DOI: 10.5061/dryad.280gb5n05
title: Genotype data of Anoplophora Glabripennis from invasive populations in North America and native population in Asia

description: This dataset provides genomic resources for the invasive Asian longhorned
 beetle (Anoplophora glabripennis Motschulsky, ALB), a significant pest
 threatening global forest ecosystems. It includes 2,768 genome-wide single
 nucleotide polymorphisms (SNPs) derived from invasive ALB populations in
 North America, enabling the study of genetic variation, invasion history,
 and population dynamics. The dataset is structured to support analyses of
 genetic bottlenecks, population expansions, and secondary spread patterns,
 offering insights into multiple independent introductions from the native
 range. The dataset is organized into genotype matrices and metadata,
 including sample locations, collection dates, and population identifiers.
 It is reusable for studies on invasion biology, biosurveillance, and
 biosecurity, providing a foundation for tracing the origins of intercepted
 individuals and informing pest management strategies. Legal and ethical
 considerations include compliance with data-sharing policies and
 restrictions on the use of genetic data for invasive species management.
 This resource is designed to enhance genome-based biosurveillance tools,
 supporting regulatory agencies in strengthening biosecurity measures
 against ALB and other invasive pests.
description: DNA was extracted
 from individual specimens using a single leg or larval thoracic muscle,
 surface-sterilized with ethanol, flash frozen in liquid nitrogen, and
 homogenized. The samples were processed using the DNeasy 96 Blood
 & Tissue Kit (Qiagen). Additionally, previously
 published <em>A. glabripennis</em> data from China and South
 Korea were included to generate a native reference collection.
 Genotyping was performed using genotyping-by-sequencing (GBS) on
 an Ion Proton platform. The Fast-GBS v1.0 pipeline was used for variant
 calling. SNP variants were filtered using VCFtools and PLINK to retain
 high-quality biallelic SNPs. Quality filters included thresholds for
 missing data, minor allele frequency, read depth, and relatedness among
 samples.
description: # Genotype data of Anoplophora Glabripennis from invasive populations in
 North America and Native populations in Asia
 [https://doi.org/10.5061/dryad.280gb5n05](https://doi.org/10.5061/dryad.280gb5n05) ## Description of the data and file structure **490_2768.recode.vcf**: This file contains the filtered genotype data in VCF format. **metadata490.txt**: This file provides corresponding metadata for the genotype data. **FastGBS_platypus_basic.recode.vcf**: This file contains initial genotype data in VCF format generated using the Fast-GBS pipeline. The dataset includes SNPs that underwent basic filtering using VCFtools to reduce file size, by removing variants with excessive missing data or other low-quality characteristics. **FastGBS_platypus_basic.log**: This file is a log file generated during the filtering of the initial variant calls using VCFtools. ### Files and variables #### File: metadata490.txt **Description:**  ##### Variables * **INDV**: Individual sample identifier (e.g., "P1_c01c02_SKOR52.sort"). * **pop_id**: Population identifier or code (e.g., "KOR" for Korea). * **Latitude**: Geographic latitude of the collection site. * **Longitude**: Geographic longitude of the collection site. * **City**: City where the sample was collected. * **State.Region**: State or region where the sample was collected. * **Country**: Country of origin for the sample (e.g., "Korea").  * **Range**: Indicates whether the population is native or invasive. * **Fst_group**: Grouping based on genetic differentiation (Fst), typically indicating a population or region of origin (e.g., "Korea"). * **Collection_year**: The year in which the sample was collected (e.g., 2001). #### File: 490\_2768.recode.vcf **Description:** This file contains the filtered genotype data in Variant Call Format (VCF). It includes single nucleotide polymorphisms (SNPs) for the *Anoplophora glabripennis* specimens. The data has undergone quality control filtering, retaining only high-quality, biallelic SNPs that meet specific criteria for missing data, read depth, minor allele frequency, and relatedness among individuals.