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Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels.
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Our molecular clock analysis highlights the differences in the sequence divergence rates between the MC1-2 receptor subtypes, that seem to evolve fast, and the MC3-4-5 subtypevolvet evolve slower (see Figure 3).
The OsLRR-PSR gene is the true ortholog of IRI-like genes and the incongruent divergence time estimates are caused by differences in molecular clock rates.
In theory, genetic differences between closely related taxa allow the establishment of a divergence time based on a known rate of accumulation of neutral genetic differences (the molecular clock).
Since most fixed differences are neutral and accumulate at a rate proportional to the mutation rate (molecular clock), the number of fixed differences are indicative for the elapsed time since two populations evolved from a common ancestor.
We performed two different molecular clock analyses.
Firstly, if their likelihood-ratio test indicated that all sequences evolved according to a molecular clock, one would not anticipate pronounced differences in branch lengths between taxa.
Molecular clock calibration is always problematic, but this >10-fold difference offers dramatic contrast between a recent and ancient New World introduction.
Small differences between observed and estimated values suggest that the molecular clock assumption is (approximately) valid for a given dataset and tree topology, whereas large differences indicate that molecular clock is not applicable.
Assumption of a molecular clock is useful for estimating the divergence time between orthologous molecular sequences.
The differences should raise questions about how precisely the molecular clock predicts the actual dates of origin of the mammal groups, Heaney says.
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