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Patterns of gene flow in Eurasia do not explain LD decay in Central Asia Gene flow clearly occurs in , with population structure exhibiting isolation by distance everywhere, and admixture with European dogs in particular regions. Using f3 admixture statistics, we find that indeed all Old World populations geographically intermediate between two other populations appear to be genetically intermediate as well, consistent with this model of bidirectional gene flow (Table S1). As Central Asia is a population intermediate between regions previously implicated in genetic theories of origins (East Asia and Middle East / ), we used ms simulations 1 (Table S2) to examine the effect of gene flow on central and peripheral populations to ensure that the intermediate position of Central Asia within Eurasia was not driving a spurious signature of a domestication origin in the LD decay data. We explored two alternate models (Fig S1). In the first, dogs arise in a single population; this population splits as dogs move westward (serial founder model). The non-founder populations each experience a bottleneck as they split off. Gene flow then occurs between the centrally located population (Population 2) and both the founder population (Population 1) and the most diverged population (Population 3). This is the pattern we would expect in Eurasia if dogs were from South East Asia and then had spread west (or were from Europe or the Middle East, and spread east). In the second model, dogs originate in a central population, two populations branch off from the central populations and after going through a bottleneck both the Eastern and Western population experience gene flow with the central population. This is the model we would expect if dogs originated in Central Asia and spread in both directions. Under various levels of migration, in the first model Population 2 never exhibited lower LD than the founder population (Fig S2). As migration rates increased populations became more similar in LD curve. For model 2 the founding population was also the population with lowest LD. This is consistent with the interpretation that dogs arose in the Central Asia and spread outward, but not consistent with dogs arising in either East Asia or Europe / Middle East. More complicated patterns of admixture may influence patterns of LD in more complex ways. Perhaps the most likely way for LD to be reduced in a region (apart from being a domestication origin) would be substantial ancient admixture from an archaic population. While there is evidence of localized admixture with wolves in our dataset (Fig S3) and previously published datasets [14], we did not see any D tests where Central Asian dogs were outliers, indicating outsized gene flow from another population. East Asian dogs showed clear evidence of admixture with Chinese wolves, and all other dog populations showed evidence of admixture with Middle Eastern wolves. We note that Freedman et al 2014 demonstrated that admixture with Middle Eastern wolves was bidirectional, although TreeMix only identified admixture from Middle Eastern wolves into dogs in our dataset (Fig 4). We believe the lack of a reciprocal admixture edge biases the TreeMix topology, artificially putting Middle Eastern wolves as the nearest neighbor to dogs. Other TreeMix models run with different numbers of admixture edges are inconsistent about the grouping of Middle Eastern wolves with dogs. In some models, Chinese wolves are closest (but no admixture edge is seen between Chinese wolves and dogs despite highly significant D-tests supporting such admixture) and in others wolves are monophyletic. Thus, while we believe admixture edges shown in Figure 4 reflect real genetic patterns, some admixture events are not robustly detected by TreeMix, leading to inconsistent topologies at the most basal branches of dogs and wolves.

Table S1: Significant F3 tests. We tested all combinations of village dog populations from: Afghanistan, Africa, Europe, India, Middle East, Mongolia, Nepal, and Vietnam and we report the significant results. Source1 Source2 Target f3 Z Lower Upper p-value Europe India Middle East -0.00919 -21.63 0.608 0.818 4.69E-104 Europe Vietnam Mongolia -0.0160 -21.062 0.489 0.818 8.88E-99 Middle East Vietnam Mongolia -0.0130 -20.119 0.623 0.772 2.52E-90 Vietnam India Nepal -0.0124 -16.499 0.257 0.418 1.87E-61 Vietnam Africa Nepal -0.0133 -16.192 0.303 0.58 2.87E-59 Middle East Vietnam Nepal -0.0115 -15.497 0.531 0.767 1.82E-54 Vietnam Africa Mongolia -0.0111 -13.385 0.299 0.553 3.70E-41 Europe India Afghanistan -0.00849 -13.07 0.399 0.665 2.44E-39 Vietnam Afghanistan Mongolia -0.00780 -11.134 0.191 0.273 4.29E-29 Europe Vietnam Nepal -0.0102 -10.896 0.374 0.818 6.02E-28 Vietnam Afghanistan Nepal -0.00787 -10.392 0.196 0.362 1.35E-25 Europe Vietnam Afghanistan -0.00607 -7.276 0.614 0.872 1.72E-13 Middle East Vietnam Afghanistan -0.00441 -6.266 0.812 0.955 1.85E-10 Europe Nepal Afghanistan -0.00376 -6.046 0.383 0.711 7.42E-10 Europe Nepal Middle East -0.00264 -6.035 0.598 0.856 7.95E-10 India Mongolia Nepal -0.00310 -5.439 0.254 0.59 2.68E-08 Europe Africa Middle East -0.00135 -4.247 0.26 0.558 1.08E-05 Africa Mongolia Middle East -0.00145 -4.081 0.542 0.072 2.24E-05 Vietnam Africa Afghanistan -0.00322 -3.665 0.133 0.403 0.000124 Europe Vietnam Middle East -0.00142 -2.231 0.749 0.927 0.0128

1Hudson, R. R.(2002) Generating samples under a Wright-Fisher neutral model. Bioinformatics 18:337-8

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Table S2: Code for reported ms simulations

Migration Rate Model 1 Model 2 2.5 x 10-6 ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n -n 2 1 -n 3 1 -m 2 1 0.2 -m 2 3 0.2 -m 1 2 0.2 -m 3 2 1 -n 3 1 -m 2 1 0.2 -m 1 3 0.2 -m 1 2 0.2 -m 3 1 2 0.2 -eM 0.01 0 -en 0.025 3 0.01 -ej 0.0251 3 2 -en 0.2 -eM 0.04 0 -en 0.049 3 0.01 -en 0.0495 2 0.01 -ej 0.0495 2 0.01 -ej 0.05 2 1 0.0497 3 1 -ej 0.05 2 1 1.25 x 10-5 ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n 2 1 -n 3 1 -m 2 1 1 -m 2 3 1 -m 1 2 1 -m 3 2 1 -eM 2 1 -n 3 1 -m 2 1 1 -m 1 3 1 -m 1 2 1 -m 3 1 1 -eM 0.01 0 -en 0.025 3 0.01 -ej 0.0251 3 2 -en 0.0495 2 0.04 0 -en 0.049 3 0.01 -en 0.0495 2 0.01 -ej 0.0497 0.01 -ej 0.05 2 1 3 1 -ej 0.05 2 1 2.5 x 10-5 ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n 2 1 -n 3 1 -m 2 1 2 -m 2 3 2 -m 1 2 2 -m 3 2 2 -eM 2 1 -n 3 1 -m 2 1 2 -m 1 3 2 -m 1 2 2 -m 3 1 2 -eM 0.01 0 -en 0.025 3 0.01 -ej 0.0251 3 2 -en 0.0495 2 0.04 0 -en 0.049 3 0.01 -en 0.0495 2 0.01 -ej 0.0497 0.01 -ej 0.05 2 1 3 1 -ej 0.05 2 1 1 x 10-4 ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n 2 1 -n 3 1 -m 2 1 8 -m 2 3 8 -m 1 2 8 -m 3 2 8 -eM 2 1 -n 3 1 -m 2 1 8 -m 1 3 8 -m 1 2 8 -m 3 1 8 -eM 0.01 0 -en 0.025 3 0.01 -ej 0.0251 3 2 -en 0.0495 2 0.04 0 -en 0.049 3 0.01 -en 0.0495 2 0.01 -ej 0.0497 0.01 -ej 0.05 2 1 3 1 -ej 0.05 2 1 0.001 ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n 2 1 -n 3 1 -m 2 1 80 -m 2 3 80 -m 1 2 80 -m 3 2 80 2 1 -n 3 1 -m 2 1 80 -m 1 3 80 -m 1 2 80 -m 3 1 -eM 0.01 0 -en 0.025 3 0.01 -ej 0.0251 3 2 -en 0.0495 80 -eM 0.04 0 -en 0.049 3 0.01 -en 0.0495 2 0.01 -ej 2 0.01 -ej 0.05 2 1 0.0497 3 1 -ej 0.05 2 1 0.05 ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n ms 36 100 -t 80 -r 80 100000 -I 3 12 12 12 -n 1 1 -n 2 1 -n 3 1 -m 2 1 4000 -m 2 3 4000 -m 1 2 4000 -m 2 1 -n 3 1 -m 2 1 4000 -m 1 3 4000 -m 1 2 4000 -m 3 2 4000 -eM 0.01 0 -en 0.025 3 0.01 -ej 0.0251 3 2 3 1 4000 -eM 0.04 0 -en 0.049 3 0.01 -en 0.0495 2 -en 0.0495 2 0.01 -ej 0.05 2 1 0.01 -ej 0.0497 3 1 -ej 0.05 2 1

Model 1- East Asian Origin Model 2- Central Asian Origin

Pop3 Pop1 Pop2 Pop1 Pop2 Pop3

Fig. S1: Models for MS simulations.

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Model 1 Model 2 0.7 Migration 0.6 0.5 2.5x10-6 0.4 0.3 0.7 0.6 0.5 1.25x10-5 0.4 0.3 0.2 0.6 0.5 2.5x10-5 0.4 ) 2 0.3 0.7 mean LD (r 0.6 0.5 1x10-4 0.4 0.3 0.2 0.6

0.001 0.5 0.4 0.3 0.7 0.6

0.05 0.5 0.4 0.3 0.2 5 10 20 50 100 5 10 20 50 100 Inter−SNP distance (kb) Fig. S2: LD curves for two contrasting models of dog history featuring various migration rates (percentage of sink population made up of source population per generation). In all cases the red population is the founding population.

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Coyote Dog China Middle Coyote Dog China Middle Wolf East Wolf East Wolf Wolf Nepal French Polynesia Fiji Mongolia Bosnia Turkey Croatia Solomon Islands West Africa Vietnam Uganda Qatar Puerto Rico Portugal PNG Peru Namibia Mexico Liberia Lebanon Kinshasa Katanga india Egypt DR Colombia Central America Brazil Borneo Boende Afghanistan

−0.04 −0.02 0.00 0.02 0.04 Fig. S3: D tests for all village dog populations in relation to Middle Eastern and Chinese wolves. Points are colored by region.

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PC8 (3.04%) Egypt PC10 (2.90%) −0.1 −0.10 −0.2 −0.20 −0.2 −0.1 0.0 0.1 0.2 −0.2 −0.1 0.0 0.1 0.2 0.3 PC7 (3.52%) PC9 (2.99%)

Fig. S4: Principal component analysis for village dogs (PC3–PC10). Village dogs are represented by colored dots while breed dogs, which have been projected onto the PCA space, are represented by open black circles.

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Toy Fox Terrier Doberman Pinscher Weimaraner Saint Bernard 5 Ha.8 Pug Ha.3 Belgian Breeds Collie Great Dane Bernese Mountain Dog Hc.10 Whippet 2 Border Terrier Ha.4 2 Ha.7 Ha.2 Newfoundland H1a.1 2 Hc.11 Norfolk Terrier Norwich Terrier Ha.5 Ha.6 Maltese Ha.1 2 American Dog Yorkshire Terrier Havanese 3 Bedlington Terrier Silky Terrier Hc.9 Great Pyrenees H1a.2 3 H1a.3 5 German ShepherdH1a.15 H1a.12 H1a.7 2 H1a.11 H1a.10 Cairn Terrier 5 Cardigan Welsh Corgi 3 H3 Cocker Spaniel Viszla English Cocker Spaniel H1a.4 Hc.6 H1a.14 H1a.13 Brittany Pembroke Welsh Corgi Pekingese 4 Hc.2 Cavalier King Charles Spaniel H1a.16 Miniature Poodle H1a.8 Puli Hc.1 Soft Coated Wheaten Terrier 4 H1a.17 H1a.6 6 Leonberger 6 H1a.18 H1a.20 Otterhound H1a.9 Masti 6 H1a.5 Greyhound Hc.12 6 Australian Cattle Dog 8 Frise Hc.3 6 English Setter H1a.19 Giant Schnauzer 2 4 Golden Retriever Greater Swiss Mountain Dog Hc.4 Irish Wolfhound Old English Sheepdog Europe HG1 (Ding et al.) Scottish Terrier HG3 (Ding et al.) East Asia Hc.7 West Highland White Terrier SW Asia Hb.3 Hc.5 Africa 2 Arctic Hc.8 India H5a H5b Australasia 8 New Guinea Singing Dog Mix 6 H27 America Hb.1 Central Asia Afghanistan

Fig. S5: Minimum spanning network for Y-haplogroup HG1-3. Circle size is proportional to haplotype frequency and line length is determined by number of mutations separating haplotypes (indicated by numerals when > 1 mutation). Previously reported haplotypes have maintained their published names. Some haplotypes are particularly common in individual breeds. Breed name is printed next to a haplotype if we had at least 5 individuals from that breed and more than 90% of those individuals carried the haplotype. HG1 and HG3 were separate haplogroups in Ding et al. [10]. Red dotted lines connect haplotypes previously grouped in HG3 and green dotted lines connect haplotypes previously grouped in HG1.

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BULM A256 A1.1 A267 A1.2 A317 A319 NSDT A365 2 WHIP 2 A33 PGWD A367 A224 A19 A342 A374 A266 A270 A299 A262 A326 A306 GORD A303 A308 A315 A254 A17 A16/17/ A261 A361 99/100 A369 A20 A316 A304 A377 2 A244 A368 A18b A296 CKCS A30 A263 A324 A318 A243 A18/19/20/21/27/36/94/109 A340 A230 A370 A268 A313 KEES A229 A372 A231 A357 A289 2 A1.3 A291 A363 A253 A240 A18 BRTE PUG A310 A293 MSCH A332 A338 A330 A339 A290 A288 A292 GSMD 2 A356 A362 2 A51/93 A359 AFGH A331 2 A336 A1.4 A11b A41 BORZ 3 A278 A328 2 A360 A366 2 3 A312 A358 A334 A354 3 A337 2 2 A271 3 A353 A335 2 A311 A26a A350 A91/11 A378 A329 A347 A352 A351 SOFT A341 A349 3 A305 A355 3 A89 10 A255 A15 6 A346 A375 A364 A10 A11 A333 A325 A348 A298 A371 A344 A43 A11a A251 ROTT A297 Europe A49 WHPG East Asia CANE SW Asia A269 A247 Africa A1.3 A248 Arctic A250 India A249 Australasia A1.5 2 A252 Mix America A1.4 A1.2 Central Asia A1.1 All A1 Afghanistan

Fig. S6: Minimum spanning networks for haplogroup A1. A1 is the largest Mt haplogroup and we have subdivided it in the interest of readability. Circle size is proportional to haplotype frequency and line length is determined by number of mutations separating haplotypes (indicated by numerals when > 1 mutation). Previously reported haplotypes have maintained their published names. Novel haplotypes, or published haplotypes which did not follow the naming convention from Pang [8], have names larger than A200. Some haplotypes are particularly common in individual breeds. Breed name is printed next to a haplotype if we had at least 5 individuals from that breed and more than 80% (or 50% in italics) of those individuals carried the haplotype. The network in the bottom left corner indicates how the subhaplogroups fit together.

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A78 2

IRIW A158 BRIT GRPY 3 A286 A287VIZS A241 A227 A284 A34 A343 LEON A129 A285 A225 A314 A258 A228 2 5 3 A274 A234 3 A5 A1 2 A237 A235 A257 A154 A273 5 A25 A239 3 BELS A307 2 A236 A272 2 A242 A295 A226 A148 A232 TIBT A26b A238 A376 A277 2 A9b 2 A282 8 A321 A2b A233 A265 3 A322 5 2 A264 A279 2 2 A275 NMAS A294 A22 A246 2 2 A345 A260 3 4 BNMD 3 A283 5 A276 A74 A320 A280 A245 3 3 A281 A163 Europe A2a 3 East Asia A373 A259 SW Asia 4 Africa A309 A3 Arctic A2 India A149 Australasia A102 2 3 A301 Mix 2 2 A300 America 3 A327 Central Asia 3 Afghanistan 3 3

A302 Fig. S7: A minimum spanning network for Mt subhaplogroup A1.5. Circle size is proportional to haplotype frequency and line length is determined by number of mutations separating haplotypes (indicated by numerals when > 1 mutation). Previously reported haplotypes have maintained their published names. Novel haplotypes, or published haplotypes which did not follow the naming convention from Pang [8], have names larger than A200. Some haplotypes are particularly common in individual breeds. Breed name is printed next to a haplotype if we had at least 5 individuals from that breed and more than 80% (or 50% in italics) of those individuals carried the haplotype. Ancient American haplotypes are from Thalmann et al. [11]. Modern American haplotypes clustering with the ancient haplotypes are from a village dog in Puerto Rico, a village dog in the Dominican Republican, and several Alaskan Village .

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A2 A212 A3 A84 A222 A39 3 A220 A38 A213 A86/87 3 A85 4 /122 A44 3 3 4 A106 A97 4 4 2 A103 A217 A1192 A215 2 2 A125 4 2 2 A4 4 2 A9a 2 4 2 A218 2 2 A45/59 A209 3 3 5 A65 A219 2 3 A221 3 22 3 A73 A75 6 A114 A214 A55 A208 A105 B63 A216 A29b 5 A211 A210 A64 B67 B59 A207 A223 B1 SIBE A29a BICH TNSP B50 LHAS B6/8 A5 PEKI BASS 8 STZU B42 A141 RHRB B41 A116 B54 WEIM B53 B51 A204 B1d B28 3 6 2 2 OTTH B64 B52 B65 A200 GOLD 2 A130 3 A201 B68 A205 GREY B1/13 A136 POOD B40 2 2 3 B1b A202 B69 B55 A206 B57 A110 BELT A203 B56 3 B66 B48 B47 2 B38 B2 A8a CARD B46 B62 B45 B37 B36 CANA B1a 4 B32 B49 B58 B1c B44 B34 5 Europe 2 East Asia B39 SW Asia B35 B33 B61 B2a Africa B60 Arctic B43 B5/23 2 India 3 B22 Australasia HAVA 2 B24/29 Mix B2b B30 America Central Asia B9 Afghanistan B70

Fig. S8: Minimum spanning Mt haplotype networks for A and B haplogroups. Circle size is proportional to haplotype frequency and line length is determined by number of mutations separating haplotypes (indicated by numerals when > 1 mutation). Previously reported haplotypes have maintained their published names. Novel haplotypes, or published haplotypes which did not follow the naming convention from Pang et al [8], have names larger than A200 or B32. Some haplotypes are particularly common in individual breeds. Breed abbreviation is printed next to a haplotype if we had at least 5 individuals from that breed and more than 80% (or 50% in italics) of those individuals carried the haplotype. Ancient American haplotypes are from Thalmann et al. [11].

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Congo Congo Liberia Namibia Liberia Uganda Namibia Alaska Uganda Fiji Alaska French Polynesia Fiji Papua New Guinea French Polynesia Solomon Islands Papau New Guinea Brazil Colombia Dominican Republic Honduras Mexico Mexico Peru Peru Mongolia Mongolia Nepal Nepal Borneo Borneo China Vietnam Vietnam Croatia Portugal India India Egypt Afghanistan Lebanon Egypt Qatar Iran Turkey Lebanon Basenji Qatar Samoyed Turkey Basenji Tibetan Spaniel Alaskan Malamute Chinese Shar−Pei Samoyed Lhasa Apso Pekingese Akita Chinese Crested Pug Lhasa Apso Shih Tzu Pekingese Tibetan Terrier Pug Afghan Shih Tzu Chihuahua Tibetan Spaniel Xoloitzcuintli Afghan Hound Airedale Terrier Canaan Dog Chihuahua Basset Hound Peruvian Inca Orchid Beagle Airedale Terrier Bernese Mountain Dog Australian Shepherd Bichon Frise Basset Hound Bloodhound Beagle Border Collie Bernese Mountain Dog Border Terrier Bichon Frise Borzoi Border Collie Borzoi Boston Terrier Boston Terrier Bouvier Des Flandres Boxer Boxer English Bulldog Brittany French Bulldog Bull Terrier Bullmastiff English Bulldog Cairn Terrier French Bulldog Cavalier King Charles Spaniel Cairn Terrier Chesapeake Bay Retriever Cavalier King Charles Spaniel Cocker Spaniel Cocker Spaniel Collie Collie Dachshund Dachshund Doberman Pinscher Doberman Pinscher English Cocker Spaniel English Cocke Spaniel English Setter English Setter English Springer Spaniel English Springer Spaniel Fox Terrier Wire German Shepherd German Shorthaired Pointer Golden Retriever Golden Retriever Gordon Setter Gordon Setter Great Dane Great Dane Greater Swiss Mountain Dog Great Pyrenees Havanese Greater Swiss Mountain Dog Irish Setter Greyhound Irish Wolfhound Havanese Jack Russell Terrier Irish Setter Irish Wolfhound Labrador Retriever Jack Russell Terrier Leonberger Keeshond Maltese Labrador Retriever Mastiff Leonberger Miniature Pinscher Maltese Miniature Schnauzer Mastiff Miniature Pinscher Newfoundland Miniature Schnauzer Otterhound Newfoundland Papillon Old English Sheepdog Pembroke Welsh Corgi Otterhound Pomeranian Papillon Poodle Pembroke Welsh Corgi Toy Poodle Pomeranian Portuguese Water Dog Poodle Rhodesian Ridgeback Toy Poodle Rottweiler Rottweiler Saint Bernard Saint Bernard Scottish Terrier Scottish Terrier Shetland Sheepdog Shetland Sheepdog Vizsla Soft Coated Wheaten Terrier Weimaraner Staffordshire Bull Terrier West Highland White Terrier Vizsla Weimaraner Wirehaired Pointing Griffon West Highland White Terrier Yorkshire Terrier Wirehaired Pointing Griffon

Yorkshire Terrier

HG6 HG9 HG8 E

D HG23 A1 A2 A3 A4 A5 B1 B2

C1 C2 HG1-3 Fig. S9: Heat maps for haplogroups found within each population containing at least 10 dogs (at least 6 males). All Mt haplogroups (left) and Y haplogroups (right) are listed. Dark purple indicates that a group of dogs is fixed for a haplogroup while white indicates that the haplogroup is not found within that group of dogs. 10 www.pnas.org/cgi/doi/10.1073/pnas.0709640104 Footline Author

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Europe C1 C2 C24 East Asia C22 C25 C16 SW Asia 4 Africa C26 C17 Arctic C30 India C23 Oceania C31 C1 C21 America C15 C3/14 Mix BOVE Central Asia 2 Europe Wolf C19 SW Asia Wolf C28 C20 India Wolf C18 C3 East Asia Wolf C1/2 C27 America Wolf D D2 Ancient Europe Dog E38 E37 E5 C29 E4 E6 3 2 4 4 E39 5 E2 C12 E D1/3/8 W2 6 JAMA C5/12 C32 E35 2 E34 9 7 E3 C2 E33 4 7 C33 4 3 C7/10 2 E21 E20 3 E26 2 2 2 E2 E25 3 E24 2 5 E14 E22 4 E32 10 E11 W5 5 E28 E12 11 D1 D2 E36 19 2 11

E16 E13 D5 19 2 6 E17 E15 E23 3 2 E27 E19 E31 E9 D6

E18 3 3 4 E10 2 D4 E1 E30 E29 E7 E8 Fig. S10: Minimum spanning haplotype networks for C, D, and E haplogroups. Circle size is proportional to haplotype frequency and line length is determined by number of mutations separating haplotypes (indicated by numerals when > 1 mutation). Previously reported haplotypes have maintained their published names. Novel haplotypes, or published haplotypes which did not follow the naming convention from Pang et al. [8], have names larger than C15, or E1 (all D haplotypes have been previously reported). Some haplotypes are particularly common in individual breeds. Breed abbreviation is printed next to a haplotype if we had at least 5 individuals from that breed and more than 80% (or 50% in italics) of those individuals carried the haplotype. Ancient European wolf haplotypes are from Thalmann et al. [11].

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2

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16 America BreedAmerica Mexico Belize Honduras Costa Rica Panama Colombia Brazil Peru Republic Dominican Rico Puerto NGSD Palau PNG Islands Solomon Kadavu Viti Levu French Polynesia Arctic Breed Alaska Herding Hound Non-Sporting Sporting Working Portugal Croatia Bosnia Guinea Liberia FasoBurkina Ghana Namibia Uganda Sudan SW Asia Breed Egypt Lebanon Qatar East Asia Breed Vietnam Kinshasa Boende Katanga Mumbai Dehli Chennai Orissa Hazaribagh West Bengal Nepal Mongolia Terrier Toy Turkey Borneo Java Basenji Iraq Afghanistan Fiji DRC Indonesia

Arctic Europe Sub-Saharan Africa South West Asia India Central East Oceania Americas Asia Asia Fig. S11: ADMIXTURE analysis of village and purebred dogs at all K between 2 and 16. European components are in gray scale while regional components are in color. Each vertical line represents an individual, breeds are represented by a single individual with the exception of Basenjis, New Guinea Singing Dogs, and Carolina Dogs for which all unrelated individuals are included.

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A Europe

Eurasier Shar-Pei

Vietnam Carolina Dog Samoyed Akita Chow Chow Shiba Inu Belize Brazil Europe Asia Chihuahua B Colombia Chow Chow | Shar−Pei Costa Rica | Akita | Dominican Republic Shiba Inu Siberian Husky | Honduras Sledge Dog | Mexico Alaskan Malamute | Panama Alaskan Malamute Siberian Husky | Peru | Peruvian Inca Orchid Samoyed | Carolina Dog | Puerto Rico Puerto Rico Xoloitzcuintli | Greenland Sledge Dog Peru | English Bulldog Panama | Cocker Spaniel Mexico | Papillion Honduras | Dominican Republic | Costa Rica Alaska | Colombia | Brazil | Belize | Chihuahua | Peruvian Inca Orchid | Xoloitzcuintli | Papillon | Cocker Spaniel | English Bulldog |

−0.2 −0.1 0.0 0.1 0.2

Fig. S12: A. Principal component analysis of European, Vietnamese, and Alaskan village dogs with American dogs (and representative European and Asian breed dogs) projected onto the PCA space. B. Mean value for PC1 of breed and village populations. Error bars indicate two standard deviations from the mean.

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HG6 H15.9 HG8 H8.6 H15.10 2 9

2 H15.8 2

H15.11 H15.12 H15.7 H8.1

H15.3 3 2 2 H8.2

H15.4 H15.2 H8.7 3 H15.5 H15.1 2

H8.3 H15.6 Europe H8.4 East Asia SW Asia Africa H8.5 India Australasia Mix Afghanistan HG23 H10.3 America Central Asia H10.2

Hd.1 H10.1 Boxer

Hd.4 3 Hd.2 Afghan Hound H7 Bull Terrier French Bulldog Wire Fox Terrier

Fig. S13: Minimum spanning networks for the smaller Y haplotypes. Circle size is proportional to haplotype frequency and line length is determined by number of mutations separating haplotypes (indicated by numerals when > 1 mutation). Previously reported haplotypes have maintained their published names. Some haplotypes are particularly common in individual breeds. Breed name is printed next to a haplotype if we had at least 5 individuals from that breed and more than 90% of those individuals carried the haplotype.

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Wolf Basenji Canaan Dog Saluki Afghan Hound Chinese Shar−Pei Sighthounds Eurasier Shiba Inu NGSD Mountain Dogs Chow Chow Samoyed Akita Terriers Siberian Husky Alaskan Malamute East Asia Greenland Sledge Dog Finnish Tibetan Terrier South West Asia/Africa Tibetan Spaniel Pekingese Herding Shih Tzu Lhasa Apso Masti Elkhound Pug Arctic Keeshond Pomeranian Sporting Chinese Crested Bull Terrier Chihuahua Miniature Schnauzer Papillon Asian Toy Poodle Toy Poodle Scenthounds Miniature Poodle Maltese Havanese Bichon Frise Xoloitzcuintli Great Pyrenees Peruvian Inca Orchid Vizsla Wirehaired Pointing Griffon German Shorthaired Pointer English Setter AKC Groupings Gordon Setter Irish Setter Herding Brittany Weimaraner Hound Cavalier King Charles Spaniel English Springer Spaniel Non-Sporting English Cocker Spaniel Sporting Dalmatian Portuguese Water Dog Terrier Miniature Dachshund Dachshund Toy Basset Hound Working Beagle Otterhound Bloodhound Miniature Pinscher Italian Greyhound Borzoi Giant Schnauzer Belgian MalinoisDoberman Pinscher Belgian Sheepdog Belgian Tervuren Migration German Shepherd Dog Nova Scotia Duck Tolling Retriever weight Australian Cattle Dog Australian Shepherd Border CollieShetland Sheepdog 0.5 Pembroke Welsh Corgi Norfolk Terrier Scottish Terrier Cairn Terrier West Highland White Terrier Jack Russell Terrier Wire Fox Terrier Border Terrier Yorkshire Terrier Silky Terrier Labrador Retriever Flat−Coated Retriever Golden Retriever Chesapeake Bay Retriever Old English Sheepdog Bernese Mountain Dog Greater Swiss Mountain Dog Airedale Terrier Bouvier Des Flandres Rottweiler Saint Bernard Leonberger Newfoundland 0 Rhodesian Ridgeback Irish Wolfhound Whippet Greyhound Great Dane Soft Coated Wheaten Terrier Cane Corso Neapolitan Mastiff French Bulldog 10 s.e. American Staffordshire Terrier Staffordshire Bull Terrier Boxer English Bulldog Boston Terrier Bull Terrier Mastiff Bullmastiff

0.00 0.05 0.10 0.15 0.20 Drift parameter Fig. S14: Breeds form genetic clusters primarily according to geography in TreeMix (left) and ADMIXTURE (right). In both analyses, four basal clusters correspond to the Middle East, Africa, East Asia, and the Arctic with the fifth (European) cluster containing distinct subgroups corresponding to Sight , Scent Hounds, Sporting Dogs, Retrievers, Terriers, Mastiffs, and Herding Dogs, although many AKC groups (e.g. Toy, Working and Non-sporting) are spread throughout the tree. A few non-European breeds (Rhodesian Ridgeback, Chihuahua, Xoloitzcuintli and Peruvian Inca Orchid) group with European dogs, having been reconstituted over time from European stock. Four Asian breeds—Tibetan Spaniel, Lhasa Apso, Pekingese and Shih Tzu—also lie within the European cluster but retain between 18% and 44% Asian ancestry depending on breed (Fig. S15), consistent with their origins in East Asia followed by introgression from European dogs during modern times. Other admixture edges are consistent with known origins of modern breeds—Cane Corso as a mix of Rottweiler and Mastiff, Chinooks as a mix of German Shepherds and other dogs. The remaining admixture edges suggest gene flow between more ancient populations.

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A Borneo

Bichon Frise Papillon Maltese Europe Pomeranian Chinese Crested Pug Havanese

Shiba Inu Akita Pekingese Shar-pei Tibetan Terrier Shih Tzu Lhasa Apso

Chow Chow Tibetan Spaniel Vietnam B Europe Asia

Chow Chow | Shar−pei | Akita | Mongolia Shiba Inu | Tibetan Spaniel | Lhasa Apso | Japanese Chin | | Nepal Pekingese Shih Tzu | Tibetan Terrier | Chinese Crested | Pomeranian | Pug | Maltese | Havanese | Bichon Frise | Papillon | −0.15 −0.10 −0.05 0.00 0.05 0.10 0.15 PC1 Fig. S15: A. Principal component analysis of European, Vietnamese, Bornese, Mongolian, and Nepalese village dogs with toy dogs (and representative Asian breed dogs) projected onto the PCA space. B. Mean value for PC1 of breed and village populations. Error bars indicate two standard deviations from the mean.

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12 Bosnia Croatia Portugal Vietnam Breeds Alaska Breeds Carolina Belize Brazil Colombia CR DR Honduras Mexico Panama Peru PR

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12 Bosnia Croatia Portugal Basenji Boende Katanga Kinshasa BF Ghana Guinea Liberia Namibia Sudan Uganda

Fig. S16: Regional ADMIXTURE analyses. Top: New World Dogs, including Carolina dogs, American and Arctic breeds (Chihuahua, Peruvian Inca Orchid, Xoloitzcuintli, Greenland Sledge Dog, Alaskan Malamute, Siberian Husky, Eurasier, and Samoyed) with one individual per breed, and European and East Asian village dogs as outgroups. PR is Puerto Rico, DR is Dominican Republic, and CR is Costa Rica. Middle: Village dogs from Oceania and Island Southeast Asia, with select East Asian and European dogs. BB stands for Bora Bora. The breeds referenced here are Staffordshire Bull Terrier and Mastiff. Bottom: Village dogs from Africa with European village dogs as an out group. BF stands for Burkina Faso.

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Fig. S17: Regional ADMIXTURE analyses, with two subsets of Eurasian village dogs–spanning the entire continent (top) and focused on Europe and South West Asia(bottom). In both cases an Afghan Hound and a Saluki are included as breeds.).

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A Europe Arctic B Africa America 0.8

0.8 Australasia India Middle East

Afghanistan ) Vietnam 2 Central Asia 0.6 Wolf mean LD (r 0.4 0.7 ) 2 0.2

mean LD (r 2 5 10 20 50 100 200 Ln Inter−SNP distance (kb)

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0.4 0.002 0.005 0.01 0.02 0.05 0.1 0.2 Inter−SNP distance (cM)

2 4 6 8 Inter−SNP distance (cM)

Fig. S18: LD decay for village dog populations worldwide. (A) LD at small inter-SNP distances. Dark lines represent means and lighter shading represent 1 s.e. interval calculated from 100 replicates. For each replicate, N = 6 individuals were selected randomly. This is a subsection of Fig 5 enlarged to make the 1 s.e. intervals visible. (B) LD curves for the same populations calculated in the same way as in A but with inter-SNP distance measured in kb. (C) LD curves calculated in the same way as A but for N = 20, a smaller number of populations were considered based which populations contained more than 20 individuals. Although the mean LD is lower, the relative ordering of populations stays the same.

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Table S3: Shared vs. regional haplotypes in 651 village dogs

Mt Y region population both local both local Burkina Faso 0 2 0 1 Congo 18 15 16 6 Ghana 4 1 1 1 Guinea 1 0 1 0 Africa Liberia 10 11 15 1 Namibia 13 2 6 5 Nigeria 0 1 - - Sudan 0 1 - - Uganda 7 5 9 2 Belize 4 0 3 0 Brazil 11 2 4 0 Colombia 9 0 6 0 Costa Rica 7 1 2 0 Dominican Republic 10 2 2 0 America Honduras 8 0 6 0 Mexico 15 0 10 0 Panama 2 0 - - Peru 83 8 61 0 Puerto Rico 7 2 5 0 Arctic Alaska 7 4 4 2 Fiji 29 0 14 0 French Polynesia 35 1 15 0 Oceania Palau 1 0 - - Papua New Guinea 16 4 9 6 Solomon Island 14 1 3 0 Mongolia 5 9 1 10 Central Asia Nepal 6 6 2 4 Borneo 2 7 0 6 China 29 51 - - East Asia Java 2 0 2 0 Thailand 4 3 - - Vietnam 0 20 6 10 Bosnia 3 0 3 0 Europe Croatia 6 0 6 0 Portugal 6 3 5 0 India India 15 20 2 25 Afghanistan 8 5 1 2 Egypt 7 8 2 6 Iran 12 1 - - South West Asia Iraq 1 0 1 0 Lebanon 9 7 9 6 Qatar 5 4 2 5 Turkey 11 2 9 1

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Table S4: Mt haplotype diversity in novel and combined Mt data sets Semi-Custom CanineHD Array Combined Population N H HT(HG) HT(SD) N H HT(HG) HT(SD) Africa Breed 30 0.93 15(1) 11.06(3.36) 33 0.93 15(1) 11.92(1.10) Africa Village 91 0.96 41(4) 14.05(3.81) 91 0.96 41(4) 14.91(1.66) America Breed 46 0.92 20(6) 12.06(1.53) 48 0.93 21(6) 12.38(1.67) America Village 171 0.94 49(7) 13.45(1.92) 171 0.94 49(7) 13.82(1.66) Arctic Breed 39 0.84 11(4) 8.77(1.07) 42 0.83 12(4) 8.92(1.24) Arctic Village 11 0.82 5(2) - 11 0.82 5(2) - Oceania Breed 5 0 1(1) - 6 0.33 2(1) - Oceania Village 101 0.93 29(5) 12.44(1.64) 105 0.93 29(5) 12.48(1.79) Cental Asia Village 25 0.95 16(5) 13.83(0.95) 26 0.95 17(5) 13.92(1.04) East Asia Breed 151 0.85 32(10) 10.68(1.76) 166 0.86 38(10) 11.67(2.05) East Asia Village 31 0.96 19(5) 14.36(1.42) 118 0.99 74(10) 17.95(1.11) Europe Breed 3414 0.95 151(7) 13.99(1.82) 3534 0.95 164(8) 14.20(1.92) Europe Village 18 0.96 15(3) - 18 0.96 15(3) - India Village 31 0.98 23(7) 16.41(1.12) 35 0.97 24(7) 15.44(1.44) South West Asia Breed 31 0.85 10(4) 8.60(0.88) 37 0.90 16(4) 11.00(1.36) South West Asia Village 67 0.97 34(6) 15.26(1.47) 80 0.96 36(6) 14.74(1.67) Sample size (N) and haplotype heterozygosity (H) by region. HT(HG) is the number of unique haplotypes (haplogroups) and HT(SD) is the average number (standard deviation) of haplotypes from a sub-sample of 20 dogs.

Table S5: Y haplotype diversity in breed dogs (top) and village dogs (bottom) Population N H HT(HG) HT(SD) Africa 10 0.51 3(3) - America 26 0.67 7(1) 5.91(0.78) Arctic 15 0.79 5(1) - East Asia 83 0.88 12(3) 9.17(1.35) Europe 1708 0.91 34(3) 10.65(1.64) South West Asia 14 0.59 5(3) - Africa 64 0.93 16(5) 11.58(1.49) America 99 0.86 15(2) 8.09(1.33) Arctic 6 0.87 4(1) - Oceania 47 0.94 19(3) 12.36(1.34) Central Asia 17 0.84 6(4) - East Asia 24 0.92 13(2) 11.68(0.85) Europe 14 0.93 9(1) India 27 0.89 12(4) 10.19(1.01) South West Asia 46 0.94 20(4) 12.41(1.38) Sample size (N) and haplotype heterozygosity (H) by region. HT(HG) is the number of unique haplotypes (haplogroups) and HT(SD) is the average number (standard deviation) of haplotypes from a sub-sample of 20 dogs.

Table S6: Ancestry percentages for African and island populations estimated by F3 tests

Source population 1 Source population 2 Target population F3 Z score Ancestry proportion from source 1 Europe Vietnam French Polynesia 0.01 14.82 0.958-0.991 Europe Borneo French Polynesia 0.01 13.02 0.958-0.981 Europe Vietnam Fiji 0.01 15.34 0.952-0.966 Europe Borneo Fiji 0.01 12.57 0.951-0.959 Europe Vietnam Solomon Islands -0.00 -2.28 0.785-0.855 Europe Borneo Solomon Islands -0.01 -6.48 0.783-0.863 Europe Vietnam PNG -0.02 -32.26 0.680-0.715 Europe Borneo PNG -0.02 -30.68 0.678-0.784 Europe Basenji Katanga -0.01 -5.02 0.884-0.856 Europe Basenji Kinshasa -0.03 -27.66 0.749-0.730 Europe Basenji Uganda -0.03 -40.38 0.580-0.638 Europe Basenji Namibia -0.03 -32.83 0.525-0.609 Europe Basenji Liberia -0.03 -39.95 0.522-0.599 Europe Basenji Boende -0.031 -33.72 0.394-0.355

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i i i i “SupplementalFigures˙v3” — 2015/10/1 — 11:53 — page 22 — #22 i i between American populations st F Table S7: Alaska ArcB Bos Cro EAB EurB Por Vie Mon AmB Car Mex Hon CR Col Bra Peru DR Arctic breedBosniaCroatiaEast 0.02 Asia breedEurope breedPortugal 0.04 0.08Vietnam 0.07 0.05 0.03Mongolia 0.06 America breed 0.02 0.06 0.03Carolina 0.07 Dog 0.02 0.00 0.00Mexico 0.11 0.09 0.05Honduras 0.07 0.00 0.06Costa 0.09 0.06 Rica 0.01 0.03 0.04Colombia 0.15 0.00 0.00 0.05Brazil 0.05 0.15 0.01 0.06 0.03 0.07 0.02Peru 0.04 0.07 0.06 0.02Dominican 0.02 0.00 Rep 0.06 0.02 0.07 0.07Puerto Rico 0.13 0.00 0.02 0.06 0.01 0.06 0.04 0.02 0.15 0.07 0.02 0.01 0.00 0.00 0.01 0.07 0.05 0.07 0.14 0.00 0.01 0.03 0.06 0.02 0.03 0.08 0.06 0.07 0.01 0.06 0.01 0.02 0.13 0.00 0.00 0.06 0.01 0.01 0.04 0.02 0.04 0.00 0.00 0.01 0.01 0.03 0.00 0.00 0.00 0.04 0.01 0.13 0.15 0.01 0.03 0.00 0.00 0.14 0.01 0.04 0.05 0.02 0.03 0.00 0.01 0.14 0.04 0.01 0.02 0.00 0.14 0.00 0.00 0.04 0.01 0.02 0.02 0.00 0.04 0.14 0.01 0.02 0.02 0.01 0.13 0.04 0.02 0.13 0.00 0.02 0.04 0.02 0.04 0.02 0.01 0.00 0.02 0.00 0.02 0.01 0.00 0.02 0.01 0.00 0.01 0.01 0.00 0.01 0.01 0.00 0.01 0.01 0.00 0.01 0.00 0.00 0.01 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00

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i i i i “SupplementalFigures˙v3” — 2015/10/1 — 11:53 — page 23 — #23 i i between African populations st between Pacific Island populations F st F Table S9: Table S8: Basenji Boende Bosnia Croatia Egypt Europe Breeds Ghana Katanga Kinshasa Liberia Namibia Portugal Kadavu Europe Huahine Moorea Raiatea PNG NGSD Borneo Vietnam Hiva Oa Solomon Islands Bora Bora BoendeBosniaCroatiaEgyptEurope Breeds 0.06 Ghana 0.21Katanga 0.17 0.21KinshasaLiberia 0.13 0.09 0.07 0.08Namibia 0.06Portugal 0.17 0.06 0.00 0.14Uganda 0.00 0.04 0.06 0.06 0.08 0.00 0.09 0.04 0.20 0.08 0.02 0.05 0.05 0.03 0.10 0.03 0.02 0.08 0.08 0.01 0.05 0.04 0.06 0.01 0.01 0.06 0.05 0.05 0.05 0.05 0.04 0.00 0.04 0.05 0.02 0.04 0.01 0.05 0.00 0.04 0.05 0.04 0.07 0.00 0.05 0.03 0.02 0.04 0.01 0.08 0.04 0.04 0.04 0.02 0.03 0.03 0.02 0.02 0.02 0.03 0.05 0.02 0.05 0.03 0.04 EuropeHuahineMooreaRaiateaPNGNGSD 0.04 0.04BorenoVietnam 0.04Hiva 0.04 0.01 OaSolomon Islands 0.01Bora 0.04 Bora 0.01 0.39Viti 0.04 0.17 Levu 0.16 0.00 0.03 0.14 0.00 0.04 0.03 0.09 0.14 0.04 0.02 0.41 0.00 0.02 0.02 0.03 0.16 0.15 0.01 0.02 0.46 0.01 0.02 0.02 0.17 0.15 0.00 0.02 0.44 0.01 0.02 0.03 0.17 0.15 0.00 0.29 0.01 0.01 0.10 0.01 0.08 0.00 0.32 0.32 0.03 0.26 0.02 0.02 0.39 0.12 0.05 0.02 0.46 0.17 0.11 0.37 0.17 0.15 0.16 0.032 0.15 0.14 0.01 0.02 0.03 0.03 0.02

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i i i i “SupplementalFigures˙v3” — 2015/10/1 — 11:53 — page 24 — #24 i i o Tur n Qatar SWAB m Por l Nepal Ori k Mum j Mon i Leb h between Asian populations Egypt EB st F g Table S10: Dehli EAB f Cro e Che d Bos c Ben b Bas a Vie Portugal South West Asian Breed Europe Breed Croatia Mumbai Vietnam East Asia Breed Bosnia Turkey Chennai Mongolia Bengal Basenji Lebanon Orissa b c i BasBenBos 0.25 Che 0.13Cro 0.15 0.17 Dehli 0.14 0.21EAB 0.15 0.16 0.12Egypt 0.13 0.21 0.06 0.03EB 0.16 0.14Leb 0.12 0.13 0.08 0.03 0.13Mon 0.00 0.13 0.07 0.05Mum 0.07 0.13 0.17 0.07 Nepal 0.08 0.02 0.01 0.16 0.06 0.13Ori 0.08 0.18 0.07 0.05 0.04 Por 0.16 0.08 0.05 0.07 0.00 0.16 0.02Qatar 0.04 0.02 0.15 0.05SWAB 0.05 0.05 0.04 0.15 0.03 0.13 0.17 0.05 0.05Tur 0.03 0.14 0.00 0.05 0.20 0.06 0.16Afg 0.01 0.01 0.01 0.18 0.05 a 0.04 0.03 0.12 0.04 0.08 0.13 0.13 0.05 0.03 0.09 0.11 0.03 0.01 0.05 0.17 0.03 0.03 0.02 0.00 0.02 0.03 0.16 0.08 0.09 0.02 0.05d 0.02 0.05 0.12 0.05 0.03 0.06e 0.03 0.00 0.01 0.03 0.02 0.05 0.03 0.04f 0.03 0.04 0.01 0.05 0.06 0.03 0.04g 0.04 0.03 0.08 0.04 0.03 0.00 0.03h 0.03 0.03 0.05 0.03 0.03 0.03 0.07 0.03 0.04 0.05 0.03j 0.02 0.04 0.07 0.04 0.02 0.02 0.00 0.02 0.09 0.02 0.01 0.02 0.01 0.04 0.03 0.08 0.02 0.03 0.05 0.03 0.01 0.04 0.03 0.02 0.00 0.05 0.03 0.01 0.04 0.05 0.03 0.06 0.04 0.02 0.04 0.03 0.12 0.08 0.02 0.09 0.04 0.03 0.04 0.02 0.10 0.01 0.07 0.01 0.03 0.01 0.01 0.02 0.02 0.01 k l m n o

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Table S11: Sampling locations for village dogs

region country location Nmal Nfem notes Africa Guinea Kankan 1 0 US import Africa South Sudan Sudan 0 1 US import Africa Nigeria unknown 1 0 sampled in Monrovia Africa Namibia northern 10 4 see Boyko et al 2009 Africa Namibia central 1 0 see Boyko et al 2009 Africa Uganda mainland 11 1 see Boyko et al 2009 Africa Liberia Lofa 13 6 various districts Africa Liberia Monrovia 3 1 Africa DR Congo Boende 8 7 Africa DR Congo Kinshasa 5 1 Africa DR Congo Katanga 9 3 Africa Ghana Cape Coast 2 3 Africa Burkina Faso Bobo-Dioulasso 1 1 America Peru Arequipa 11 5 various communities America Peru Cusco 18 7 various communities America Peru Ica 7 1 Nazca America Peru Loreto 13 12 various communities America Peru Puno 12 5 various communities America Panama various 0 2 US imports America Mexico Mexico City 5 1 America Mexico Morelia 5 4 America Brazil various 4 9 America Dominican Republic Sosua 2 10 America Honduras Roat´an 6 2 America Colombia Colombia 6 3 America United States Puerto Rico 5 4 see Boyko et al 2009 America Belize Belize 3 1 America Costa Rica Costa Rica 2 6 Arctic United States Alaska 6 5 coastal and interior Alaskan Village Huskies Central Asia Mongolia various 11 2 Bankhar Central Asia Nepal various 6 6 East Asia Indonesia Borneo 6 3 East Asia Vietnam L`aoCai 4 0 East Asia Vietnam H`aGiang 4 1 East Asia Vietnam Cao Bang 4 2 East Asia Vietnam Lang Son 4 1 East Asia Indonesia Jakarta 2 0 Europe Portugal various 5 4 Europe Croatia various 6 0 Europe Bosnia various 3 0 India India Orissa 6 0 India India Chennai 4 2 India India Dehli 6 0 India India Hazaribagh 1 1 India India Mumbai 6 0 India India West Bengal 5 1 Australasia Papua New Guinea Port Moresby 8 1 Australasia Papua New Guinea Eastern Highlands 7 4 Australasia Palau Palau 0 1 US import Australasia French Polynesia Society Islands 10 14 Bora Bora, Huahine, Moorea, Raiatea Australasia French Polynesia Marquesas 5 7 Hiva Oa Australasia Fiji Viti Levu 5 11 various villages Australasia Fiji Kadavu 8 4 Australasia Fiji Tavenui 1 0 sampled in Kadavu Australasia Solomon Islands Guadalcanal 1 2 Australasia Solomon Islands Makira 1 3 Australasia Solomon Islands Central 1 3 Australasia Solomon Islands Western 0 4 Middle East Qatar various 7 2 Middle East Egypt Luxor 8 4 see Boyko et al 2009 Middle East Egypt Giza 1 2 see Boyko et al 2009 Middle East Egypt Kharga 1 0 see Boyko et al 2009 Middle East Lebanon Beruit 8 1 Middle East Lebanon Bekaa 7 0 Middle East Iraq various 1 0 US import Middle East Afghanistan various 3 10 US imports Footline AuthorMiddle East Turkey Istanbul 8 2 PNAS Issue Date Volume Issue Number 25 Middle East Turkey Giresun 2 1

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