4DTV

4DTV stands for four-fold synonymous (degenerative) third-codon transversion. It represents a transversion in the third nucleotide position within four codons that does not result in a change in corresponding amino acid identity within the protein it codes for. Such an estimate of synonymous mutation rate within a transcribed region of a gene but not in region that experiences selection is a conserved means of estimating divergence within the more recent evolutionary past. Distances corresponding to the 'salicoid' whole-genome duplication events were delineated based on discrete peaks in 4DTV distributions. Duplicated segments were defined as regions on different linkage groups or scaffolds containing six or more homeologous pairs with similar 4DTV values, with fewer than 25 nonhomeologous genes intervening. Gene pairs resulting from the 'salicoid' duplication (apparently common to the Salicaceae) were defined by 4DTV values between 0.04 and 0.17. Microsynteny in flanking regions of segmental duplicates was verified using the Genome Browser. Tandemly duplicated genes that matched the same homeolog were only counted once for this analysis.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174922/

Synonymous substitution (K_s) and fourfold degenerate site transversion (4DTV) calculation

For each pair of homologs, we aligned their protein sequences using CLUSTALW (Thompson et al. 1994) and converted the protein alignment to DNA alignment using PAL2NAL (Suyama et al. 2006). Some homologous genes could not produce reliable CLUSTALW alignment for various reasons and were discarded from further analysis. K_s values were calculated using the Nei-Gojobori algorithm (Nei and Gojobori 1986) implemented in the PAML package (Yang 1997). We repeated theK_s calculation using other algorithms and found that the differences are small, systematic biases that do not affect major conclusions. We calculated 4DTV values between gene pairs using in-house Perl scripts. 4DTV values are calculated for gene pairs having ≥10 fourfold degenerate sites. Fourfold degenerate sites are codons of amino acid residues G, A, T, P, V, and R, S, L. Raw 4DTV values are then corrected for possible multiple transversions at the same site using this formula:

http://genome.cshlp.org/content/18/12/1944.long