DOI: 10.5061/dryad.b2rbnzss7
title: Data from: Genetic identification of lamprey genera and anadromous ecotypes in watersheds of the Northeastern Pacific Ocean

description: Non-parasitic, non-migratory 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=1,474), 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
 (&gt;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 (&gt;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 efficiency of surveys
 by eliminating time-intensive morphological data collection.
description: # Data from: Genetic identification of lamprey genera and anadromous
 ecotypes in watersheds of the Northeastern Pacific Ocean Dataset DOI:
 [10.5061/dryad.b2rbnzss7](10.5061/dryad.b2rbnzss7) ## Description of the
 data and file structure This dataset accompanies the article with the same
 title with the aim to develop genetic ID applications for lampreys. 
 Sample collections were comprised of the following overlapping subsets of
 samples (a – e) and used in various combinations to address our
 objectives: a) morphologically-confirmed ocean-phase Western River Lamprey
 (Lampetra ayresii; WRL) collected at sea by Fisheries and Oceans Canada
 between 2013 – 2019 from “site 1” in the Georgia Basin (Salish Sea,
 British Columbia, Canada; N=91), which served as a positive control
 collection of the anadromous ecotype WRL for testing purposes (Table 1,
 Fig. 1), b) WBL and WRL voucher specimen (N = 39) that were a portion of
 the confident morphologically identified voucher specimen from Ksi Ts’oohl
 Ts’ap Creek (Nass River Northern B.C., Canada) that could be used for
 candidate SNP discovery, c) broadly distributed specimen with both
 morphological photo documentation and genetic data for testing genus ID
 concordance (N = 1170), d) broadly distributed specimen with both
 morphological photo documentation and genetic data for testing *Lampetra*
 ecotype ID concordance (N = 514), and e) genotyped individuals lacking
 morphological ID (N = 747) that were combined with all other genotyped
 individuals for characterizing the spatial distributions of genera and
 ecotypes across the entire geographic area of our study (Table 1).  The
 grand total of unique individuals (N = 1917, Table 1) was constructed into
 24 collections that represented 15 unique geographical sites and multiple
 collection years (Table 1).  ### Files and variables #### File:
 Dryad\_Repository\_EVA-2025-010-OA\_R1Data.xlsx: Sampling data tab #####
 Variables * Order- individual order # * Individual name- unique databse ID
 * Collection Group- standard group naming convention (collection agency,
 collection method, collection subbasin, collection site and year,
 collection Rkm for stream sites or latitude interval * Location- Site
 description and Latitude Longitude coordinates in decimal degrees *
 Collection Year- Date or year only * Life Stage- (Adult, juvenile, or
 larva) * Total length- body length in mm * LampSD- the allele 1 and allele
 2 for the SNPs for genus ID * Genetic ID Genus- The determination of genus
 (Lampetra or Entosphenus) based on genotypes * Region- name of the
 collection region * Region#- collection regions numbered 1 - 7 * Site-
 sites numbered 1 - 15 * Collection#- collections (site + collection year)
 numbered 1 -24 * Morph ID Genus- the morphological ID of lamprey genera
 (Lampetra or Entosphenus) * Morph ID SPP- the morphological ID of lamprey
 species/ecotypes (WRL, WBL, Lampetra spp, Entosphenus tridentatus) * a, b,
 c, d, e - the type of collection described in Table 1 based on the
 objective for its collection.  The letters indicate which individuals were
 in each of the following overlapping subsamples (a – e) used to address
 multiple objectives: a) WRL positive control, b) voucher specimen from Ksi
 Ts’oohl Ts’ap Creek used for candidate SNP discovery, c) Specimen with
 both morphological photo documentation and genetic data for testing genus
 ID concordance, d) Specimen with both morphological photo documentation
 and genetic data for testing *Lampetra* ecotype ID concordance, and e)
 individuals with only genetic data. * %_WRL - the percent of WRL alleles
 among the 5-SNP candidate assay  * Genetic ID Ecotype - classification of
 ecotypes (WRL or WBL) based on the Genetic ID "%_WRL" * Missing
 - number of loci (total 5) missing from the 5-SNP candidate assay *
 N_alleles - number of alleles successfully genotyped of the 5-SNP
 candidate assay (total 10) * Missing Chr2 - the number of loci (total 2)
 missing from chromosome 2 loci in the 5-SNP candidate assay  Missing data
 are indicated as "NA" #### File:
 Dryad\_Repository\_EVA-2025-010-OA\_R1Data.xlsx**:** SNP\_genotypes tab
 ##### Variables * Order- individual order # (same as sampling_data tab) *
 Region#- Region numbers  (same as sampling_data tab) * Site- Site numbers 
 (same as sampling_data tab) * Collection#- Collection numbers (same as
 sampling_data tab) * Genetic ID Genus - (data  same as sampling_data tab)
 * Morph ID Genus - (data same as sampling_data tab) * Morph ID SPP -
 (data  same as sampling_data tab) * Individual Name - (Specimen IDs same
 as sampling_data tab) * Lri2P16333005 - Genotype for this Chromosome 2 SNP
 locus that is part of the 5-SNP candidate assay; blue genotypes indicate
 homozygous for WRL alleles; gray genotypes are heterozygous; red genotypes
 are homozygous for WBL alleles) * Lri2P16367064 - Genotype for this
 Chromosome 2 SNP locus that is part of the 5-SNP candidate assay; blue
 genotypes indicate homozygous for WRL alleles; gray genotypes are
 heterozygous; red genotypes are homozygous for WBL alleles) * Lri5P4640927
 - Genotype for this Chromosome 5 SNP locus that is part of the 5-SNP
 candidate assay; blue genotypes indicate homozygous for WRL alleles; gray
 genotypes are heterozygous; red genotypes are homozygous for WBL alleles)
 * Lri12P6060911 - Genotype for this Chromosome 12 SNP locus that is part
 of the 5-SNP candidate assay; blue genotypes indicate homozygous for WRL
 alleles; gray genotypes are heterozygous; red genotypes are homozygous for
 WBL alleles) * Lri14P4079387 - Genotype for this Chromosome 14 SNP locus
 that is part of the 5-SNP candidate assay; blue genotypes indicate
 homozygous for WRL alleles; gray genotypes are heterozygous; red genotypes
 are homozygous for WBL alleles) Missing data are indicated as
 "NA" #### File: Dryad\_Repository\_EVA-2025-010-OA\_R1Data.xlsx:
 SNPList*low*coverage\_genotypes tab ##### Variables * Order- locus order #
 (as ordered in SNP*low*coverage_genotypes tab) * Locus- locus name *
 Scaffold- Scaffold number or Chromosome # which are used synonymously *
 position- bp position on the reference genome * GenomeOrder- Order of loci
 based on scaffold and position * RetainFILTER- Y if retained, N if
 excluded from the 349 SNP filtered dataset (see methods in article) *
 Distance-value- the distance in bp that a particular SNP is located away
 from the neighboring SNP on the same scaffold.  One SNP from each pair of
 SNPs within 1000bp from each other was excluded in the filtered dataset
 which resulted in trimming to 349 total SNP loci. #### File:
 Dryad\_Repository\_EVA-2025-010-OA\_R1Data.xlsx:
 SNP*low*coverage\_genotypes tab ##### Variables * MorphID- whether the
 specimen was morphologically classified as WRL or WBL ecotype *
 Individual.Name- specimen database ID * Order- same order as the specimen
 in Table 2 in article * LPT_scaf_8_3352124.A1 - allele 1 for this locus. 
 All loci are listed in columns from the SNPlist for this low coverage
 whole genome resequencing dataset #### File:
 Dryad\_Repository\_EVA-2025-010-OA\_R1Data.xlsx: SNP\_primers tab #####
 Variables * MarkerType- Species ID, Genus ID, or one of the 47 candidate
 Ecotype ID SNPs (Table S3) * Assay- Name of the locus * A1- letter code
 for allele 1 * A2- letter code for allele 2 * A1-Probe-  the probe allele
 1 sequence for genotyping-by-sequencing pipeline * A2-Probe-  the probe
 allele 2 sequence for genotyping-by-sequencing pipeline * Forward primer
 sequence * reverse primer sequence ## Access information Other publicly
 accessible locations of the data: * *Lampetra richardsoni* (recently
 synonymized as *Lampetra ayresii*; this particular specimen is designated
 as Western Brook Lamprey ecotype) whole genome sequence: GenBank Accession
 Number: JARYGF000000000, JASBGX000000000 * WBL and WRL whole genome
 resequencing data: GenBank Accession Number PRJNA953978