Table 2 Open in new tab Count of...

	Neo-X	Neo-Y	Ratio	α	P Value
Synonymous sites
All	811	1165	1.44	1.84	<0.001
P → U	476	722	1.52	2.05	<0.001
U → P	208	240	1.15	1.25	>0.1
P → P	58	80	1.38	1.70	<0.03
U → U	69	123	1.78	2.93	<0.001
Neutral	127	203	1.60	2.28	<0.001
Short introns
<100 bp	261	318	1.22	1.37	<0.001

	Neo-X	Neo-Y	Ratio	α	P Value
Synonymous sites
All	811	1165	1.44	1.84	<0.001
P → U	476	722	1.52	2.05	<0.001
U → P	208	240	1.15	1.25	>0.1
P → P	58	80	1.38	1.70	<0.03
U → U	69	123	1.78	2.93	<0.001
Neutral	127	203	1.60	2.28	<0.001
Short introns
<100 bp	261	318	1.22	1.37	<0.001

Table 2

Count of Synonymous Substitutions and Substitutions in Short Introns (<100 bp) along the Neo-X and Neo-Y Chromosome at 205 Homologous Genes

	Neo-X	Neo-Y	Ratio	α	P Value
Synonymous sites
All	811	1165	1.44	1.84	<0.001
P → U	476	722	1.52	2.05	<0.001
U → P	208	240	1.15	1.25	>0.1
P → P	58	80	1.38	1.70	<0.03
U → U	69	123	1.78	2.93	<0.001
Neutral	127	203	1.60	2.28	<0.001
Short introns
<100 bp	261	318	1.22	1.37	<0.001

	Neo-X	Neo-Y	Ratio	α	P Value
Synonymous sites
All	811	1165	1.44	1.84	<0.001
P → U	476	722	1.52	2.05	<0.001
U → P	208	240	1.15	1.25	>0.1
P → P	58	80	1.38	1.70	<0.03
U → U	69	123	1.78	2.93	<0.001
Neutral	127	203	1.60	2.28	<0.001
Short introns
<100 bp	261	318	1.22	1.37	<0.001

NOTE.—A total of 60,788 synonymous sites and 20,723 short intron sites were compared on the neo-X and neo-Y chromosome. P → U refers to a change from a preferred to an unpreferred codon, and U → P refers to a change from an unpreferred to a preferred codon; P → P or U → U are substitutions within a class and considered neutral. P values are given using a Sign test to test for an equal number of substitutions on the neo-X and neo-Y branch.

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