Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis

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 ..., 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., 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.
, # 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 f...,