Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis
Data files
May 31, 2023 version files 6.63 GB
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Axiom_Canine_SetA_SetB_cels_112.zip
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Axiom_CanineHD_CEL.zip
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Cairnsetal_admix_dataset_20221012.bed
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Cairnsetal_admix_dataset_20221012.bim
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Cairnsetal_admix_dataset_20221012.fam
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GA_affy_SNP_meta_mec16998.xls
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MS1_sample_metadata_v5_upload.xlsx
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README.md
Abstract
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.
Methods
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.
Usage notes
Included is a readme .txt file, a excel .xlsx file with sample metadata for all 543 samples, a 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.