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Positive Darwinian selection after gene duplication in primate ribonuclease genes.
TLDR
It was found that the number of arginine residues increased substantially in a short period of evolutionary time after gene duplication, and these amino acid changes probably produced the novel anti-pathogen function of ECP.
Detection of convergent and parallel evolution at the amino acid sequence level.
TLDR
Computer simulations to assess the efficiencies, of the parsimony and Bayesian methods of ancestral sequence inference in identifying convergent and parallel-change sites showed that the Bayesian method performs better than the Parsimony method in identifying parallel changes, and both methods are inefficient in identifying convertergent changes.
Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes.
TLDR
This letter addresses how well the t-test performs when the sample size is small and whether there is a better way of testing positive selection by using a recently published data set of primate lysozyme sequences as an example.
A simple method for estimating the parameter of substitution rate variation among sites.
  • X. Gu, J. Zhang
  • Computer Science
    Molecular biology and evolution
  • 1 November 1997
TLDR
A new method is developed that first estimates the expected number of substitutions at each site, which is corrected for multiple hits, and then estimates the shape parameter alpha, an index of the degree of among-site rate variation.
Evolution of Antennapedia-class homeobox genes.
TLDR
The results show that the genes that are phylogenetically close are also closely located in the chromosome, suggesting that the colinearity between the gene expression and gene arrangement was generated by successive tandem gene duplications and that the gene arrangement has been maintained by some sort of selection.
The crystal structure of a high oxygen affinity species of haemoglobin (bar-headed goose haemoglobin in the oxy form).
TLDR
The well-ordered conformation and the three-dimensional distribution of positive charges clearly indicate this area to be the inositol pentaphosphate binding site of bird haemoglobins.
Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models.
  • J. Zhang
  • Biology
    Molecular biology and evolution
  • 1 June 1999
TLDR
Computer simulation was used to examine performance of LRTs of the molecular clock, transition/transversion bias, and among-site rate variation under different substitution models and showed that when correct models are used,LRTs perform quite well even when the DNA sequences are as short as 300 nt; however, L RTs were found to be biased under incorrect models.
An unusual form of purifying selection in a sperm protein.
TLDR
It was found that both the total number of amino acids and the positions of arginine residues have changed considerably during the course of mammalian evolution, suggesting that arginin-rich selection is a general feature of protamine evolution.
Correlation between the substitution rate and rate variation among sites in protein evolution.
TLDR
A negative correlation between the extent of among-site rate variation and the average substitution rate of a protein is found and it is concluded that slowly evolving proteins tend to have a high level of rate variation among sites, and vice versa.
Rapid evolution of a primate sperm protein: relaxation of functional constraint or positive Darwinian selection?
TLDR
It is found that the nucleotide substitution rate at nonsynonymous sites is significantly higher than the rate at synonymous and intron sites for protamine P1 of hominoids and Old World monkeys, which suggests that positive selection has been operating on protamineP1 of these species.
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