DOI: 10.5061/dryad.r4xgxd2q6
title: Reference population and gametophyte culture genotypes

description: Many challenges arise when monitoring organisms with cryptic life
 histories. For example, cryptic stages are hard to identify or sample due
 to their microscopic nature, which creates unknowns surrounding an
 organism’s population dynamics. Environmental DNA (eDNA) is a non-invasive
 sampling technique used to monitor cryptic species when traditional survey
 methods are challenging. Generally, eDNA has been used to quantify the
 presence/absence of species in various habitats. However, recent advances
 in next-generation sequencing have enabled researchers to detect
 intraspecific species abundances with eDNA. In this study, we present two
 complementary R packages that can be used to estimate the number of
 individuals in an eDNA sample. The first package (Amplicomsat) cleans
 high-throughput amplicon microsatellite sequences and counts the observed
 alleles identified in eDNA. Our second package (GenotypeQuant) then uses a
 numerical maximum likelihood estimator (NMLE) to estimate the number of
 contributors most likely to have produced the sequenced panel of
 microsatellite alleles amplified from eDNA. We first present simulations
 to characterize the accuracy and precision of the method. We then
 estimated densities of Nereocystis luetkeana (bull kelp)
 microscopic gametophytes from eDNA collected from an experiment with a
 manipulated number of gametophytes. Finally, we analyzed benthic eDNA from
 kelp forest habitats. We found that gametophyte estimates produced by the
 NMLE varied within +3/-2 individuals when processing eDNA from rocks with
 8 seeded gametophytes. eDNA harvested from the field showed that
 gametophyte estimates scaled with the sampling area, and total densities
 in July ranged between 500 to 800 m2.
description: Both kelp gametophyte biobank samples and tissue samples were
 genotyped for 11 microsatellite loci using high-throughput amplicon
 sequecing. Gentoyped gametophyte cultures were used in two seperate
 studies (creating artificial eDNA and a gametophyte seeding study) to test
 the affectiveness of estimating numbers of gametophytes from an eDNA
 sample, using a reference of population allele frequencies and a numerical
 maximum likelihood estimator. Reference population allele frequencies were
 estimated by genotyping the same 11 microsatellite loci with sporophyte
 (2n) samples from 12 neighboring sites in Hakai Passage British Columbia,
 Canada. We collected 32 individuals from each site and pooled all the
 samples (n=384), as their genetic structure was negligible
 (F<sub>st</sub> = 0.02).  An additional reference population
 was produced from Owen Bay British Columbia, Canada, where 40 sporophytes
 (2n) were sampled and genotyped at the same loci. Alleles were scored
 using the R package Amplicomsat (github.com/UWMAlberto-Lab/Amplicomsat),
 where both fragment-length and sequence variant alleles were
 identified. 
description: # Reference population and gametophyte culture genotypes for Liggan et al.
 2025
 [https://doi.org/10.5061/dryad.r4xgxd2q6](https://doi.org/10.5061/dryad.r4xgxd2q6) ## Description of the data and file structure This data represents genotypes for gametophyte cultures and sporophyte tissue of Nereocystis luetkeana published in Liggan et al. 2025. Genotypes were obtained using high-throughput sequencing of amplicons and 11 microsatellite loci. Genotypes are reported with scored fragment-length (bp) and sequence variant alleles.         ### Files and variables #### File: Biobank\_genotypes\_HakaiMarnaLab.txt **Description:** Genotypes of gametophyte cultures used in a seeding study published in Liggan et al. 2025.  ##### Variables * Sample Name: gametophyte culture name * Ner2: microsatellite marker name * NL24: microsatellite marker name * NL25: microsatellite marker name * NL26: microsatellite marker name * NL27: microsatellite marker name * NL30: microsatellite marker name * NL40: microsatellite marker name * NL47: microsatellite marker name * NL50: microsatellite marker name * NL59: microsatellite marker name #### File: Reference\_population\_allele\_genotypes.txt **Description:** Genotypes of sporophyte tissue used as two reference population datasets (Hakai Passage and Owen Bay BC, Canada) published in Liggan et al. 2025. The dataset consists of TableS4a) fragment length allele genotypes in bp and TableS4b) sequence variant allele genotypes.  #### Variables * Reference Population: Population name * Ner2: microsatellite marker name * NL24: microsatellite marker name * NL25: microsatellite marker name * NL26: microsatellite marker name * NL27: microsatellite marker name * NL30: microsatellite marker name * NL40: microsatellite marker name * NL47: microsatellite marker name * NL50: microsatellite marker name * NL59: microsatellite marker name #### File: biobank\_genotypes\_AlbertoLab.txt **Description:** Genotypes of gametophyte cultures used to created artificial eDNA published in Liggan et al. 2025.  ##### Variables * Sample Name: gametophyte culture name * NL26: microsatellite marker name * NL27: microsatellite marker name * Ner2: microsatellite marker name ## Code/software NA