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Research develops genetic tools to aid In recovery of pacific lamprey in Columbia river basin

A set of 96 genetic markers, or single nucleotide polymorphisms (SNPs), winnowed by Columbia River basin researchers from a list of 4,439 previously identified in Pacific lamprey could help give researchers insights into the lives and life influences faced by the diminished, but highly valued, fish species, according to a research paper made available last week online.

“The manuscript describes the development of genetic tools that are highly versatile for conservation applications in Pacific lamprey,” according to the article’s lead author, Jon E. Hess. “Those genetic tools have been optimized for performing multiple functions, including parentage analysis, species identification, and characterizing neutral and adaptive population structure.”

The article, “Use of genotyping-by-sequencing data to develop a high-throughput and multi-functional SNP panel for conservation applications in Pacific lamprey,” was accepted for publication in the scientific journal “Molecular Ecology Resources. It is available online at

Hess and contributing authors Nathan R. Campbell and Shawn R. Narum are Columbia River Inter-Tribal Fish Commission researchers based in Hagerman, Idaho. Other contributing authors include Margaret F. Docker from the University of Manitoba in Winnipeg, Cyndi Baker and Andrew J. Wildbill of the Confederated Tribes of the Warm Springs Reservation of Oregon, Aaron Jackson of the Confederated Tribes of the Umatilla Indian Reservation, Ralph Lampman of the Yakama Nation, CRITFC’s Brian McIlraith, Mary L. Moser of NOAA Fisheries’ Northwest Fisheries Science Center and David P. Statler and William P. Young of the Nez Perce Tribe.

A better understanding to lamprey life history and activities is needed to guide management actions aimed at restoring populations, according to the researchers.

“Pacific lamprey (Entosphenus tridentatus) populations are in decline (Close et al. 2002) and are relatively understudied,” the research paper says. “Hence, research to address critical biological and management related uncertainties is urgently needed.”

Counts of 400,000 adult lamprey were recorded at Bonneville Dam 60 years ago, according to CRITFC. Current annual counts are less than 20,000, according to CRITFC. And, generally speaking, lamprey returns are diminished more greatly in relation to the distance upstream in the Columbia/Snake river system.

Bonneville is the first dam the lamprey must pass if they want to spawn in the mid or upper Columbia or the Snake River drainages. Tribal interests in particular have been experimenting with translocation – capturing lamprey at, primarily, Bonneville Dam, and transporting them to tributaries upstream in hope they will spawn and reinvigorate local populations.

“Translocation (i.e. transporting individuals from a source population to a recipient site), artificial propagation, and habitat improvement are all being used to rebuild the Pacific lamprey abundance in the interior Columbia River Basin, where declines have been most severe,” the research paper notes.

A better understanding of the traits in specific fish populations that might give them a better chance to succeed reproductively in translocation, or as broodstock for lamprey hatchery introductions, is needed. And refined interpretation of a growing genetic data bank could help.

“Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species,” according to the research paper. “As Pacific lamprey populations are undergoing rapid decline, these SNPs provide an important resource to address critical uncertainties associated with the conservation and recovery of this imperiled species.

“The idea is that these genetic markers must somehow be associated with functional characteristics,” Hess said.

The parental analysis allows researchers to mine data banks developed through fish samples to determine where a fish was born, and who its parents were. And over time the new genetic tools may help judge what lineage, and/or set of genetic traits is most likely to produce lamprey that survive and reproduce in the wild.

Fish size, for example seems to enable lamprey to sustain upstream migrations, studies indicate.

“Larger bodied lamprey tend to go further” upstream, Hess said.

“Genetic markers indicate minimal population structure throughout a large portion of the Pacific lamprey range (Goodman et al. 2008, Spice et al. 2012, Hess et al. 2013), and only the northernmost populations appear to show significant genetic differentiation from the rest of the eastern Pacific range (Lin et al. 2008, Hess et al. 2013),” the research paper says. That relative homogenization stems from the fact that Pacific lamprey, unlike salmon that also are spawned in freshwater, go to the ocean to mature and return to rivers to spawn, do not necessarily home back in on their natal stream.

“Thus translocation is an appealing option because the potential benefits (Ward et al. 2012) may vastly outweigh the potential risks for disrupting neutral population structure (Weeks et al. 2011).

“However, despite minimal levels of neutral population genetic structure, there is evidence for significant adaptive genetic divergence among lamprey collections (Hess et al. 2013) and migration fate of adults appears to be associated with passage-timing and morphology (e.g. Keefer et al. 2009, 2013), which suggests that selection is acting strongly on returning lamprey.

“Therefore, adaptive genetic markers associated with phenotypes may help to understand the influence of genetic background on reproductive success of individuals in particular habitats,” the researchers say.

“The study describes some significant conservation success stories. For example, we use parentage analysis to directly validate the reproductive success of translocated Pacific lamprey in the Snake River basin. In fact a set of translocated adults from the first Nez Perce translocation event in 2007 successfully produced 5-year-old offspring that we could age using the results from parentage assignments,” Hess said.

“A translocation strategy may also require a means to validate reproductive success of initial translocation efforts and track the long term viability of offspring. Therefore genetic markers optimized to perform these functions are critical; however, for relatively understudied species, this can be challenging,” the research paper says.

“Also we show that natural reintroduction of Pacific lamprey is possible following dam removal (Hood River, removal of Powerdale dam),” according to Hess.

“Finally, some of the genetic markers are associated with adult traits, such as length and passage-timing at Willamette Falls... so we know that these ‘adaptive’ genetic markers are associated with functional regions of the Pacific lamprey genome,” Hess said

He noted that the research involved efforts from all four CRITFC member tribes (Warm Springs, Umatilla, Yakama Nation, and Nez Perce), as well as international and federal entities.

Columbia Basin Bulletin The Columbia Basin Bulletin e-mail newsletter is produced by Intermountain Communications of Bend, Oregon and supported with Bonneville Power Administration fish and wildlife funds through the Northwest Power and Conservation Council's Columbia Basin Fish and Wildlife Program. Articles republished by The Dalles Chronicle with permission.


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