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Supporting Information Guillermo Friisand Borja Milá Color 1 Supporting Information 2 3 Guillermo Friis and Borja Milá 4 5 Color divergence, sexual dichromatism and the role of sexual selection in the rapid 6 postglacial radiation of dark-eyed juncos (Aves: Passerellidae) 7 8 Sequencing and assembly of the sexual chromosome 9 To recover the Z chromosome for which DoveTails Hi-C sequencing failed, we 10 assembled a consensus draft genome by combining low-coverage genomes of eight 11 different junco individuals from a parallel study, consisting in 2 samples of J. bairdi, 2 12 J. p. palliatus, 2 J. h. caniceps, 1 J. h. thurberi and 1 J. h. dorsalis. Libraries for seven 13 of the genomes were prepared with the Kapa Library Preparation Kit (Kapa Biosystems, 14 Inc.) using TruSeq-style adapters (Faircloth and Glenn 2012). They were pooled after 15 random shearing and individual barcoding and sequenced in a single lane of an Illumina 16 HiSeq platform. The eighth genome, corresponding to the dorsalis individual, was 17 sequenced at a higher coverage by means of two 101-bp paired-end shotgun libraries 18 and two 101-bp mate-paired libraries with insert sizes of 8 Kb in length at Macrogen 19 Inc. The TruSeq Nano DNA Kit (Illumina) was used for the preparation of the shotgun 20 libraries, while the mate-paired libraries were prepared with Nextera Mate Pair Kit 21 (Illumina). We used FASTQC (Andrews 2010) to evaluate the quality of the sequenced 22 data, and quality filtering was carried out with NextClip (Leggett et al. 2013) in the case 23 of the mate paired libraries. For the rest of them we used Trimmomatic (Bolger et al. 24 2014), applying a sliding window filtering approach with a size of 4 bp and a phred 25 quality score threshold of 25. We also set a minimum length of 50 bp, below which 1 26 reads were filtered out after trimming. We used the software SOAPDENOVO2 (Luo et 27 al. 2012) to perform the assembly. The average insert size for each library was 28 estimated in a preliminary run, and we set a Kmer size of 27 and minimum edge 29 coverage of 2. Gaps that emerged during the scaffolding process were removed with the 30 GapCloser tool from SOAPDENOVO2. Finally, we filtered out all the scaffolds shorter 31 than 500 bp so the genome was functional as a mapping reference. The final assembled 32 genome had 37,904 scaffolds with an N50 of 147,816 bases, a L50 of 1,951 scaffolds, a 33 total size of 1.09 Gb, 17.5 Mb of missing sites, and an overall coverage of ~56X, as 34 computed with VCFTOOLS version 0.1.13 (Danecek et al. 2011). To recover the Z 35 chromosome specifically, we mapped the 37,904 scaffolds against the zebra finch 36 (Taeniopygia guttata) genome v87 available in Ensembl (Yates et al. 2016) by means of 37 the Chromosembler tool available in Satsuma (Grabherr et al. 2010). The assembled Z 38 chromosome was 71.1 Mb long. 39 40 41 42 43 44 2 45 Table S1. List of samples sequenced by genotyping-by-sequencing (GBS). State 46 abbreviations are the following: Virginia (VA), Wyoming (WY), California (CA), 47 Colorado (CO), Utah (UT), Maine (ME), New Hampshire (NH), New Mexico (NM), 48 Nevada (NV), , Utah (UT), Wyoming (WY), and Arizona (AZ) in the USA; British 49 Columbia (BC) in Canada; and Chihuahua (CHIH), Mexico City (CM) and Durango 50 (DGO), in Mexico. 51 Taxonomy Field name State Country LAT LONG Collection date SEX J. h. aikeni 05N0522 WY USA 44.48614 -104.45108 7/13/2005 M J. h. aikeni 05N0523 WY USA 44.48614 -104.45108 7/13/2005 M J. h. aikeni 05N0524 WY USA 44.59476 -104.41141 7/13/2005 M J. h. aikeni 05N0525 WY USA 44.59476 -104.41141 7/14/2005 M J. h. aikeni 05N0526 WY USA 44.59476 -104.41141 7/14/2005 M J. h. aikeni 05N0527 WY USA 44.50185 -104.45238 7/14/2005 M J. h. aikeni 05N0528 WY USA 44.50185 -104.45238 7/14/2005 M J. h. aikeni 05N0529 WY USA 44.50185 -104.45238 7/14/2005 M J. h. aikeni 05N0531 WY USA 44.48349 -107.45811 7/14/2005 M J. h. aikeni 05N0532 WY USA 44.48349 -107.45811 7/14/2005 M J. h. aikeni 05N0534 WY USA 44.48349 -107.45811 7/14/2005 M J. h. aikeni 05N0535 WY USA 44.48349 -107.45811 7/14/2005 M J. h. caniceps 14-0368 CO USA 6/12/2014 M J. h. caniceps 14-0379 CO USA 37.80702 -107.90788 6/13/2014 M J. h. caniceps 14-0380 CO USA 37.80536 -107.90508 6/13/2014 M J. h. caniceps 14-0365 CO USA 6/12/2014 M J. h. caniceps 14-0366 CO USA 6/12/2014 M J. h. caniceps 14-0367 CO USA 6/12/2014 M J. h. caniceps 14-0369 CO USA 6/12/2014 M J. h. caniceps 14-0370 CO USA 6/12/2014 M J. h. caniceps 14-0371 CO USA 6/12/2014 M J. h. caniceps 14-0373 CO USA 6/12/2014 M J. h. caniceps 14-0374 CO USA 37.80629 -107.90349 6/13/2014 M J. h. caniceps 14-0375 CO USA 37.80491 -107.90621 6/13/2014 M J. h. caniceps 14-0376 CO USA 37.80715 -107.90481 6/13/2014 M J. h. caniceps 14-0405 CO USA 38.24164 -105.66933 6/18/2014 M J. h. caniceps 14-0406 CO USA 38.2527 -105.67553 6/18/2014 M J. h. caniceps 14-0407 CO USA 38.25445 -105.67116 6/18/2014 M J. h. caniceps 14-0408 CO USA 6/18/2014 M J. h. caniceps 14-0411 CO USA 38.25371 -105.66551 6/19/2014 M J. h. caniceps 14-0412 CO USA 38.05197 -105.53458 6/19/2014 M J. h. caniceps 14-0413 CO USA 38.05247 -105.53736 6/19/2014 M J. h. caniceps 14-0404 CO USA 38.25366 -105.67282 6/18/2014 M J. h. caniceps 12-158 NV USA 39.29206 -117.11548 4/28/2012 M J. h. caniceps 12-159 NV USA 39.29206 -117.11548 4/28/2012 M 3 J. h. caniceps 12-160 NV USA 39.29206 -117.11548 4/29/2012 M J. h. caniceps 14-0395 UT USA 39.33038 -106.66054 6/17/2014 M J. h. caniceps 14-0383 UT USA 6/15/2014 M J. h. caniceps 14-0384 UT USA 39.30839 -106.63971 6/15/2014 M J. h. caniceps 14-0385 UT USA 39.30835 -106.64185 6/16/2014 M J. h. caniceps 14-0388 UT USA 39.30939 -106.64325 6/16/2014 M J. h. caniceps 14-0389 UT USA 39.31047 -106.64441 6/16/2014 M J. h. caniceps 14-0390 UT USA 39.31016 -106.64459 6/16/2014 M J. h. caniceps 14-0391 UT USA 39.30652 -106.64223 6/16/2014 M J. h. caniceps 14-0392 UT USA 39.30553 -106.64254 6/16/2014 M J. h. caniceps 14-0393 UT USA 6/16/2014 M J. h. caniceps 14-0394 UT USA 6/16/2014 M J. h. caniceps 14-0396 UT USA 39.33174 -106.66293 6/17/2014 M J. h. caniceps 14-0387 UT USA 39.30991 -106.64361 6/16/2014 M J. h. caniceps 14-0397 UT USA 39.33203 -106.6641 6/17/2014 M J. h. caniceps 14-0398 UT USA 39.33216 -106.66359 6/17/2014 M J. h. caniceps 14-0399 UT USA 39.33311 -106.66375 6/17/2014 M J. h. caniceps 14-0401 UT USA 39.33472 -106.6643 6/17/2014 M J. h. caniceps 14-0402 UT USA 39.33547 -106.66398 6/17/2014 M J. h. caniceps 14-0381 UT USA 39.30025 -106.60064 6/15/2014 M J. h. caniceps 14-0382 UT USA 39.30839 -106.63971 6/15/2014 M J. h. caniceps 05N0548 UT USA 40.68944 -110.89545 7/16/2005 M J. h. caniceps 05N0549 UT USA 40.68944 -110.89545 7/16/2005 M J. h. caniceps 05N0550 UT USA 40.68944 -110.89545 7/16/2005 M J. h. caniceps 05N0551 UT USA 40.66553 -110.96137 7/16/2005 M J. h. caniceps 05N0552 UT USA 40.66553 -110.96137 7/16/2005 M J. h. caniceps 05N0554 UT USA 37.49955 -112.54743 7/17/2005 M J. h. caniceps 05N0557 UT USA 37.49955 -112.54743 7/17/2005 M J. h. caniceps 05N0560 UT USA 37.48084 -112.57668 7/18/2005 M J. h. caniceps 06N25689 UT USA 37.52909 -112.75322 6/11/2006 M J. h. caniceps 05N0558 UT USA 37.48084 -112.57668 7/17/2005 M J. h. caniceps 05N0562 UT USA 37.48084 -112.57668 7/18/2005 M J. h. caniceps 05N0564 UT USA 37.48084 -112.57668 7/18/2005 M J. h. caniceps 06N25679 UT USA 37.52909 -112.75322 6/10/2006 M J. h. caniceps 06N25699 UT USA 40.44078 -111.62781 6/12/2006 M J. h. caniceps 06N26252 UT USA 40.44078 -111.62781 6/12/2006 M J. h. caniceps 05N0540 UT USA 40.8046 -110.87705 7/15/2005 M J. h. caniceps 05N0541 UT USA 40.8046 -110.87705 7/15/2005 M J.
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