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Other peptide families with multiple forms such as allatostatins [ 8] have both conserved and fast-evolving peptide sequences and are certainly more significant in this context but less extensively studied.
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As well as for de novo ncRNA annotation, they have been used to detect protein-coding genes [17], [18], conserved regions [19] and fast-evolving ones [20].
As expected, the quantitative estimates of past temperatures inferred by both slow- and fast-evolving sites are different from those obtained with the complete dataset.
This is because nonrecombining haplotypes composed of both slow-evolving markers (DIP) and fast-evolving markers (STR) combine the benefits of both tools [de Knijff, 2000; Mountain et al., 2002].
Both slowly (e.g. PRDM2) and fast-evolving (e.g. PRDM6) paralogs show methyltransferase activity, which implies the repartition of the putative ancestral function among several duplicates.
Subtelomeres are dynamic and fast-evolving regions of eukaryotic genomes owing to their remarkable plasticity [1] [3].
AARs are highly polymorphic and fast-evolving sequences [ 9, 16].
We place a separate HMM on the root sequence, allowing it to switch between emitting slow-evolving characters and fast-evolving characters with specific probabilities.
We sorted genes by their Ka values from smallest to largest in each lineage, and defined genes corresponding to the lowest, middle, and highest 10% of Ka values to be slow-evolving, intermediately-evolving, and fast-evolving genes, respectively.
These genes have distinct functions and cannot be associated with recent large and fast-evolving duplicated gene families.
Repeated domains and fast-evolving mucin domains also hamper the automatic sequence alignment of the family 15.
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