>>The reliability of molecular clocks in reptile phylogenies?
>>
>>Hi folks,
>>
>>I read about molecular clocks and the Neutralist Theory and, the more I read, the more I’m getting curious about how reliable these models are when applied to reptile phylogeny to determine the evolutionary age of lineages (at least when using mtDNA for phylogenies).

Different people have different believes about the accuracy of the molecular clock. In general, I think most scientists would agree that it is fairly accurate.

>>I understand that the basic principal on which the molecular clock theory is based is the constant rate of neutral mutations (those that do not affect the phenotyp) in genes. Furthermore, rate of neutral mutation is also independent from population size (sensu Kimura), whereas in advantageous mutations population size has to be considered as well…

Neutral mutations are those that do not affect the fitness of an organism. A classic example is the mutation of the third nucleotide in a codon, since the net result is no change in the amino acid being coded. Of course another well known example are some of the mitochondrial genes.

>>Well, today we know that there is nothing like a “universal molecular clock”. Slopes and upswings in mutation rates must be calculated for every lineage and a priori assumptions have to be made to “set” the clock.

Not all genes are suitable for ascertaining phylogenies, and certainly not all of them are suitable for use as molecular clocks. Adaptive characters are subject to natural selection, with chance playing a relatively small or even nonexistent role, so these characters are poorly suited for ascertaining phylogenies and/or for use as molecular clocks. I think many people simply erred in ignoring this simple fact, which is well known even to Darwin and his contemporaries, who distrust adaptive characters when dealing with systematics.

>>I recall some papers on reptile phylogeny worked with the pseudo-standard rate of 2% MYA for mtDNA (e.g. Keogh et al., 2001), although the authors mentioned that more recent studies revealed slower or faster clocks (=levels of gene divergence) (e.g. Zamudio & Greene (1997) for allopatric populations of Lachechis (0.47 – 1.32% /My) or more recently Wüster et al. (2002) with 1.09 – 1.77% for the cyt b of the crotaline genus Porthidium. The latter rates were also used by Malotra and Thorpe (2004) for Trimeresurus.). So, at the end, how relieable is the usage of the 2% rate in Keogh et al. (2001). I recall a paper (ARBOGAST, B. S. and J. B. SLOWINSKI 1998) taking apart a priviously published paper from Klicka and Zink due to errornous assumptions and for not providing measures of errors...

Molecular clocks have to be calibrated using the fossil record. So, a disagreement on rates is understandable. I think it is more important to figure out how these authors come up with the mutation rates they are quoting than how fast or slow they think a particular gene is mutating. The reliability of a particular molecular clock is therefore dependent on the soundness of the method of calibration.

>>What about all these side-effects that may have more or less impact on the rate of mutation in genes such as the negative body size correlation and some life-history traits (temperature), gene repair capabilities, selective pressure, advantageous mutations rather than neutral mutations and implied within population size, evolving geographic barriers and diseases that may kill most of a population, other traits of population dynamics, high UV-radiation causing more mutations, and others). How do we handle these? There are lots of stochastic models around but, who decides which of these side-effects (if any) may have taken place?
>>
>>Cheers,
>>Wulf
>>-----
>>http://www.leiopython.de - the white-lipped python site -
>>http://www.herpers-digest.com - herp related eBooks search -

These are all very good questions. When most individuals of a population has perished, the result is a genetic bottleneck, and it is well known that great changes in the genotype can be expected when a population goes through a bottleneck. Another factor that you mentioned, such as increased UV radiation causing more mutations, may not be important as these mutations may not be neutral. A frog egg that has been exposed to too much UV radiation, for example, may not survive to reproduce. Do remember that it is neutral mutations that are most likely to be useful for calibrating the molecular clock.

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