DOI: 10.5061/dryad.80gb5mm1t
title: Development of a cost-effective, multifunctional SNP panel and analysis workflow for wolf monitoring in Finland

description: Genetic monitoring is an essential tool for managing threatened or
 commercially valuable wildlife species. Ideally, genetic monitoring relies
 on straightforward protocols for genotyping and data handling,
 accommodates varying sample volumes, applies to non-invasive samples such
 as scat and hair, produces reliable and repeatable genotypes, and is
 cost-effective. Moreover, the marker panel itself should be tailored to
 specific species and/or population management information needs. We
 describe the development of a microarray-based 96-SNP panel specifically
 designed for non-invasive genetic monitoring of the Finnish wolf
 population. The panel was developed to meet four specific needs for this
 population: identification of wolf genotypes from the non-target species
 (fox, raccoon dog, golden jackal), species detection, sexing, individual
 identification, and kinship resolution. Detection of potential dog or
 hybrid samples is addressed with a separate 93-SNP wolf-dog panel
 (Harmoinen et al. 2021) used in parallel. We demonstrate the utility of
 the SNP panel using a subset of the genetic monitoring data collected in
 2022–2023, including an overview of the data analysis workflow. The
 development and successful application of this SNP panel, along with a
 comparison with similar studies in the field, provide valuable insights
 for researchers and conservationists aiming to implement similar
 strategies for other species.
description: Data is genotyped with microfluidic 96.96 Dynamic Arrays™
 (Standard BioTools Inc, formerly Fluidigm) using the 96 SNP panel
 developed in the corresponding article.
description: # Development of a cost-effective, multifunctional SNP panel and analysis
 workflow for wolf monitoring in Finland Dataset DOI:
 [10.5061/dryad.80gb5mm1t](10.5061/dryad.80gb5mm1t) ## Description of the
 data and file structure The data were genotyped using microfluidic 96.96
 Dynamic Arrays™ with a 96-SNP panel developed in the corresponding
 article. Some files also include data genotyped with the Illumina CanineHD
 Whole-Genome BeadChip microarray (Illumina, Inc., San Diego, California,
 USA), from which the corresponding 96 SNPs were extracted. ### Files and
 variables #### File: Subset_MonitoringData.csv
 **Description:** Tab-delimited file including all unique individuals from
 the subset of monitoring data (supplementary table 5). Output from Allele
 match software. Missing values indicated by -9. ##### Variables: Sample
 name in the first column, and then allele a and b for each loci #### File:
 Pedigree_SNP_data.ped **Description:** PLINK PED file of inbred wolf packs
 comprising 81 SNPs and 65 individuals from southwestern Finland, used for
 pedigree analyses. Missing values indicated by 0. #### File:
 Pedigree_SNP_data.map **Description:** PLINK MAP file
 for Pedigree_SNP_data.ped #### File: Pedigree_MSAT_data.txt
 **Description:** GENEPOP-format data from inbred wolf packs comprising 65
 individuals from southwestern Finland, genotyped with 17 microsatellites
 and used for pedigree analysis. Missing values indicated by 0. #### File:
 PCA_data.ped **Description:** PLINK PED file containing 86 SNPs from
 individuals used in PCA and RUBIAS analyses. The first column indicates
 the genotyping method and species for each sample. 'Illumina'
 refers to genotyping with the Illumina CanineHD BeadChip, while
 'MoPa' refers to the monitoring panel developed in the article
 and genotyped using Dynamic Array™ IFC plates (Standard BioTools).
 'Testsample' indicates individuals from the monitoring data
 subset that were analyzed to determine their species of origin. Missing
 values indicated by 0. #### File: PCA_data.map **Description:** PLINK MAP
 file for PCA_data.ped #### File: Sexing_Xchromosome.ped
 **Description:** PLINK PED file containing 9 X-chromosomal SNPs from 87
 wolves of known sex, used for testing the accuracy of sex
 determination. Missing values indicated by 0. #### File:
 Sexing_Xchromosome.map **Description:** PLINK MAP file
 for Sexing_Xchromosome.ped #### File: ErrorRate.ped **Description:** PLINK
 PED file containing 95 SNP genotypes from 15 wolves, used for error rate
 estimation. The first column indicates the genotyping method:
 'Illumina' refers to the Illumina CanineHD BeadChip, while
 'MoPa' refers to the monitoring panel developed in the article
 and genotyped using Dynamic Array™ IFC plates (Standard BioTools). Missing
 values indicated by 0. #### File: ErrorRate.map **Description:** PLINK MAP
 file for ErrorRate.ped #### File: HWE_MAF_LD_36UnrelatedFinnishWolves.ped
 **Description:** PLINK PED file containing 36 unrelated Finnish wolves
 used for HWE, MAF, LD and PID analyses. Missing values indicated by 0.
 #### File: HWE_MAF_LD_36UnrelatedFinnishWolves.map **Description:** PLINK
 MAP file for HWE_MAF_LD_36UnrelatedFinnishWolves.ped