Fig 1.
The timetree of the 32 primate species used in this study.
The green areas display the partition of the six large clades, while the orange areas further divide them into the eight small clades as described in Section Mapping absent genes to primate clades. The divergence times of the species were obtained from the TimeTree database [38]. Numeric labels represent large clades, while alphabetic labels represent small clades. One species Carlito syrichta is not included in any clade as it is far away from other species on the timetree. Human (Homo sapiens) is not included in any clade during further analysis processes in human genes, but included in the tree to show the distances from other species to human.
Table 1.
The distribution of ,
,
,
, and
among 31 non-human primates and 4 non-primate species. We use N to represent the total number of genes of a gene set, J to represent the total number of genes out from each gene set that were identified in all 31 non-human primates, K to represent the total number of genes out from each gene set that were identified in a proper subset of 31 non-human primates, L to represent the total number of genes out from each gene set that were identified in none of 4 non-primate species. We call
the “primate specific ratio”.
Table 2.
Contingency tables and Fisher’s exact test results for pairwise comparisons. Positive cases are primate-specific genes, while negative cases are genes that are not primate specific. Statistical significance is denoted by asterisks: results with p-values less than 0.01 are indicated by two asterisks (**), whereas results with p-values less than 0.05 are indicated by one asterisk (*). An odds ratio larger than 1 suggests the group is more likely to be primate specific compared to or
.
Table 3.
Proportion of positive or negative outcomes for each group, and Cohen’s h values for pairwise comparisons between and the other two groups:
and
. Here, positive cases are primate-specific genes, while negative cases are genes that are not primate specific. A higher absolute Cohen’s h indicates a greater difference in proportions.
Fig 2.
Statistical comparisons and gene distribution summary.
(A) Cohen’s h values for pairwise comparisons between and the other two groups:
and
. Primate Specific Ratios are calculated as in Table 1. A higher absolute Cohen’s h indicates a greater difference in ratios between the two compared groups. Green bar represents
, orange bar represents
, and blue bars represent
. (B) Results of Fisher’s exact tests for pairwise comparisons between each of
,
, and
and each control group (
and
), together with the comparison between
and
. Primate Specific Ratios are calculated as in Table 1. Statistical significance is denoted by asterisks. Results with p-values less than 0.01 are indicated by two asterisks (**), results with p-values less than 0.05 are indicated by one asterisk (*), and all other results are marked as ns. Green bar represents
, orange bar represents
, blue bar represents
, gray bars represent
, and purple bars represent
. (C) The number of tissues corresponding to each quantile for the brain genes and immune-related genes. Green bars represent
, orange bars represent
, and gray bars represent all genes that have at least one highly expressed tissue in Human Protein Atlas [32,33]. (D) The number and ratio of genes highly expressed specifically in brain tissues or immune-related tissues, out of 1019 brain genes and 586 immune-related genes, respectively.
Table 4.
Contingency tables and Fisher’s exact test results for three comparisons: (1) the subsets of “wide 10” genes (genes highly expressed in at least 10 tissues) in and
, (2) the subsets of “narrow 10” genes (genes highly expressed in less than 10 tissues) in
and
, and (3) the subsets of “tissue specific” genes, the genes highly expressed exclusively in brain tissues in
and genes highly expressed exclusively in immune-related tissues in
. Positive cases are primate-specific genes, while negative cases are genes that are not primate specific. A p-value less than 0.01 are marked with two asterisks (**), indicating a more statistically significant difference. An odds ratio less than 1 suggests the group in
is less likely to be primate specific compared to the group in
. The union of “wide 10” and “narrow 10” genes corresponds to the complete gene sets (1019 and 586) reported in Table 2, where results for the full sets are shown. This separation allows assessment of whether statistical significance observed in the full gene sets is driven primarily by the “wide 10,” “narrow 10”, or “tissue specific” subset.
Table 5.
The absence of genes from ,
,
,
, and
in primate clades within 31 non-human primates, where the large and small clades are defined in Fig 1. Within the genes exist in at least one of the 31 primate species, we use N to represent the total number of genes of a gene set, P to represent the total number of genes that are absent from large clades, and Q to represent the total number of genes that are absent from small clades. We call
and
“large clade absent ratio” and “small clade absent ratio” respectively.
Table 6.
Contingency tables and Fisher’s exact test results for pairwise comparisons. Positive cases genes absent from large clades. Statistical significance is denoted by asterisks: results with p-values less than 0.01 are indicated by two asterisks (**), whereas results with p-values less than 0.05 are indicated by one asterisk (*). An odds ratio larger than 1 suggests the group is more likely to be absent from large clades compared to or
.
Table 7.
Expression and existence bit strings of selected genes. Selected genes are those in set that do not belong to set
(denoted
), and that are absent from at least two large clades. For genes that are highly expressed in no more than five tissues, the tissues are listed out.
Table 8.
Expression and existence bit strings of selected genes. Selected genes are genes in that are absent from at least two large clades. For genes that are highly expressed in no more than five tissues, the tissues are listed out.
Table 9.
Expression and existence bit strings of selected genes. Selected genes are genes that are absent from small clades and possess bit strings of 1111 or 1110, within ,
, and
. No genes from
satisfy this condition. For genes that are highly expressed in less than five tissues, the tissues are listed out.
Table 10.
The distribution of ,
,
,
, and
among 31 non-human primates and 4 non-primate species. We use N to denote the total number of genes in a gene set, J the number identified in all 31 non-human primates, K the number identified in a proper subset of the 31 non-human primates, and L the number identified in none of the 4 non-primate species. We define
as the primate-specific ratio.
Table 11.
The absence of genes from ,
,
,
, and
in primate clades within 31 non-human primates, where the large and small clades are defined in Fig 1. Within the genes exist in at least one of the 31 primate species, we use N to represent the total number of genes of a gene set, P to represent the total number of genes that are absent from large clades, and Q to represent the total number of genes that are absent from small clades. We call
and
“large clade absent ratio” and “small clade absent ratio” respectively.