Next-generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays for nonmodel organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high-throughput SNP assays from a total of 4439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus) and used them to address four disparate objectives: parentage analysis, species identification and characterization of neutral and adaptive variation. Nine of these SNPs are FST outliers, and five of these outliers are localized within genes and significantly associated with geography, run-timing and dwarf life history. Two of the 96 SNPs were diagnostic for two other lamprey species that were morphologically indistinguishable at early larval stages and were sympatric in the Pacific Northwest. The majority (85) of SNPs in the panel were highly informative for parentage analysis, that is, putatively neutral with high minor allele frequency across the species' range. Results from three case studies are presented to demonstrate the broad utility of this panel of SNP markers in this species. 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.
RESUMEN: Las poblaciones de la lamprea del Pacífico (Entosphenus tridentatus) están declinando en la cuenca del Río Columbia, y desde el año 2000 se ha implementado la translocación de individuos adultos para restablecer los corredores migratorios de esta especie. Se describen y reportan los resultados de dos programas recientes de translocación, se contextualiza el uso de la translocación y se discuten sus beneficios potenciales, riesgos e incertidumbre. Ambos programas de translocación parecen haber incrementado el número de adultos desovantes y la presencia tanto de larvas como de juveniles; sin embargo, para que sea posible cualquier incremento ulterior en el stock natural de reproductores se requerirá de al menos una, aunque muy probablemente de más, generaciones. Se observó que el número de adultos que ingresó al Río Umatilla aumentó en los primeros cuatro años después de la primera translocación. Los beneficios potenciales de los programas de translocación son un aumento en la producción de feromonas por parte de larvas ammocoetes para atraer adultos, incremento en la distribución y abundancia de lampreas en áreas objetivas, incremento en la cantidad de nutrientes derivados del medio marino y la promoción de culturas tribales. Los riesgos potenciales incluyen modificación de la estructura poblacional y las adaptaciones genéticas asociadas, transmisión de enfermedades y agotamiento de los stocks donadores. ABSTRACT: The Pacific lamprey (Entosphenus tridentatus) is in decline in the Columbia River Basin, and translocating adult lamprey to bypass difficult migration corridors has beenimplemented since 2000. We describe and report results from two current translocation programs, provide context for use of translocation, and discuss potential benefits, risks, and uncertainties. Both translocation programs appear to have increased the number of spawning adults and the presence of larvae and juveniles; however, any subsequent increase in naturally spawning adults will require at least one, and likely more, generations to be realized. It was seen that the number of adults entering the Umatilla River increased beginning four years after the first translocations. Potential benefits of translocation programs are increased pheromone production by ammocoetes to attract adults, increased lamprey distribution and abundance in target areas, increased marine-derived nutrients, and promotion of tribal culture. Potential risks include disruption of population structure and associated genetic adaptations, disease transmission, and depletion of donor stocks.
Dworshak Reservoir pool recommendations contained herein are independent of conditions for upstream or downstream anadromous fish migration and of any other purposes not specifically stated. Nothing in this report shall limit or restrict future water rights claims or flow recommendations made by the Nez perce Tribe for any purposes. The authors also recognize that the needs of the resident fish studied may conflict with the needs of downstream anadromous fish. This report makes no attempt to resolve the conflicts or recommend priorities among alternative uses of Dworshak Reservoir water. The kokanee fishery declined during our study from a harvest of 206,000 kokanee and a catch rate of 1.5 fish/hour in 1988 to 95,000 kokanee at a catch rate of 0.8 fish/hour in 1990. Limited surveys in 1991 indicated a further decline in catch rates to 0.5 fish/hour. The Nez Perce Tribe (NPT) and the Idaho Department of Fish andChanges in the kokanee fishery reflected population changes in the reservoir.Mid-water trawling in 1989 indicated the reservoir contained 13 kokanee of harvestable size per acre but that dropped to 2 kokanee per acre in 1991. Angler satisfaction also declined throughout the study from 37% rating the fishing as poor in 1988, to 55% giving it this rating in 1990.Nearly all anglers cited low numbers of fish caught as the reason for the rating.Management goals should therefore be towards more numerous but slightly smaller kokanee to maximize angler satisfaction.Dworshak kokanee have exceedingly low annual survival rates; much lower than other kokanee populations.Over 80% of yearling kokanee die before recruiting to the fishery the following year.Losses of kokanee through Dworshak Dam appear responsible for the high mortality rates. As many as 83,000 to 235,000 kokanee of a single age group were estimated to be lost annually.The resulting low densities reduced catch rates from 1.5 to 0.5 fish/hour and likely reduced fishing effort by 66%. Low kokanee density has, however, triggered good growth rates. Kokanee averaged 11 inches by July of their third summer in the reservoir. This compares to 7.5 inches in Coeur d'Alene Lake, and 8.3 inches in Lake Pend Oreille. Kokanee in these other lakes live to be 1 to 3 years older than Dworshak Reservoir kokanee and so ultimately make up some of the difference in length.During our study, Dworshak Reservoir was much more nutrient poor than when it was first filled in 1971. We would have expected nutrient input from inundated vegetation and soils to have stabilized, however, our results indicated the reservoir may still be declining in nutrient status.Near-shore habitat has also been altered since initial inundation. Vegetation along the shoreline has been eliminated due to fluctuating water levels and wave action. Cover and food production for littoral fish species have been adversely affected by this change. Abundance of redside shiners, an important forage species, peaked only a few years following initial impoundment. This species was in decline prior to the reservoirwide...
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.