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However, while in the case of Jockey elements from Drosophila melanogaster and D. funebris the rate was much higher in comparison with other pairs, CR1B retrotransposons from B. mori and Maculinea spp. showed significantly low rate of divergence.
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These seemingly conflicting results are best explained by a few species-rich genera (e.g. Dryopteris, Thelypteris, Polystichum) with low rates of divergence in trnH-psbA that skew the overall distribution of interspecific values.
Only ADH4 was significant in comparison to the control gene set (MLHKA test, P = 0.0007) (Table S3) and was characterized by both high rates of polymorphism and also low rates of divergence at synonymous sites.
This indicated that the chloroplasts maintained relatively low rate of sequence divergence to preserve its primary function.
Yet, in comparison to other regions the significance of ADH4 appears to be a partial consequence of the low rate of synonymous divergence.
One gene in the control gene set, TRX2, appeared to be an outlier characterized by both a high rate of synonymous polymorphism and a low rate of synonymous divergence.
Among the insects analysed so far, it appears that the Tribolium genes show the lowest rates of divergence.
If these six genera are examples of overall low rates of sequence divergence, then effective barcoding of such taxa will be difficult no matter which locus is selected.
Based on this observation, genomic scans for noncoding regions characterized by low rates of sequence divergence among different species have been used to identify evolutionarily conserved enhancers.
This low rate of recombination may reflect the higher divergence of the VAND genome, compared to previous crosses between the type 2 ME49 and clonal types 1 [ 30] and 3 [ 20, 29].
Taken together, these data point to a comparatively low rate of duplicate pigmentation gene loss before the euteleost divergence.
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