implications of methodologies for integrating empirical kinships into ex situ population management using PMx: a case study of Baer’s Pochard (Aythya baeri) in North America

In this study, we aimed to understand the implications of integrating empirical kinships into the genetic management of an ex situ population of the endangered waterfowl, Baer’s pochard (Aythya baeri), in North America. Single nucleotide polymorphism data were generated for 141 Baer’s pochard using double digest restriction site-associated DNA sequencing and empirical kinships were derived and integrated into the population management software PMx. We compared three different scenarios for appying empirical kinships within PMx: 1) no empirical kinships applied, 2) empirical kinships applied for pedigree terminals, 3) empirical kinships applied for the entire populations of pedigree terminals and descendants. We determined that most genetic summary statistics were impacted through the calculation of the population’s mean kinship, which increased signficantly after empirical kinships were integrated into our analyses. Our results also revealed the importance of understanding how molecular..., DNA extracted from whole blood from each of the 141 sampled individuals were sent to the Genomic and Bioinformatics Service, Texas A&M AgriLife Research laboratory for ddRAD library preparation and sequencing. A total of 500 ng of DNA from each individual were provided. Paired-end sequences approximately 150-bp in length were produced on a single lane of the Illumina NovaSeq 6000 S2 X platform. Demultiplexed sequence data was obtained in the form of compressed fastq files (fastq.gz), representing raw paired-end sequencing reads. Data filtering and SNP discovery were performed in STACKS v2.41 (Catchen et al. 2013, Rochette et al. 2019). Initially, sequence data was cleaned using the program process_radtags by removing reads with an uncalled base or low quality score (raw phred score <10). A custom bioinformatics pipeline (available at https://github.com/apwilder/StacksParameterSelection) then was used to select optimal parameters (m, M, n) for STACKS based on the guidelines of Par..., ddRAD paired-end sequence data for 141 sampled Baer's pochard:

BAPO_Seq_1_20
BAPO_Seq_21_38
BAPO_Seq_39_55
BAPO_Seq_56_72
BAPO_Seq_73_89
BAPO_Seq_90_107
BAPO_Seq_108_123
BAPO_Seq_124_141

Stacks population map input file:

PopulationMap

Stacks output file (haplotype and SNPs):

populations.snps.vcf

Empirical kinship files imported into PMx:

KinshipMatrix_N56_Scenario2.txt
KinshipMatrix_N141_Scenario3.txt
KinshipMatrix_N141_OriginalWithNegativeValues.txt

The PMx (scti.tools/pmx/) software is requried to open the PMx project files:

BaersPochard_Scenario1.pmxproj 
BaersPochard_Scenario2.pmxproj
BaersPochard_Scenario3.pmxproj
, This README file was generated on 2023-10-03 by Asako Chaille.

GENERAL INFORMATION

1. Title of Dataset: Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer’s Pochard (Aythya baeri) in North America
2. Author Information
First Author Contact Information
Name: Asako Chaille
San Diego Zoo Wildlife Alliance
Address: San Diego, CA USA
Email: [e-mail]
3. Date of data collection (single date, range, approximate date): Birds were sampled for blood between 2017 and 2019. ddRAD data was generated and analyzed between 2019-2021
4. Geographic location of data collection: Birds were sampled across 21 participating North American facilities. The ddRAD library preparation and sequencing was done at the Genomic and bioinformatics Service, Texas A&M AgriLife Research laboratory.
5. Information about funding sources that supported the collection of the data: This work was funded by Akron Z...

本研究旨在探究将经验亲缘关系（empirical kinships）整合至濒危水鸟青头潜鸭（Aythya baeri）北美迁地种群的遗传管理中的意义。本研究通过双酶切限制性位点相关DNA测序（double digest restriction site-associated DNA sequencing，ddRAD）对141只青头潜鸭开展单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分型，推导得到经验亲缘关系并将其整合至种群管理软件PMx中。我们在PMx中设置3种应用经验亲缘关系的情景进行对比：1）不应用经验亲缘关系；2）仅对谱系终端个体应用经验亲缘关系；3）对谱系终端个体及其后代的整个种群应用经验亲缘关系。结果表明，多数遗传汇总统计量会因种群平均亲缘关系的计算受到影响，且在整合经验亲缘关系至分析后，平均亲缘关系显著升高。本研究结果还揭示了理解分子手段如何……的重要性。

从141个采样个体的全血中提取的DNA被送至德克萨斯农工大学农业生命研究中心基因组与生物信息学服务实验室，用于ddRAD文库制备与测序。每个个体提供总量为500 ng的DNA。在Illumina NovaSeq 6000 S2 X平台的单个测序泳道上生成了长度约150 bp的双端测序序列。得到的双端测序原始数据以压缩FASTQ文件（fastq.gz）形式完成拆分。

数据过滤与SNP发掘在STACKS v2.41（Catchen等人，2013；Rochette等人，2019）中完成。首先，使用process_radtags工具对序列数据进行质控清洗，移除存在未调用碱基或低质量得分（原始Phred质量值<10）的reads。随后，基于相关指南，使用自定义生物信息学流程（可在https://github.com/apwilder/StacksParameterSelection获取）为STACKS筛选最优参数（m、M、n）。

141个采样青头潜鸭的ddRAD双端测序数据：
BAPO_Seq_1_20
BAPO_Seq_21_38
BAPO_Seq_39_55
BAPO_Seq_56_72
BAPO_Seq_73_89
BAPO_Seq_90_107
BAPO_Seq_108_123
BAPO_Seq_124_141

STACKS种群映射输入文件：
PopulationMap

STACKS输出文件（单倍型与SNP）：
populations.snps.vcf

导入至PMx的经验亲缘关系文件：
KinshipMatrix_N56_Scenario2.txt
KinshipMatrix_N141_Scenario3.txt
KinshipMatrix_N141_OriginalWithNegativeValues.txt

需使用PMx（scti.tools/pmx/）软件打开以下PMx项目文件：
BaersPochard_Scenario1.pmxproj
BaersPochard_Scenario2.pmxproj
BaersPochard_Scenario3.pmxproj

本README文件于2023年10月3日由Asako Chaille生成。

一、数据集标题：基于PMx的经验亲缘关系整合方法在迁地种群管理中的应用——以北美青头潜鸭（Aythya baeri）为例
二、作者信息
第一作者联系方式
姓名：Asako Chaille
所属机构：圣地亚哥动物园野生动物联盟
地址：美国加利福尼亚州圣迭戈
邮箱：[e-mail]
三、数据收集日期（单一日期、日期范围或近似日期）：2017年至2019年间采集鸟类血液样本；ddRAD数据的生成与分析工作于2019-2021年间完成
四、数据收集地理位置：在北美21家合作机构采集鸟类样本；ddRAD文库制备与测序工作在德克萨斯农工大学农业生命研究中心基因组与生物信息学服务实验室完成。
五、数据收集工作的资助方信息：本研究由Akron Z……资助