DOI: 10.5061/dryad.83bk3jb4r
title: Genetic testing predicts appearance but not behavior in dogs

description: Genetic tests for behavioral and personality traits in dogs are now being
 marketed to pet owners, but their predictive accuracy has not been
 validated. To evaluate the reliability of such tests, we analyzed data
 from Darwin’s Ark, a community science initiative that includes over 3,000
 dogs with both genetic data and individual-level behavioral phenotypes.
 None of the candidate variants had significant associations or predictive
 power for behavioral traits as previously reported. However, we found
 strong associations with aesthetic traits that differentiate breeds, such
 as height, leg length, and ear shape. Our results suggest that earlier
 studies using breed-average phenotypes, rather than individually measured
 phenotypes, were confounded by population structure. Behavior in dogs is
 polygenic and complex, and thus cannot be accurately predicted using tests
 that consider only a few genetic variants. Furthermore, behavior in dogs
 is only moderately heritable, and environmental influences inherently
 limit the potential accuracy of genomic predictions. Developing
 meaningful, accurate genetic predictions for complex traits that can
 improve dog health and welfare will require very large cohorts of
 individually phenotyped dogs.
description: # Genetic testing predicts appearance but not behavior in dogs The
 following archives contain data files associated with the manuscript:
 Kathryn A. Lord, Vista Sohrab, Kasia Bryc, Michelle E. White, Brittney
 Kenney, Kathleen Morrill Pirovich, Frances L. Chen, Elinor K. Karlsson,
 Genetic testing predicts appearance but not behavior in dogs. *PNAS*.
 2025. Data Files #### Genetic Data: `darwins_dogs_genetic_set.zip`
 Contains a subset of the gene dataset. #### Darwin's Ark Cohort A
 *PLINK1* bfile set (.bed/.bim/.fam) with sample IDs encoded as dog IDs
 matching individuals from the Darwin's Ark survey data files,
 including genotypes from 3,277 dog whole genomes sequenced under
 BioProject PRJNA675863.
 `DarwinsDogs_2024_N-3277_canfam4_gp-0.70_biallelic.bed`
 `DarwinsDogs_2024_N-3277_canfam4_gp-0.70_biallelic.bim`
 `DarwinsDogs_2024_N-3277_canfam4_gp-0.70_biallelic.fam` The following
 plink set above is then further filtered using minor allele frequency and
 Hardy-Weinberg p-value thresholds for genetic analysis. See the Methods
 section of the manuscript for more details. #### Genetic analysis input
 files `darwins_dogs_gwas_input_files.zip` contains the phenotype input
 files and covariate input files used to run the analysis.
 `phenotype_input_files` This folder contains the following files: *
 `DarwinsArk_4Q_Morphology_N-3277_rerun_20241107.tsv` Contains level
 phenotypic data for morphological questions that were recoded differently
 from the raw survey questions. *
 `DarwinsArk_13Q_Q243_coat_color_N-1930.tsv` Contains level-phenotypic data
 for the coat color question. *
 `DarwinsArk_34Q_Priorities1-3_Behavior_9Q_Morphology_N-3277.tsv` Contains
 level-phenotypic data for behavioral questions and morphological questions
 (raw data in this file and no recoding for morphological questions). *
 `DarwinsArk_8Factors_N-3277.tsv` Contains I-level behavioral factor
 scores. Each phenotype input file requires a required dog_id column
 referring to the dog_id used in both our phenotypic and genetic datasets,
 followed y columns for the phenotype of interest. The workflow used to run
 our genetic analysis creates an individual phenotype file from the
 following input files above. Workflow for analysis can be found at
 [https://github.com/VistaSohrab/dog-gwas-heritability-nextflow](https://github.com/VistaSohrab/dog-gwas-heritability-nextflow) FDarwinrwi.n's Ark questio.n key from abbreviation to full text (ie, Q121 refers to dog height), see Supplemental Table 5 (Table S5) of the manuscript. `covariate_input_files` This folder contains the following files: * `DarwinsArk_AgeComposed_Height_N-3277.tsv` contains individual-level ages and heights used in all GWAS analyses as a quantitative covariate, except for height GWAS * `DarwinsArk_AgeComposed_N-3277.tsv` contains individual-level ages used as a quantitative covariate in height GWAS * `DarwinsArk_Sex_NeuterStatus_N-3277.tsv` contains individual-level sex status (sex and neuter status) as a single discrete covariate used in all the GWAS #### Genetic analysis output files (GWAS) `darwins_dogs_gwas_output_files.zip` contains all GCTA leave-one-chromosome-out mixed linear model association output files (.loco.mlma) This folder contains GWAS output files for behavioral and morphological questions, as well as behavioral factors. #### Heritability output files (GCTA-GREML) `darwins_dogs_heritability_output_files.zip` contains heritability output files from GCTA-GREML This folder contains GCTA-GREML output files (both LD-corrected and non-LD-corrected) (both constrained and unconstrained) * `.lds.hsq` refers to LD-corrected and constrained (most reliable and reported in the manuscript) * `.lds.no-constraint.hsq` refers to LD-corrected and no constraint * `.no-lds.hsq` refers to non-LD-corrected and constrained (can refer to this file in case the LD-corrected and constrained run was unsuccessful) * `.no-lds.no-constraint.hsq` refers to non-LD-corrected and no constraint #### Supplemental information: GWAS analysis `supplemental_information_gwas.zip` contains GCTA leave-one-chromosome-out mixed linear model association output files (.loco.mlma) from 5 phenotypes (2 behavioral questions, 2 behavioral factors, and height as morphological question) pera formed on mixed breed random sampling of mixed-breed and single-breed dogs from the full dataset. * `random_dogs` In the GWAS output file name or the phenotype input file column name refers to dogs randomly sampled from the full dataset * `mixed_dogs` In the GWAS output file or the phenotype input file column name refers to mixed-breed dogs The phenotype input files can be found in the `supp_gwas_phenotype_input_files` folder. Covariate files are the same as other GWAS (age and height, sex status) or (age, sex status) for height. #### Data availability FASTQ files for all genetic information in this study are available in the NIH Sequence Read Archive (project PRJNA675863) at [https://www.ncbi.nlm.nih.gov/sra?term=PRJNA675863](https://www.ncbi.nlm.nih.gov/sra?term=PRJNA675863). The genetic data, as well a,s the GWAS and heritability input and output files are avail, are available on Dryad at (DOI: 10.5061/dryad.83bk3jb4r). The code for curating the phenotypes and predicting SNP effects on phenotype is available on GitHub at [https://github.com/broadinstitute/dog_behavioral_gwas_paper](https://github.com/broadinstitute/dog_behavioral_gwas_paper). The pipeline for GWAS and heritability is available at [https://github.com/VistaSohrab/dog-gwas-heritability-nextflow/](https://github.com/VistaSohrab/dog-gwas-heritability-nextflow/) with the necessary software packaged in a Docker container at [https://hub.docker.com/r/vistasohrab/terra-dogagingproject-gwas](https://hub.docker.com/r/vistasohrab/terra-dogagingproject-gwas). #### Contact If you have further questions about the data file archive, then contact the authors, Kathryn L. Ord ([kathryn.lord@umassmed.edu](mailto:kathryn.lord@umassmed.edu)) and Elinor Karlsson ([elinor.karlsson@umassmed.edu](mailto:elinor.karlsson@umassmed.edu)), and we will resolve them as soon as possible.