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The Wild Species Genome Ancestry of Domestic Chickens Short Title: Chicken Genome Ancestry

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The Wild Species Genome Ancestry of Domestic Chickens Short Title: Chicken Genome Ancestry Supplementary Materials Full title: The wild species genome ancestry of domestic chickens Short title: Chicken genome ancestry Raman Akinyanju Lawal1,2*#, Simon H. Martin3,4, Koen Vanmechelen5, Addie Vereijken6, Pradeepa Silva7, Raed Mahmod Al-Atiyat8, Riyadh Salah Aljumaah9, Joram M. Mwacharo10, Dong-Dong Wu11,12, Ya-Ping Zhang11,12, Paul M. Hocking13†, Jacqueline Smith13, David Wragg14 & Olivier Hanotte1, 14,15* 1Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, NG7 2RD, Nottingham, United Kingdom 2,#The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA 3Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, Edinburgh, United Kingdom 4Department of Zoology, University of Cambridge, CB2 3EJ, Cambridge, United Kingdom 5Open University of Diversity - Mouth Foundation, Hasselt, Belgium 6Hendrix Genetics, Technology and Service B.V., P.O. Box 114, 5830, AC, Boxmeer, The Netherlands 7Department of Animal Sciences, Faculty of Agriculture, University of Peradeniya, Sri Lanka 8Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan 9Department of Animal Production, King Saud University, Saudi Arabia 10Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, ILRI-Ethiopia Campus, Addis Ababa, Ethiopia 11Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China 12State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China. 13The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK 14Centre for Tropical Livestock Genetics and Health, The Roslin Institute, EH25 9RG, Edinburgh, UK 15LiveGene, International Livestock Research Institute (ILRI), P. O. 5689, Addis Ababa, Ethiopia †Deceased #Present address *Correspondence: [email protected] and [email protected] 1 The content of this supplementary materials is as below: Fig. S1A and B: Exon phylogeny and TreeMix Fig. S2 – S4: Plots for the introgression from domestic chicken/Red junglefowl to Grey junglefowl Fig. S5 – S11: Plots for the introgression from Grey junglefowl to domestic chicken/Red junglefowl Fig. S12: Genome fd plots for the comparison between Ceylon junglefowl and domestic chicken Fig. S13 – S14: Plots for the introgression from Ceylon junglefowl to domestic chicken. Fig. S15: Genome fd plots for the comparison between Green junglefowl and domestic chicken Fig. S16: Plots for the introgression from Green junglefowl to domestic chicken Table S1: Sampling, mapping and variants statistics Table S2A and B: Candidate introgressed regions Table S3: Functional annotations for the enriched genes within the introgressed regions 2 Fig. S1A. Maximum likelihood tree generated from 1,849,580 exon SNPs with GTR model. All branches are supported by 100% bootstrap values. The colour for the taxon markers are ◆: Domestic chicken, ◆: Red junglefowl, ◆: Javan red junglefowl, ◆: Grey junglefowl, ◆: Ceylon junglefowl, ◆: Green junglefowl, ◆: common Pheasant. 3 Ceylon junglefowl Grey junglefowl Red junglefowl Javan red junglefowl Green red junglefowl Fig. S1B. TreeMix across the autosomal genome 4 Fig. S2. A 26 Mb (Chr1: 141287737 - 167334186 bp) introgressed region from domestic chicken into Grey junglefowl. (A) fd plot for chromosome 1, (B) haplotype-based network and (C) maximum likelihood tree for the introgressed region, (D) Twisst plot and the proportion of each topology in the introgressed region, (E) DXY and (F) FST. Eth, Sau, SriLanka, Lang, Ked, Sum represent chicken samples from Ethiopia, Saudi, Sri Lanka, Langshan, Kedu Hitam and Sumatra, respectively, GreyJ represent Grey junglefowl, and targetGreyJ are the introgressed (*) Grey junglefowl haplotypes. domestic include all the domestic chicken populations. The colours for (B) and (C) defining each species are; ◆: Domestic chicken ◆: Red junglefowl, ◆: Javan red junglefowl, ◆: Grey junglefowl, ◆: Ceylon junglefowl, ◆: Green junglefowl, ◆: common Pheasant. 5 (*) (*) Fig. S3. A 9 Mb (Chr2: 11022874 - 19972089 bp) introgressed region from domestic chicken to Grey junglefowl. (A) fd plot for chromosome 1, (B) maximum likelihood tree for the introgressed region, (C) haplotype-based network, (D) Twisst plot and the proportion of each topology in the introgressed region, (E) DXY and (F) FST. Eth, Sau, SriLanka, Lang, Ked, Sum represent chicken samples from Ethiopia, Saudi, Sri Lanka, Langshan, Kedu Hitam and Sumatra, respectively, GreyJ represent Grey junglefowl, and targetGreyJ are the introgressed (*) Grey junglefowl haplotypes. Domestic include all the domestic chicken populations. The colours for (B) and (C) defining each species are; ◆: Domestic chicken ◆: Red junglefowl, ◆: Javan red junglefowl, ◆: Grey junglefowl, ◆: Ceylon junglefowl, ◆: Green junglefowl, ◆: common Pheasant. 6 (*) (*) Fig. S4. A 2.8 Mb (Chr4: 76429662 - 79206239bp) introgressed region from domestic chicken/Red junglefowl into Grey junglefowl. (A) fd plot for chromosome 4, (B) haplotype- based network, (C) maximum likelihood tree, (D) Twisst plot, its topologies and their proportions, (E) DXY and (E) FST. Eth, Sau, SriLanka, Lang, Ked and Sum are domestic chicken from Ethiopia, Saudi, Sri Lanka and Langshan, KeduHitam and Sumatra breeds, respectively. GreyJ is Grey junglefowl, and targetGreyJ are the introgressed Grey junglefowl haplotypes (*). Domestic includes all the chicken domestic populations. ◆: Domestic chicken; ◆: Red junglefowl, ◆: Javan red junglefowl, ◆: Grey junglefowl, ◆: Ceylon junglefowl, ◆: Green junglefowl, ◆: common Pheasant. 7 Description for Fig. S5 - S11 The plots are zoomed close to the region. (A) fd plot, (B) haplotype-based network and (C) maximum likelihood tree for the introgressed region (D) Twisst plot and the proportion of each topology in the introgressed region (E) DXY and (F) FST. Eth, Sau, SriLanka, Lang, Ked, Sum represent chicken samples from Ethiopia, Saudi, Sri Lanka, Langshan, Kedu Hitam and Sumatra, respectively, GreyJ represent Grey junglefowl, and targetDom are the introgressed (*) domestic haplotypes. The colours for (B) and (C) defining each species are ◆: Domestic chicken ◆: Red junglefowl, ◆: Javan red junglefowl, ◆: Grey junglefowl, ◆: Ceylon junglefowl, ◆: Green junglefowl, ◆: common Pheasant. Fig. S5. A 220 kb (Chr 2: 119676880 - 119901132bp) candidate introgressed region from Grey junglefowl to domestic chicken/Red junglefowl. targetDom here include the introgressed domestic chicken and a single Red junglefowl haplotypes (*). 8 Fig. S6. A 100 kb (Chr 3: 50759656 - 50859645 bp) introgressed region from Grey junglefowl into domestic chicken. 9 Fig. S7. A 200 kb (Chr 4: 62097304 - 62297319 bp) introgressed region from Grey junglefowl into domestic chicken. 10 Fig. S8. A 280 kb (Chr 5: 45674368 - 45954418 bp) introgressed region from Grey junglefowl into domestic chicken. 11 Fig. S9. A 140 kb (Chr 7: 22652767 - 22792759 bp) introgressed region from Grey junglefowl into domestic chicken. 12 Fig. S10. A 500 kb (Chr 9: 23052049 - 23552045 bp) introgressed region from Grey junglefowl into domestic chicken. 13 Fig. S11. A 100 kb (Chr 12: 12914268 - 13014266 bp) introgressed region from (*) Grey junglefowl into domestic and (**) vice versa. The Twisst values and plots are based on the introgressed domestic haplotypes from the Grey junglefowl and does not account for the reverse introgression. 14 A B C Fig. S12. The fd plots test for the comparison between Ceylon junglefowl and domestic chicken population from (A) Ethiopia and Saudi, (B) Sri Lanka and (C) Southeast and East Asia. The Y-axis fd value and X-axis 1 – 28 autosomes. 15 Fig. S13. Network and Twisst proportion of topologies for three Ceylon candidate introgressed regions into domestic chicken (A - C). (A1) and (A2) 6.52 Mb region Chr 1: 2895616 - 9418660 bp, (B1) and (B2) 3.95 Mb Chr 1: 25261354 - 29205161 bp, (C1) and (C2) 1.38 Mb region Chr 1: 147936229 - 149316591 bp. (C1) also shows support for introgression from domestic chicken to some Grey junglefowl haplotypes at the same region. 16 Fig. S14. A 600 kb (Chr 3: 108325801 - 108925723 bp) introgressed region from Ceylon junglefowl to domestic chicken. (A) fd plot (B) haplotype-based network, (C) maximum likelihood tree, (D) Twisst plot and the proportion of each topology, (E) DXY and (E) FST. Eth, Sau, SriLanka, Lang, Ked, Sum are domestic chicken from Ethiopia, Saudi, Sri Lanka and Langshan, Kedu Hitam and Sumatra breeds, respectively, CeylonJ is Ceylon junglefowl and targetDom are the introgressed domestic chicken haplotypes (*). ◆: Domestic chicken; ◆: Red junglefowl, ◆: Javan red junglefowl, ◆: Grey junglefowl, ◆: Ceylon junglefowl, ◆: Green junglefowl, ◆: common Pheasant. 17 A A C Fig. S15. The fd plots test for the comparison between Green junglefowl and domestic chicken population from (A) Ethiopia and Saudi, (B) Sri Lanka and (C) Southeast and East Asia. The Y-axis fd value and X-axis 1 – 28 autosomes. 18 Fig. S16: A 100 kb (Chr 5: 9538715 - 9638713 bp) introgressed region from Green junglefowl into domestic chicken. (A) fd plot, (B) haplotype-based network, (C) maximum likelihood tree, (D) TWISST plot and the proportion of each topology, (E) DXY and (E) FST. Eth, Sau, SriLanka, Lang, Ked, Sum are domestic chicken from Ethiopia, Saudi, Sri Lanka and Langshan, Kedu Hitam and Sumatra breeds, respectively,
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