Genetic Identification of Lamprey Genera and Anadromous Ecotypes in Watersheds of the Northeastern Pacific Ocean

Nonparasitic, nonmigratory Western Brook Lamprey (WBL; Lampetra ayresii), and parasitic, anadromous Western River Lamprey (WRL; L. ayresii) are sympatric lampreys that likely represent different life history variations of a single species. Novel genetic tools are critical for differentiating WBL and WRL, whose larvae preclude morphological identification (ID) and will enable comprehensive assessment of imperiled native lampreys of the Northeastern Pacific (including WBL, WRL, and Pacific Lamprey, Entosphenus tridentatus). We developed 47 candidate single nucleotide polymorphism (SNP) markers using whole genome resequencing of WBL (N = 24) and WRL (N = 15) from Ksi Ts'oohl Ts'ap Creek (Nass River, British Columbia, Canada) which are likely ecotypes distinguished by few divergent SNPs across multiple chromosomes. We used five novel candidate SNPs to perform genetic ID of WBL and WRL ecotypes in collections of mixed native lampreys from lower Columbia River tributaries (N = 1474), Ksi Ts'oohl Ts'ap Creek (N = 352), and ocean phase WRL from the Georgia Basin (Salish Sea, British Columbia, Canada; N = 91). Two previously published SNPs were used to ID genera, Entosphenus versus Lampetra. Morphological ID utilized photographs collected from a subset of genotyped lampreys, and high concordance was demonstrated between ID methods for genera (99%) and Lampetra ecotypes (> 98%). We characterized spatial and temporal composition of lamprey genera and ecotypes surveyed across NE Pacific tributaries under the expectation these compositions would be similar across nearby sites and across years at the same site. Proportions of lamprey genera were highly variable within regions and across years; however, Lampetra ecotypic proportions were spatially and temporally stable. WRL were rare in lower Columbia tributaries (~1% average rate among Lampetra) and common further north (> 40% of Lampetra). Genetic ID methods are powerful monitoring tools that create the novel ability to ascertain genera and ecotypes regardless of life stage, while increasing the efficiency of surveys by eliminating time-intensive morphological data collection.