Payoff matrix of the “donation game”.

<p>The entries in the matrix refer to the payoffs of player A. The benefit of cooperation (<i>b</i>), the cost of cooperation (<i>c</i>), and <i>b</i> − <i>c</i> are greater than 0.</p

The average fitness payoff for five homogeneous groups which adopt the error-prone strategies at four different error rates.

<p>TWTH stands for TFT-with-trembling-hand. SDH stands for shame-driven-hiding. SDD stands for shame-driven-denying. GDA stands for guilt-driven-amending. P stands for Pavlov. (A) When <i>b</i> = 1, <i>c</i> = 0.25 and <i>n</i> = 10. (B) When <i>b</i> = 1, <i>c</i> = 0.25 and <i>n</i> = 20. (C) When <i>b</i> = 1, <i>c</i> = 0.25 and <i>n</i> = 50. (D) When <i>b</i> = 1, <i>c</i> = 0.25 and <i>n</i> = 100.</p

The number of dominant results for nine strategies tested in pairwise contests.

<p>AC stands for always-cooperate. AD stands for always-defect. AT stands for always-trembling. TFT stands for tit-for-tat. GTFT stands for generous tit-for-tat. TWTH stands for TFT-with-trembling-hand. SDH stands for shame-driven-hiding. SDD stands for shame-driven-denying. GDA stands for guilt-driven-amending. P stands for Pavlov. (A) When <i>b</i> = 1 and <i>c</i> = 0.75, the ranking of nine strategies. (B) When <i>b</i> = 1 and <i>c</i> = 0.5, the ranking of the strategies. (C) When <i>b</i> = 1 and <i>c</i> = 0.25, the ranking of nine strategies.</p

The average fitness payoff for ten strategies competing in a group under the conditions that group size is 50 (<i>n</i> = 50), benefit equals 1 and cost equals 0.25 (<i>b</i> = 1 and <i>c</i> = 0.25).

<p>The average fitness payoff for ten strategies competing in a group under the conditions that group size is 50 (<i>n</i> = 50), benefit equals 1 and cost equals 0.25 (<i>b</i> = 1 and <i>c</i> = 0.25).</p

Large Genomic Region Free of GWAS-Based Common Variants Contains Fertility-Related Genes

<div><p>DNA variants, such as single nucleotide polymorphisms (SNPs) and copy number variants (CNVs), are unevenly distributed across the human genome. Currently, dbSNP contains more than 6 million human SNPs, and whole-genome genotyping arrays can assay more than 4 million of them simultaneously. In our study, we first questioned whether published genome-wide association studies (GWASs) assays cover all regions well in the genome. Using dbSNP build 135 data, we identified 50 genomic regions longer than 100 Kb that do not contain any common SNPs, i.e., those with minor allele frequency (MAF)≥1%. Secondly, because conserved regions are generally of functional importance, we tested genes in those large genomic regions without common SNPs. We found 97 genes and were enriched for reproduction function. In addition, we further filtered out regions with CNVs listed in the Database of Genomic Variants (DGV), segmental duplications from Human Genome Project and common variants identified by personal genome sequencing (UCSC). No region survived after those filtering. Our analysis suggests that, while there may not be many large genomic regions free of common variants, there are still some “holes” in the current human genomic map for common SNPs. Because GWAS only focused on common SNPs, interpretation of GWAS results should take this limitation into account. Particularly, two recent GWAS of fertility may be incomplete due to the map deficit. Additional SNP discovery efforts should pay close attention to these regions.</p></div

The Evolutionary Panorama of Organ-Specifically Expressed or Repressed Orthologous Genes in Nine Vertebrate Species

<div><p>RNA sequencing (RNA-Seq) technology provides the detailed transcriptomic information for a biological sample. Using the RNA-Seq data of six organs from nine vertebrate species, we identified a number of organ-specifically expressed or repressed orthologous genes whose expression patterns are mostly conserved across nine species. Our analyses show the following results: (i) About 80% of these genes have a chordate or more ancient origin and more than half of them are the legacy of one or multiple rounds of large-scale gene duplication events. (ii) Their evolutionary rates are shaped by the organ in which they are expressed or repressed, e.g. the genes specially expressed in testis and liver generally evolve more than twice as fast as the ones specially expressed in brain and cerebellum. The organ-specific transcription factors were discriminated from these genes. The ChIP-seq data from the ENCODE project also revealed the transcription-related factors that might be involved in regulating human organ-specifically expressed or repressed genes. Some of them are shared by all six human organs. The comparison of ENCODE data with mouse/chicken ChIP-seq data proposes that organ-specifically expressed or repressed orthologous genes are regulated in various combinatorial fashions in different species, although their expression features are conserved among these species. We found that the duplication events in some gene families might help explain the quick organ/tissue divergence in vertebrate lineage. The phylogenetic analysis of testis-specifically expressed genes suggests that some of them are prone to develop new functions for other organs/tissues.</p></div

The number of specifically expressed or repressed (OSER) orthologous clusters in each organ/tissue.

<p>*The OSER clusters in nervous tissue show no significant expression difference between brain and cerebellum while have a distinct expression pattern between nervous tissues and the other organs.</p><p>The number of specifically expressed or repressed (OSER) orthologous clusters in each organ/tissue.</p

Comparison of the evolutionary rate of specifically expressed and repressed clusters in seven organs/tissues.

<p>The total phylogenetic tree branch length of each one-to-one OSER cluster was used to represent its evolutionary rate.</p

Comparison of human ChIPseq data with mouse/chicken ChIPseq data.

<p>Comparison of human ChIPseq data with mouse/chicken ChIPseq data.</p

The evolutionary origins of OSER clusters in each organ/tissue.

<p>The evolutionary origins of OSER clusters in each organ/tissue.</p