Spreadsheet: 05454673-2851-4e8e-9182-cb91b62e782c
Sheet: ST11

Supplementary Table 11 ([NAME] et al.) Results showing human-specific acceleration or conservation
Baseml was used to estimate branch-specific nucleotide substitution rates for alignments containing human, chimpanzee, orangutan, and macaque sequences. Of the
32 peak regions below, 23 showed 1:1 orthology between all 4 primate species, using UCSC's liftover utility. Nucleotide substitution rates were not estimates for the
remaining 9 regions. Codeml was used to anlyze boh site-specific, and human-branch-specific amino acid substitution rates. The alignments for codeml contained
sequences from 5 primate species: human, chimpanzee, gorila, ornagutan, and macaque. Only 19 out of 30 genes contained annotated 1:1 orthologs in all 5 primate
species, using Ensembl's BioMart tool. Only significant results with p < 0.01 are shown.
 |  |  |  | baseml branch model |  | codeml sites model |  | codeml branch model
Coordinates | NearestTSS | TSS | DistanceToTSS | p < 0.01 | nucleotide subsitution rate (human branch) | p < 0.01 | dN/dSe | p < 0.01 | dN/dS     (human branch)
chr1:145037804-145040692 | 143787436 | PDE4DIPd | 35387
chr1:147717685-147719570c,d | 146076705 | NBPF11d | 107604
chr10:103328874-103331401 | 103337963 | POLL | 16572
chr10:109673385-109675834 | 108914282 | SORCS1 | 749093 |  |  |  |  | 0.0004169877743212621 | 0.0001
chr10:81741180-81742583b,d | 81698841 | SFTPD | 32319
chr10:830316-831468 | 725608 | DIP2C | 94708 |  |  |  |  | 1.004182381545235e-06 | 0.03
chr11:857724-860732 | 834445 | TSPAN4 | 13279 | 1.038059166657432e-05 | 0.29628
chr13:31626584-31631064 | 30634117 | HSPH1 | 105053 |  |  |  |  | 0.01578101076401193 | 0.0001
chr15:98195675-98196486 | 96218663 | LOC91948d | 221173
chr17:21475991-21477731 | 21395534 | C17orf51d | 21050
chr18:73627718-73628912 | 71268577 | C18orf62d | 488129
chr18:74798658-74800451 | 72973762 | MBP | 44323
chr18:903446-909852 | 895296 | ADCYAP1 | 0 | 1.169957604746943e-24 | 4.89596
chr19:17558365-17559781a | 17432725 | NXNL1 | 11944 |  |  |  |  | 0.01543857853270976 | 0.0001
chr19:51016136-51018764 | 55709759 | ASPDH | 0 |  |  | 0.005600500035571601 | 7.284
chr2:115419153-115420608 | 114916368 | DPP10 | 219255 | 1.158057926733316e-07 | 4.17615
chr2:115917965-115921773 | 115636201 | DPP10 | 0 | 1.748568868387822e-16 | 4.38868
chr2:132794729-132796576b,d | 132635995 | [NAME] | 122949
chr2:133013735-133016150b,d | 132732012 | [NAME] | 0
chr20:1782608-1784925 | 1822812 | SIRPAd | 89887 | 0.001259383635672717 | 2.24267
chr20:326778-329498 | 275369 | NRSN2 | 0 | 0.001091635584479858 | 1.92204
chr20:361304-363330a | 309307 | TRIB3 | 0 |  |  |  |  | 0.0009914819456773789 | 0.1822
chr20:5484588-5485659c | 5433242 | LOC149837d | 0
chr22:27040777-27045045c | 25383483 | MIATd | 8438
chr22:47549899-47551490 | 45537212 | TBC1D22A | 391351
chr3:2139182-2142802 | 2117246 | CNTN4 | 0 | 9.499100325249451e-12 | 3.08255 |  |  | 6.966822378970457e-05 | 0.0443
chr3:237095-242136 | 213649 | CHL1 | 0 | 6.820761826547704e-06 | 1.99227 | 0.01849444066542104 | 3.323 | 0.009679914478873128 | 0.1822
chr3:87137688-87139305 | 87122947 | VGLL3 | 97431
chr5:146762173-146763181 | 146813453 | DPYSL3 | 70079 |  |  |  |  | 0.01434513180354241 | 0.0001
chr6:151814531-151816287 | 151856867 | C6orf97 | 0
chr7:152621856-152623442 | 152087783 | ACTR3B | 165006
chr7:51538748-51540078 | 51352009 | COBL | 154233
aregions that were deleted in chimpanzee, i.e. intersected no chains using liftover
bregions that were duplicated in chimpanzee, i.e. intersected more than one chain in liftover
cregions that were duplicated in orangutan, i.e. intersected more than one chain using liftover
dregions that were duplicated in macaque
egenes that did not contain an ortholog in all five primate species used for codem
f Probability > 0.95 that dN/dS at that site is greater than 1
Regarding significances in codeml  human branch model:Note that coding sequences show a highly significant decrease in dN/dS ratios , strongly suggesting purifying selection and increased constraint in the human branch as compared to the rest of the tree.