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: ...,

监测具有隐秘生活史的生物时，会面临诸多挑战。例如，隐秘生活史阶段因体型微小难以识别或采样，进而导致生物种群动态相关的未知性。环境DNA（environmental DNA, eDNA）是一种非侵入性采样技术，当传统调查方法难以开展时，可用于监测隐秘物种。通常而言，eDNA技术已被用于量化不同生境中物种的存在与否。然而，下一代测序技术的最新进展，使得研究者能够借助eDNA检测物种的种内丰度。本研究推出两款互补的R语言工具包，可用于估算eDNA样本中的个体数量。第一款工具包（Amplicomsat）可对高通量扩增子微卫星序列进行质控清洗，并统计eDNA样本中检测到的等位基因。第二款工具包（GenotypeQuant）则通过数值最大似然估计器（numerical maximum likelihood estimator, NMLE）来估算……的个体数量。本研究通过高通量扩增子测序，对巨藻（Nereocystis luetkeana）配子体生物样本库样本与组织样本的11个微卫星位点进行基因分型。经基因分型的配子体培养物被用于两项独立研究（分别为人工eDNA构建实验与配子体播种实验），以种群等位基因频率作为参考，结合数值最大似然估计器，验证通过eDNA样本估算配子体数量的有效性。参考种群的等位基因频率，通过对加拿大不列颠哥伦比亚省哈凯航道12个邻近位点的孢子体（2n）样本进行上述11个微卫星位点的基因分型来估算。每个位点采集32个个体，最终合并所有样本（总样本量n=384），因为这些样本的遗传结构可忽略不计（Fst = 0.02）。另有一个参考种群来自加拿大不列颠哥伦比亚省欧文湾，该种群采集了40个孢子体（2n）样本，并在相同的微卫星位点进行了基因分型。等位基因的分型工作通过R语言工具包Amplicomsat完成（……）。

# 2025年Liggan等人研究的参考种群与配子体培养物基因型数据
https://doi.org/10.5061/dryad.r4xgxd2q6

## 数据与文件结构说明
本数据集对应Liggan等人2025年发表的研究中，巨藻（Nereocystis luetkeana）的配子体培养物与孢子体组织的基因型数据。基因型通过11个微卫星位点的扩增子高通量测序获得，结果以已分型的片段长度（bp）与序列变异等位基因形式呈现。

### 文件与变量
#### 文件：Biobank_genotypes_HakaiMarnaLab.txt
**文件说明：** 本文件包含Liggan等人2025年播种实验中所用配子体培养物的基因型数据。

##### 变量说明
* 样本名称：配子体培养物名称
* Ner2：微卫星标记名称
* NL24：微卫星标记名称
* NL25：微卫星标记名称
* NL26：微卫星标记名称
* NL27：微卫星标记名称
* NL30：微卫星标记名称
* NL40：……