Ten strategies tested in the model.

Ten strategies tested in the model.</p

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

Top 6 GO terms from the functional annotation analysis of 97 CSFR genes by DAVID.

1<p>gene included RBMY1A1, RBMY1B, RBMY1J, RBMY1F, XKRY, XKRY2, BPY2C, BPY2B, BPY2, CDY1, CDY1B, CDY2B, CDY2A, DAZ2, DAZ3, DAZ4, DAZ1, and TSPY2.</p>2<p>gene included RBMY1A1, RBMY1B, RBMY1J, RBMY1F, BPY2C, BPY2B, BPY2, CDY1, CDY1B, CDY2B, CDY2A, DAZ2, DAZ3, DAZ4, DAZ1, and TSPY2.</p

MOESM2 of Convergent degeneration of olfactory receptor gene repertoires in marine mammals

Additional file 2: Table S1. OR number distribution of 23 mammals. Intact genes indicate coding sequences starting from start codons and ending with stop codons without any interference mutations. Pseudogenes indicate sequences containing nonsense mutations, coding shifts, deletions in conserved regions, or combinatorial features. Truncated genes indicate sequences with partial sequences or located at the end of a contig. Truncated genes can also be pseudogenes. Pseudogene proportion refers to the number of pseudogenes divided by the total number of OR genes in the species

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

Phylogenetic tree of GATA transcription factor family.

<p>A <i>Ciona intestinalis</i> gene was selected as the outgroup to root the tree and only the cladogram is shown. The tree node where a possible large-scale duplication event happened is marked with a filled black square ■. 7 means the gene’s expression level is higher than 95% of all genes expressed in the organ. 6 is between 95% and 85%. 5 is between 85% and 65%. 4 is between 65% and 35%. 3 is between 35% and 15%. 2 is between 15% and 5%. 1 is lower than 5%. 0 means no expression at all. N is not available.</p

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

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