PhastCons analysis

Pairwise alignments were generated using lastz v1.02⁷¹, with the following parameters: “B = 2 C = 0 E = 150 H = 0 K = 4500 L = 3000 M = 254 O = 600 Q = human_chimp.v2.q T = 2 Y = 15,000”. This was followed by using USCS genome utilities (https://genome.ucsc.edu/util.html, https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/FOOTER) axtChain tool with -minScore = 5000. Additional tools with default parameters were then used following the UCSC whole-genome alignment paradigm (http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto) in order to obtain a contiguous pairwise alignment. Multiple alignments were generated from pairwise alignments with the multiz v11.2⁷² program, using default parameters and the following pre-determined phylogenetic tree: ((((M. zebra, P. nyererei), A. burtoni), N. brichardi), O. niloticus) in agreement with Brawand et al.³⁵. Sequence conservation scores were then obtained using PhastCons⁷³ with a phylogenetic model estimated by the phyloFit⁷⁴ program, both from the PHAST software package (v.1.3). The model fitting was done using default parameters. PhastCons was run in two iterations, first to obtain the free parameters of the model (-estimate-trees and -no-post-probs) and then using the output from this we ran PhastCons again to attain the conservation scores with—target-coverage 0.3—expected-length 100.