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Supplemental Material.Pdf Supplemental Material Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers Reto Burri1*, Alexander Nater1, Takeshi Kawakami1, Carina F. Mugal1, Pall I. Olason2, Linnea Smeds1, Alexander Suh1, Ludovic Dutoit1, Stanislav Bureš3, Laszlo Z. Garamszegi4, Silje Hogner5,6, Juan Moreno7, Anna Qvarnström8 9, Stein-Are Sæther5,10, 5 11 1* Glenn-Peter Sætre , Janos Török & Hans Ellegren, Milan Ružić 1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden; 2 Wallenberg Advanced Bioinformatics Infrastructure (WABI), Science for Life Lab, Uppsala University, 75123 Uppsala, Sweden; 3 Laboratory of Ornithology, Department of Zoology, Palacky University, 77146 Olomouc, Czech Republic; 4 Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, 41092, Seville, Spain; 5 Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway; 6 Natural History Museum, University of Oslo, 0318 Oslo, Norway; 7 Museo Nacional de Ciencias Naturales-CSIC, 28006 Madrid, Spain; 8 Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, 75236 Uppsala, Sweden; 9 Bird Protection and Study Society of ; 10 Norwegian Institute for Nature Research 11 Serbia,(NINA), Radnička 7034 Trondheim, 20a, 21000 Norway; Novi Sad, Behavioural Serbia Ecology Group, Department of Systematic Zoology and Ecology, Eötvös Loránd University, 1117 Budapest, Hungary. * Correspondence to: [email protected], Tel +46 70 534 00 71, Fax +46 18 471 63 10 (RB) [email protected], Tel +46 18 471 64 60, Fax +46 18 471 63 10 (HE) Supplemental Figure S1. Species tree topology as inferred from the distribution of gene trees under the multispecies coalescent. Branch lengths are depicted in units of 4Ne generations, and external branch lengths are not estimated. Numbers on internal branches show bootstrap support values in percent from 1,000 bootstrap replicates. Supplemental Figure S2. Population genomic parameters along the genome. Color codes, species-specific parameters: blue, collared; green, pied; orange, Atlas; red, semicollared. FST and dxy: green, collared-pied; light blue, collared-Atlas; blue, collared-semicollared; orange, pied-Atlas; red, pied-semicollared; black, Atlas-semicollared. Chromosome 25 has been omitted due to its short length. Chr1 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 10 8 6 4 [cM/Mb] r 2 0 0 20 40 60 80 100 120 Position [Mb] Chr1A 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 10 20 30 40 50 60 70 Position [Mb] Chr2 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 12 10 8 6 4 [cM/Mb] r 2 0 0 50 100 150 Position [Mb] Chr3 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 20 40 60 80 100 Position [Mb] Chr4 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 10 8 6 4 [cM/Mb] r 2 0 0 10 20 30 40 50 60 70 Position [Mb] Chr4A 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 5 10 15 20 Position [Mb] Chr5 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 12 10 8 6 [cM/Mb] 4 r 2 0 0 10 20 30 40 50 60 Position [Mb] Chr6 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 10 8 6 4 [cM/Mb] r 2 0 0 5 10 15 20 25 30 35 Position [Mb] Chr7 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 10 20 30 Position [Mb] Chr8 0.5 0.4 10Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 14 12 10 8 6 [cM/Mb] 4 r 2 0 0 5 10 15 20 25 30 Position [Mb] Chr9 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 5 10 15 20 25 Position [Mb] Chr10 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 5 10 15 20 Position [Mb] Chr11 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 5 10 15 20 Position [Mb] Chr12 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 14 12 10 8 6 [cM/Mb] 4 r 2 0 0 5 10 15 20 Position [Mb] Chr13 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 5 10 15 Position [Mb] Chr14 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 [cM/Mb] 5 r 0 0 5 10 15 Position [Mb] Chr15 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 5 [cM/Mb] r 0 0 2 4 6 8 12 Position [Mb] Chr17 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 25 20 15 10 [cM/Mb] r 5 0 0 2 4 6 8 10 12 Position [Mb] Chr18 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 15 10 [cM/Mb] 5 r 0 0 2 4 6 8 10 Position [Mb] Chr19 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 8 6 4 [cM/Mb] 2 r 0 0 2 4 6 8 10 12 Position [Mb] Chr20 0.5 0.4 5Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 8 6 4 [cM/Mb] 2 r 0 0 2 4 6 8 10 12 14 Position [Mb] Chr21 0.5 0.4 1Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 12 10 8 6 4 [cM/Mb] r 2 0 0 1 2 3 4 5 6 7 Position [Mb] Chr22 0.5 0.4 1Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1 0 6 ] 5 3 − 4 10 3 [ 2 π 1 0 ] 3.0 3 − 2.5 2.0 10 [ 1.5 e t a 1.0 v i r 0.5 p π 0.0 0.5 D 0.0 −0.5 −1.0 Tajima's −1.5 −2.0 0.5 H 0.0 −0.5 Fay&Wu's −1.0 14 12 10 8 6 [cM/Mb] r 4 2 0.5 2.0 3.5 Position [Mb] Chr23 0.5 0.4 1Mb S 0.3 B 0.2 P 0.1 0.0 1.0 0.8 T 0.6 S F 0.4 0.2 0.0 7 ] 6 3 − 5 10 4 [ 3 Y 2 X d 1
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