Table 4. SMACv1.0 simple de novo outlier contigs from a genome-wide analysis of divergence with the chicken.

Predicted Outlier Contig Genes and Pathways1	Known Function or GWAS Trait Classification	References
Mitochondrial Genome	Energy Production	[64]
SEMA3A, RARB, PRICKLE1, SNW1	Neuronal Development	[65]–[69]
SEMA3A, ATXN1, CNTNAP2, INPP5E,	Neurological Disorders	[70]–[80]
Intergenic TTLL7 and LPHN2, GPR37,
FOXP1/FOXP2-CNTNAP2 Pathway
ATXN1	Motor Coordination	[71]
GPR37, ATXN1, NRCAM	Cognition, Learning	[81]–[83]
ATXN1, INPP5E, TRMT1, ADK	Intelligence	[72], [77], [84]
FOXP1/FOXP2-CNTNAP2 Pathway	Speech	[74], [80]
CDK5RAP2	Brain Size	[85]–[86]
LHFP	Hippocampal Volume and Intelligence	[87]–[88]
ADAMTSL3, TEAD1, EXT1	Height	[89]–[93]
Intergenic BTG1, Intergenic PRICKLE1,	Heart Failure	[94]–[95]
PARVA
VTI1A, NFIA	Heart Ventricular Conduction	[96]
PTPRG, TTN	Heart Q-wave T-wave Interval Length	[97]
CAMK4	Blood Pressure	[98]
Intergenic WNK1 and NINJ2	Stroke	[99]
CNTNAP2, COLEC10	Bone Mass	[100]–[101]
UBE2L3, THRB	Blood Traits	[102]
LIMK2, ST6Gal1	Diabetes	[103]–[104]
PARD3B, CHSY3	Response or Susceptibility to Viruses	[105]–[106]
WDR36, Intergenic CHD7 and CLVS1,	Asthma, Lung Function, Respiratory	[107]–[109]
TTN
VEGFA, COL8A1	Age-Related Macular Degeneration	[110]
POT1	Longevity	[57]

¹For outlier direction, see Table S14.