Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia

Reducing the illegal wildlife trade requires an understanding of its origins. Here we present a genomic approach for tracing confiscated scales from the world’s most trafficked mammal, the white-bellied pangolin (Phataginus tricuspis), to their geographic origins. Analyzing scales seized in Hong Kong SAR, China from 2012–2018 revealed intense poaching along Cameroon’s southern border. Poaching pressures shifted over time from West to Central Africa. Using data from seizures representing nearly one million African pangolins, we identified Nigeria as a significant hub for trafficking, where scales are amassed and shipped to Vietnam and Hong Kong SAR, China, with final transit to markets in Guangdong and Guangxi, China. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures., , , # Genomic analyses reveal poaching hotspots and illegal trade in pangolins from Africa to Asia

Here we present a genomic approach for tracing confiscated scales from the world’s most trafficked mammal, the white-bellied pangolin (*Phataginus tricuspis*), to their geographic origins. Analyzing scales seized in Hong Kong SAR, China from 2012-2018 revealed intense poaching along Cameroon’s southern border. We utilized whole genome resequencing of white-bellied pangolins across their range to identify population structure, and then designed Fluidigm SNP-type assays diagnostic of the distinct genetic clusters to assign confiscated pangolin scales back to their origin. This data set includes the called genotypes using whole genome sequencing (in vcf form), the raw data of targeted SNP genotyping of georeferenced pangolins and confiscated pangolin scales, and custom scripts used for assignment analyses.

## Description of the data and file structure

1. pangolin_samples_for_code.xlsx: This...

打击非法野生动物贸易，需先明晰其源头。本研究提出一种基因组学溯源方法，可追踪全球被非法贩运最多的哺乳动物——白腹穿山甲（*Phataginus tricuspis*）的没收鳞片的地理来源。对2012至2018年间在中国香港特别行政区（Hong Kong SAR）查获的穿山甲鳞片进行分析后发现，喀麦隆南部边境沿线存在高强度盗猎活动。盗猎压力随时间推移从西非地区转向中非地区。通过分析涵盖近百万头非洲穿山甲的查获数据，我们确定尼日利亚是重要的非法贩运枢纽：鳞片在此处聚集，随后运往越南及中国香港特别行政区，最终转运至中国广东、广西的市场。这种“源头-目的地”溯源方法为打击非法野生动物贸易、制定反贩运措施提供了全新契机。

# 基因组分析揭示非洲穿山甲至亚洲的盗猎热点与非法贸易

本研究提出一种基因组学溯源方法，用于追踪被没收的白腹穿山甲（*Phataginus tricuspis*，全球被非法贩运最多的哺乳动物）鳞片的地理来源。此前针对2012至2018年间中国香港特别行政区查获的鳞片所开展的分析显示，喀麦隆南部边境沿线盗猎活动猖獗。我们对分布范围内的白腹穿山甲开展全基因组重测序（whole genome resequencing）以解析种群遗传结构，随后设计针对不同遗传聚类的Fluidigm SNP分型检测（Fluidigm SNP-type assays），将查获的穿山甲鳞片溯源至其原生种群。本数据集包含：全基因组测序得到的基因型分型结果（VCF格式）、带有地理坐标的穿山甲个体与查获穿山甲鳞片的靶向SNP基因分型原始数据，以及用于溯源分析的自定义脚本。

## 数据与文件结构说明
1. pangolin_samples_for_code.xlsx: This...