DOI: 10.5061/dryad.g4f4qrfr0
title: Associated data files and scripts for 'Ancestry-inclusive dog genomics challenges popular breed stereotypes'

description: Behavioral genetics in dogs has focused on modern breeds, isolated
 subgroups &lt;200 years old with distinctive physical, and,
 purportedly, behavioral characteristics. We interrogated breed stereotypes
 by surveying owners of 18,371 purebred and mixed-breed dogs, and densely
 genotyping (~45 million markers) a subset of 2,155 dogs. Most behavioral
 traits are heritable (h2&gt;25%), and admixture patterns in
 mixed-breed dogs can reveal breed propensities. However, breed poorly
 predicts an individual purebred dog’s behavioral phenotype, explaining
 just 9% of variation. Using genome-wide association, we identify 11 loci
 significantly associated with howling and other behaviors, and show
 characteristic breed behaviors are genetically complex.
 Behavior-associated loci are not unusually differentiated in modern
 breeds, but breed propensities do align, albeit weakly, with ancestral
 function. We propose behaviors now perceived as characteristic of modern
 breeds likely derive from thousands of years of polygenic adaptation
 predating breed formation, with modern breeds distinguished primarily by
 aesthetic, not behavioral, traits.
description: <strong>Survey Data.</strong> Upon enrollment in
 Darwin’s Ark (https://darwinsark.org), owners were asked to provide
 consent for participation and information about their dog’s approximate
 birth date, sex and spay/neuter status, suspected or known breed(s),
 purebred registration, and/or photograph. We presented owners with 22
 surveys composed of 10-12 questions, for which any number or order can be
 answered. The majority offered response choices of agreement with
 statements presented or the frequency of behavior in question on a 5-point
 Likert scale. Among these surveys, 123 questions were sourced from
 published and validated canine behavioral and health surveys, including
 the Dog Personality Questionnaire (DPQ / DPQL), the Canine Health-related
 Quality of Life Survey (CHQLS), the Dog Impulsivity Assessment Scale
 (DIAS), the Canine Cognitive Dysfunction Rating scale (CCDR), the
 Certified Dog Trainer Test (CDTT, International Association of Canine
 Professionals), and the Dog Obesity Risk and Appetite questionnaire
 (DORA). The remainder of surveys were developed in collaboration with the
 International Association of Animal Behavior Consultants (IAABC) (MBT) or
 include original questions about personality (NEO Five-Factor Inventory),
 allergies, environment, and physical traits or morphology. We performed a
 data freeze on sureys obtained until November 15th,
 2019.<br><br><strong>Genetic Data.</strong> We
 sent owners saliva collection kits (DNA Genotek PG-100 saliva swabs) to
 sample their dogs. We preferentially sampled dogs with complete survey
 data as well as dogs from several underrepresented breeds to expand the
 breed calling panel to include the 100 most common breeds in the US. 159
 samples (7.4% of 2,155 dogs included in the genetic data set) had
 sequencing funded by owner donations to the Darwin’s Ark Foundation. 1,715
 dogs were sequenced at coverages of 0.5x to 1.1x depth on the Gencove
 sequencing platform. Sequencing reads were processed into imputed
 autosomal (chromosomes 1-38) variant calls through Gencove’s loimpute
 software and an imputation reference panel containing publicly available
 whole genome sequence data (mean coverage 22.9x (SD: 14.2x)) for 435
 canids and representing 287 dogs of known pure breed ancestry, 6 dogs of
 unknown ancestry, 100 worldwide indigenous or village dogs, 36 wolves, and
 6 other wild canids provided by Elaine Ostrander. 440 dogs underwent
 genotyping on the Axiom Canine Genotyping Array Set A & B for
 1,268,920 variant call sites (1,267,416 SNPs and 1,504 indels), and had
 genotyped imputed using the same method. For each sample processed by
 low-pass sequencing or genotyping array with imputation, genotypes with
 genotype probability below 70% were removed. Then, all VCFs were merged by
 BCFtools and converted to a PLINK data set. SNPs below a minor allele
 frequency of 2% and missing in over 20% of individuals were filtered out.
 Only biallelic SNPs with extreme deviation from Hardy-Weinberg
 equilibrium, given p-values below 1e-20 in the exact test with mid-p
 adjustment and at observed/expected heterozygosity ratios under 0.25 or
 above 1.0, were excluded. After filtering data, 8,518,951 SNPs and 2,155
 dogs remained with a total genotyping rate of 97.5%. Owner-reported sexes
 were encoded in the sample information file, confirmed by relative
 X-chromosome coverage for sequencing data and the autosomal genotypes of X
 for genotyping data; in total, 1084 males and 1071 females. Variant IDs
 were assigned to include chromosome, position, reference allele, and
 alternate allele. <strong>MuttMix
 Data. </strong>In order to assess perceptions of breed ancestry in
 mixed-breed dogs by non-owner observers, we designed a survey hosted at
 https://muttmix.org by which participants guess the three breeds detected
 at the largest percentage in each dog. Images and videos were collected
 from the owners of 30 mixed-breed dogs and one undeclared purebred dog
 with ancestry assignments. In addition to visual aids, participants were
 provided with each dog’s size relative to an average person and other
 physical descriptors such as coat texture or markings. Participants
 indicated whether they belong to the general public or are a dog
 professional and/or breeder. Participants were provided with 59 breed
 options to select as well as a “no choice” option for the third breed
 slot. Dogs were displayed in random order to participants. Participants
 were permitted to exit the survey at any time, return later, or leave the
 survey incomplete but could not skip dogs. The survey launched on April
 16th, 2018 and closed on June 16th, 2018, collecting responses from 26,639
 people over a two-month period. For genetic breed ancestry, any call below
 5% was removed before analysis against survey data, and only breeds
 offered as survey options were examined.