Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

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Table 4.

Likelihood ratio statistic and model parameters for each model of sequence evolution

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Table 4.

  • aSequence evolution further analyzed for reverse transcriptase and integrase among gypsy and copia phylogenies

  • bM0 model, one rate ratio across all codon sites and all branches of phylogeny.

  • cNearly neutral model, constrains w ratio to nearly 0 and 1.

  • dPositive selection model.

  • eDiscrete model of sequence evolution with four categories (k).

  • fDiscrete model of sequence evolution estimated by fitModeL for comparison to M3 + 1.

  • gDiscrete model of sequence evolution, which allows “switches” of rates along phylogeny.

This Article

  1. Published in Advance November 24, 2008, doi: 10.1101/gr.083360.108 Genome Res. 19: 243-254

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