Here we use full length cDNA alignments comprising more than 700,000 nucleotides from human, mouse, pig and the Japanese pufferfish Fugu rubrices in order to investigate 1) the relationships between three major lineages of mammals: rodents, artiodactyls and primates, and 2) the rate of evolution and the occurrence of positive Darwinian selection using codon based models of sequence evolution.
We test this hypothesis using a population based model of protein evolution.
Berezovskaya and associates present here a differential equation based model of the evolution of CRISPR-Cas based immunity.
In addition to the codon-based models of evolution, we wished to identify bowhead whale specific amino acid replacement substitutions.
To explore variation in selective pressure between Ddx3a and Ddx3b genes in teleosts, we used codon-based models of evolution, as implemented in PAML (Yang 2007).
We analyzed each of the 319 refined SGOs using the nested codon-based models of evolution under a maximum likelihood framework.
The relative rates of sequence divergence and dN/dS ratio were determined for the protein coding genes using codon-based models of evolution in PAML v4.4 [ 25].
Likelihood analyses using codon-based models of evolution reveal significant changes in selective constraint along two of the guppy LWS opsin lineages.
In a complementary and more detailed analysis of selective pressure variation, we used codon-based models of evolution (Yang, 2007) to identify candidate genes with evidence of lineage-specific positive selection (see Experimental Procedures).
Tina Koestler (CIBIV, Vienna, Austria) and Jean-Baka Domelevo (LIRMM, Montpellier, France) presented profile-based models of evolution, taking into account particularities of functional or structural regions of protein sequences.
