Reference population and gametophyte culture genotypes

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 c..., 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 (Fst = 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 (gi..., , # 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: ...,