence productivity, reduce the efficacy of management, exacerbate ongoing climate‐driven changes in phenology and reduce resilience to environmental change. We provide an overview of mechanisms by which management can impact salmon phenology, and then describe a case study in which we combined retrospective analysis and evolutionary models to disentangle the contributions of environmental change and unintended artificial selection to dramatically altered reproductive timing in a population of sockeye salmon. We find strong evidence that hatchery practices have contributed to a phenological mismatch, and conclude that this change has likely contributed to recent declines in reproductive success.
8:20AM Phylogeny of Native California Rainbow Trout Subspecies and a New SNP Panel for Monitoring Upper Mccloud River Redband Trout
Ensieh Habibi, Jeff Rodzen, David Lentz, Daphne Gille, Amanda Finger
The McCloud River Redband Trout (Oncorhynchus mykiss stonei; MRRT) is a unique subspecies of coastal Rainbow Trout found only in California’s McCloud River basin, and the only O. mykiss native to the Upper McCloud River. Before the 2014-2016 drought there were ~14 isolated populations. During the drought of 2014-15, approximately 1,000 MRRT were rescued by CDFW personnel and placed into the Mt. Shasta Hatchery (MSH) for safe harbor until conditions improved. These fish spawned successfully at MSH, founding a new captive MRRT broodstock whose progeny are being stocked into waters with existing O. mykiss populations for recreational angling and to reintroduce MRRT across their native range. A genetic monitoring method is needed to track changes in introgression levels in the receiving waters. We developed a SNP panel for this purpose using RAD-sequencing and will discuss the results. In addition, we developed a phylogeny of inland native California Rainbow Trout subspecies, including Eagle Lake Rainbow, California and Little Kern Golden Trout, and Kern River Rainbow Trout, among others. We hope this work will elucidate relationships between these unique taxa, and provide a useful high throughput means for monitoring MRRT.
8:40AM Management Implications of Hybridization between Coastal Cutthroat Trout Oncorhynchus Clarki Clarki and Steelhead O. mykiss
Sam Rizza, Kitty Griswold, Thomas Williams
Coastal Cutthroat Trout Oncorhynchus clarki clarki (CCT) and Rainbow Trout and steelhead O. mykiss (SH) naturally hybridize throughout their sympatric range from Alaska to Northern California. Populations in the CCT/SH hybrid zone have been found to depict highly variable genotypic distributions, ranging from hybrid swarms, asymmetric hybridization, and near complete reproductive isolation. A detailed genetic analysis of CCT and SH populations in the Smith River, California found 20% of the 876 sampled individuals displayed some degree of hybridization. Genomic regions of reproductive isolation maintain divergence between species despite consistent gene flow across other regions of the genome resulting in an ambiguous species status of individuals produced in natural hybrid zones. It is unknown if natural hybridization acts as a mechanism to introduce novel gene combinations, results in outbreeding depression, or is simply the byproduct of the process of speciation. Limited understanding of factors that induce hybridization and the designation of Northern California steelhead as threatened increase management implications. Further development of genetic identification protocols and monitoring programs are needed to address conservation and management at the southern range of the CCT/SH hybrid zone.
9:00AM The Legacy of Translocation and Isolation on the Genetic Diversity of Sacramento Perch (Archoplites interruptus)
Amanda Coen, Rachel Schwartz, Max Fish, Randy Lovell, Jeff Rodzen, Andrea Schreier
The once widely distributed California endemic Sacramento Perch (Archoplites interruptus) has been extirpated from its native range throughout the Sacramento-San Joaquin drainage by anthropogenic activities. A handful of translocated populations survive, confined to isolated reservoirs and lakes in California and Nevada. Left unmanaged, these populations risk further genetic diversity declines and threats to the species continued persistence. To promote native species conservation, the California Department of Fish and Wildlife is interested in partnering with private aquaculture to develop captive breeding programs which could provide individuals for conservation supplementation. We conducted a range-wide genetic assessment of previously surveyed (2008) and newly discovered populations to determine the genetic health of candidate populations for use in captive breeding programs. Using 12 microsatellite markers, we found two primary genetic clusters, each containing sub-structure and exhibiting high degrees of differentiation from each other. Most populations showed evidence of past bottlenecks and limited effective population sizes, reducing their suitability as candidates for use as captive broodstock. Identification of genetically diverse, healthy populations for use in supplementation efforts will aid management efforts to prevent further declines in this species.
9:20AM Microsatellite Analysis Supports Introduced Status for Klamath Smallscale Sucker (Catostomus rimiculus) in the Smith River, California.
Andrew Kinziger, Jason White, Rodney Nakamoto, Bret Harvey
Historical and recent accounts of the Klamath smallscale sucker (Catostomus rimiculus) describe the species occurring in the Klamath and Rogue rivers of northern California and southern Oregon. Curiously these accounts do not recognize the existence of the species in the Smith River, a basin that is sandwiched between the Rogue and Klamath rivers, and that presently contains a broadly distributed population of Klamath smallscale suckers. To determine if genetic structure of the Klamath smallscale sucker population in the Smith River is consistent with expectations of an introduced species (e.g., founder effects) we genotyped >800 individuals from the Klamath, Rogue, and Smith rivers at 15 microsatellite loci. Our results revealed pattern consistent with a strong founder effect, including: (1) substantial reductions in allelic richness in the Smith River (4.26) versus the Klamath (19.18) and Rogue (16.7) rivers, and (2) a major shift in allele frequency between the Smith River and the Klamath (Fst = 0.19) and Rogue (Fst=0.20) rivers. By contrast, the Rogue and Smith rivers were genetically similar (Fst=0.03). These results suggest that the Klamath smallscale sucker population in the Smith River was most likely established as a product of a single introduction event involving a small number of founders.
09:40AM Break
10:10AM Non-Invasive Genetic Approach for Monitoring of the Threatened Valley Elderberry Longhorn Beetle
Raman Nagarajan, Alisha Goodbla, Melinda Baerwald, Emilie Graves, Marcel Holyoak, Andrea Schreier
The Valley Elderberry Longhorn Beetle (Desmocerus californicus dimorphus; VELB) is a federally threatened subspecies endemic to the Central Valley of California. Current monitoring methods are limited to direct visual surveys and counting new larval exit holes in elderberry shrubs (Sambucus mexicana), the obligate VELB host plant, into which larvae bore and excavate feeding galleries. An indirect, genetic method could provide a much needed complementary approach. In this study we developed a DNA sequencing-based method for indirect detection of VELB from frass (fecal matter). Frass samples were collected from exit holes at multiple sites across the VELB range and different DNA extraction techniques were evaluated for maximal quality and yield. Two mitochondrial genes (12S and 16S) were partially sequenced after nested PCR amplification. Three frass-derived sequences showed 100% sequence identity to VELB museum specimens, confirming indirect genetic detection. DNA database queries of other frass-derived sequences revealed high similarity to earwigs, flies, and other beetles. Overall, this non-invasive approach has great potential for augmenting existing VELB monitoring, and paves the way for genetic assays that accurately discriminate between VELB and its unlisted sister taxon, the California Elderberry Longhorn Beetle (Desmocerus californicus californicus) in regions of range overlap.
10:30AM Field Evaluations of Myy Brook Trout in Idaho Streams and Alpine Lakes: Stocking, Survival, and Reproductive Success
Curtis J. Roth, Patrick Kennedy, Kevin A. Meyer, Daniel J. Schill, Matthew Campbell
Brook Trout Salvelinus fontinalis have been introduced throughout western North America, resulting in nonnative populations that are difficult to eradicate and often threaten native salmonid populations. A novel approach to eradicating undesirable Brook Trout populations is using YY male (MYY) Brook Trout. Since 2015, the Idaho Department of Fish and Game has been stocking fingerling (i.e., ~125 mm) and catchable-sized (~250 mm) MYY Brook Trout to eradicate existing wild Brook Trout populations. Prior to stocking, we are suppressing wild abundance via electrofishing to potentially decrease time to eradication. Suppression rates generally vary ~25-50% between years and waters. Annual survival in streams for wild Brook Trout averaged 46%, whereas 11 month post-release survival for fingerlings averaged 43%. Genetic assignment tests are being used to detect successful reproduction because it is too early in the program to evaluate sex ratio changes. Within the next few years we hope to have learned: 1) whether stocking MYY fingerlings or catchables is more effective at achieving sex ratio changes in wild Brook Trout populations; 2) to what extent suppressing the abundance of wild Brook Trout speeds this process; and 3) to what extent the type of system (i.e., stream or alpine lake) affects this process.
10:50AM Population Genetics and Conservation Units of the Endangered Candy Darter
Brin Kessinger, Amy Welsh, Stuart A. Welsh, Daniel A. Cincotta
The Candy Darter Etheostoma osburni is a narrow endemic to the New River drainage of the upper Kanawha River basin in West Virginia and Virginia. It has been extirpated from much of its historic range in West Virginia, restricting it to sections of two New River tributaries (the Gauley and Greenbrier river drainages). Shrinking populations and introgressive hybridization with the introduced Variegate Darter E. variatum contributed to it being listed as endangered throughout its entire range under the U.S. Endangered Species Act in November 2018. Establishing the population genetic structure of pure Candy Darters and delineating their conservation units are the fundamental steps for the species’ conservation. We genotyped 127 individuals from seven sites in the New River Drainage with 12 microsatellite loci. Multiple genetic analyses revealed significantly high levels of genetic differentiation between the Gauley and Greenbrier River drainages (K=2; FST = 0.117). Based on our results, Candy Darters in the Gauley and Greenbrier River drainages have been separated long enough to result in high levels of genetic distinctness. The two populations should be treated as evolutionarily significant units (ESUs) where the loss of one would be a significant loss to the species’ genetic diversity.
11:10AM Assessing Genetic Connectivity in Scamp (Mycteroperca phenax), a Long-Lived Protogynous Reef Fish
Elizabeth Wallace, Marta Rodriguez-Lopez, Michael Tringali
In the southeast US, groupers are prized targets for recreational and commercial fisheries. Scamp are an important component of the grouper fishery and there is some evidence for catch and sex ratio declines in recent years. Yet little research has been conducted and no genetic data is available, thus population structure and connectivity across the region remain unknown. A stock assessment on scamp is currently underway, for which we are conducting a regional genetic population analysis to evaluate gene flow and stock structure. Specimens (N=682) collected from the Atlantic Ocean and Gulf of Mexico commercial and recreational fisheries are being genotyped with an array of 32 microsatellite loci. These data will be used for effective population size estimation, as well as to assess geographic patterns of gene flow and genetic stock structure. Study results will be incorporated into the ongoing southeast data assessment and review (SEDAR 68) to support data-driven management of this species.



Contributed Paper Session
Location: Reno-Sparks CC Date: October 2, 2019 Time: 8:00 am - 11:50 am