DOI: 10.5061/dryad.vq83bk3ww
title: Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis

description: Admixture between species is a cause for concern in wildlife management.
 Canids are particularly vulnerable to inter-specific hybridisation, and
 genetic admixture has shaped their evolutionary history. Microsatellite
 DNA testing, relying on a small number of genetic markers and
 geographically restricted reference populations, has identified extensive
 domestic dog admixture in Australian dingoes and driven conservation
 management policy. There has been concern that geographic variation in
 dingo genotypes could confound ancestry analyses that use a small number
 of genetic markers. Here we apply genome-wide single nucleotide
 polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes
 from across Australia and then carry out comparisons to domestic dogs, and
 perform ancestry modelling and biogeographic analyses to characterize
 population structure in dingoes and investigate the extent of admixture
 between dingoes and dogs in different regions of the continent. We show
 that there are at least five distinct dingo populations across Australia.
 We observed limited evidence of dog admixture in wild dingoes, challenging
 previous reports regarding the occurrence and extent of dog admixture in
 dingoes, as our ancestry analyses show that previous assessments severely
 overestimate the degree of domestic dog admixture in dingo populations,
 particularly in southeastern Australia. These findings strongly support
 the use of genome-wide SNP genotyping as a refined method for wildlife
 managers and policy makers to assess and inform dingo management policy
 and legislation moving forwards.
description: This data was collected by microarray SNP genotyping using Axiom
 Canine Set A, Axiom Canine Set B and Axiom CanineHD arrays (Thermo Fischer
 Scientific Inc). Microarrays were processed at either the Ramaciotti
 Centre for Genomics (Sydney, Australia) or Thermo Scientific Microarray
 Research Services Laboratory (Santa Clara, CA, USA). Both the raw CEL
 files off the GeneTitan microarray scanner and Plink SNP datasets are
 provided.
description: Included is a readme file, an Excel .xlsx file with sample
 metadata for all 543 samples, an Excel .xlsx file with Axiom Set A and Set
 B CEL file names for the 112 dog samples, and a binary (.bed, .bim, .fam)
 Plink dataset containing the filtered SNP dataset for 543
 canids.  Raw .CEL files for the 431 dingo and domestic
 dog samples genotyped on the Axiom Canine HD array at the Ramaciotti
 Centre for Genomics are provided. Raw .CEL files for the 112 domesitc dog
 samples genotyped on the Axiom Canine Set A and Axiom Canine Set B array
 at the Thermo Scientific Microarray Research Services Laboratory are
 provided.
description: # Axiom canine microarray data from Australian dingoes and domestic dogs
 for admixture and population structure analysis This readme file was
 generated on 2022-10-10 by Kylie M Cairns GENERAL INFORMATION Date of data
 collection: 2018-2021 Geographic location of data collection: Australia
 and United States of America SHARING/ACCESS INFORMATION Links to
 publications that cite or use the data: Cairns et al. Genome-Wide Variant
 Analyses Reveals New Patterns of Admixture and Population Structure in
 Australian Dingoes. Molecular Ecology. Links to other publicly accessible
 locations of the data: na. Links/relationships to ancillary data sets: na.
 Was data derived from another source?: No. DATA & FILE OVERVIEW File
 List: MS1_sample_metadata_v5_upload.xlsx - metadata
 Cairnsetal_admix_dataset_20221012.fam - plink files - fixed order.
 Cairnsetal_admix_dataset_20221012.bim - plink files
 Cairnsetal_admix_dataset_20221012.bed - plink files
 Axiom_Canine_SetA_SetB_cels_112.zip - Cel files for dog samples typed at
 NIH Axiom_CanineHD_CEL.zip - Cel files - for dingo and dog samples typed
 at UNSW GA_affy_SNP_meta_mec16998.xls - metadata METHODOLOGICAL
 INFORMATION Description of methods used for collection/generation of data:
 described in Cairns et al. Genome-Wide Variant Analyses Reveals New
 Patterns of Admixture and Population Structure in Australian Dingoes.
 Molecular Ecology. Published in 2023. Methods for processing the data: CEL
 files processed with Axiom Analysis Suite Software and exported for
 analysis with Plink 1.9. Instrument- or software-specific information
 needed to interpret the data: Plink 1.9 or Plink 2.0, Axiom Analysis Suite
 VERSION CHANGES 2025-September-21: Corrected order of .fam file (note
 there is a column containing the sample order, but it was mistakenly
 sorted incorrectly).