Third, we measured sequence divergence within duplicate gene groups, using a homology-based clustering coefficient, which increases inversely to sequence divergence.
Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence.
To conduct an evolutionary analysis of the data, we make use of the phylogeny, both branching pattern and branch lengths with branch lengths measuring sequence divergence in the unit of the number of subtitutions per site, inferred by [ 53].
Next generation sequencing of plastid genomes should be able to provide more data, and in turn more accurate measures of sequence divergence and of plastid DNA ages in Callitropsis [37].
Measures of sequence divergence were used as in [ 26], including dN, dN/dS, Ka, and Ka/Ks as previously calculated [ 7, 79].
This lack of a consistent association implies that divergence times obtained by applying a molecular clock to one of these measures of sequence divergence will rarely match those calibrated to another.
This problem is particularly acute with previous studies of mammalian transposons and non-LTR retrotransposons that have relied upon measures of sequence divergence between extant elements and their ancestral consensus sequences as estimates of element age.
Of the 16 annotated genome pairs, ten possessed >100 orthologous gene pairs with K s values between 0.3 and 1.5 and K18 s values >95% and could thus provide reliable genome-wide measures of sequence divergence.
For gene duplicate pairs displaying structural heterogeneity in their coding regions (partial and chimeric structure discussed in the subsequent section), all measures of sequence divergence (synonymous divergence K S and degree of sequence asymmetry/symmetry via Tajima's relative rate test) were calculated using only the homologous regions between the focal C. elegans paralogs.
As alternative measures of sequence divergence, we calculated the synonymous (Ks) and nonsynonymous (Ka) substitution rates for all protein-coding genes shared between the two members of a genome-pair; to avoid the distortion caused by genes that are under strong positive or purifying selection, we used the median value as the genome-wide level of sequence divergence.
