Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples

Genetic tools for wildlife monitoring can provide valuable information on spatiotemporal population trends and connectivity, particularly in systems experiencing rapid environmental change. Though many DNA sequencing approaches still require high quality and quantity of DNA obtained from traditional sources (e.g. blood and tissue), rapid genotyping tools such as Genotyping-in-Thousands by sequencing (GT-seq) have improved our ability to make use of degraded and less concentrated DNA commonly obtained from non-invasive and archival samples. Here, we developed a multi-purpose GT-seq panel (307 single nucleotide polymorphisms) for a climate sentinel mammal (the American pika, Ochotona princeps) for use as a genetic tool for monitoring populations in the Canadian Rocky Mountains. We optimized the panel using contemporary tissue samples (n = 77) and subsequently applied it to archival tissue (n = 17) and contemporary fecal pellet samples (n = 129) to evaluate its effectiveness at identifying..., Samples were genotyped using Genotyping-in-Thousands by sequencing (GTseq; Campbell et al. 2015) panel as modified in Burgess et al. (2022; https://doi.org/10.1002/ece3.8993). Raw data were processed using the GTseq workflow., NA, # Data from: Evaluating genotyping-in-thousands by sequencing as a genetic monitoring tool for a climate sentinel mammal using non-invasive and archival samples

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This dataset contains genotypic data of American pika (*Ochotona princeps*) scat (n=143), archival skin tissue (n=18), and liver tissue (n=85) samples at 307 single nucleotide polymorphisms (SNPs), genotyped using Genotyping-in-Thousands by sequencing (described by Campbell et al. (2015), as modified in Burgess et al. (2022)). Tissue samples were collected across North America in 2004; scat and archival skin samples were collected in the Canadian Rocky Mountain National Parks (specifically, Banff, Kootenay, Yoho, and Jasper National Parks) in 2021-2022 and 1930/1945, respectively.

## Description of the data and file structure

Ocp_liver_genotypes_307snps.vcf - this is a VCF file containing SNP and genotypic information collected using for 85 liver tissue samples (including 8 technical replicates) at 307 SNPs

Ocp_scat_arc...

用于野生动物监测的遗传工具可提供极具价值的时空种群动态与种群连通性信息，在环境快速变化的生态系统中尤为关键。尽管多数DNA测序方法仍需从传统采样来源（如血液与组织）获取高质量、高浓度的DNA，但诸如测序千人分型法（Genotyping-in-Thousands by sequencing, GT-seq）这类快速分型工具，显著提升了我们利用常见于非损伤性采样与馆藏样本中的降解、低浓度DNA的能力。本研究针对气候指示性哺乳动物——北美鼠兔（*Ochotona princeps*）开发了一款多功能GT-seq分型面板，包含307个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点，旨在作为遗传工具用于加拿大落基山脉的种群监测。我们使用77份当代组织样本对该分型面板进行优化，随后将其应用于17份馆藏组织样本与129份当代粪便颗粒样本，以评估其在识别...方面的有效性。所有样本均通过经Burgess等（2022; https://doi.org/10.1002/ece3.8993）修改的测序千人分型法（GTseq; Campbell等，2015）完成分型，原始数据通过GTseq分析流程进行处理。NA
# 数据来源：《利用非损伤性与馆藏样本评估测序千人分型法作为气候指示性哺乳动物遗传监测工具的有效性》

本数据集包含北美鼠兔（*Ochotona princeps*）的307个单核苷酸多态性（SNPs）位点基因型数据，涉及粪便样本（n=143）、馆藏皮肤组织样本（n=18）与肝脏组织样本（n=85），所有样本均采用经Burgess等（2022）修订的测序千人分型法（Campbell等，2015年最初提出）完成分型。其中肝脏组织样本于2004年在北美全境采集；粪便样本与馆藏皮肤样本分别于2021-2022年、1930/1945年采自加拿大落基山脉国家公园（具体包括班夫、库特尼、约霍与贾斯珀国家公园）。

## 数据与文件结构说明
Ocp_liver_genotypes_307snps.vcf：该VCF文件包含85份肝脏组织样本（含8份技术重复样本）在307个SNP位点的SNP与基因型信息。
Ocp_scat_arc...