Wounded King writes:
In what way? molbiogirl said were were 1% different 'genetically', a vague term that could encompass any level of genetic organisation. Skeptic faith simply said he had heard a value for genetic divergence of 5-7%. In what way is his assertion any more flawed than molbiogirl's? They are both using the vague concept of genetic similarity but providing figures base on different specific genetic metrics.
I guess I have to agree with this: the two ideas kind of delineate the outer boundaries of the argument, don't they?
Wounded King writes:
Why is a single nucleotide substitution a better guage than a 2bp deletion for evolutionary distance?
It's not: the two are equal gauges, because they both represent a
single change in the genome. A view based on sequence-divergence puts the deletion as more influential, when in fact it represents no more evolutionary distance than the point-mutation.
This is a quote from the article you cited by Britten (PNAS, 2002), which is the only one I have been able to read yet:
It appears appropriate to me to consider the full length of the gaps in estimating the interspecies divergence. These stretches of DNA are actually absent from one and present in the other genome. In the past, indels have often simply been counted regardless of length and added to the base substitution count, because that is convenient for phylogenetics. (emphasis added)
It
is convenient for phylogenetics, and it makes more sense when dealing with evolutionary distances. Sequence divergence only shows how different the two species are, not how long they've been separated from one another. Using deletion lengths (as Britten did) to represent how close humans are to chimpanzees would inflate their importance relative to point mutations, making it look like we diverged X+Y mya when, in fact, we diverged only X mya (X and Y >0).
In fact, Britten acknowledges this later in the paper:
More nucleotides are included in insertion/deletion events (3.4%) than base substitutions (1.4%) by much more than a factor of two. However, the number of events is small in comparison. About 1,000 indels listed in Tables 2 and 3 compared with about 10,000 base substitution events in this comparison of 779,142 nt between chimp and human. (emphasis added)
So, a big deletion is still just one deletion, and still happened at one time, even if it removed hundreds of nucleotides of base-pair homology. Deleting 54,773 base pairs in one swoop (or several swoops) is very different from changing 54,773 base pairs slowly over 54,773 separate mutation events. They would have the same end result, and so may represent the same amount of "sequence divergence," as per Britten's standards. But the first could have happened between me and my son (i.e. in 1 generation), while the second probably won't have happened in my evolutionary descendants 51 million years down the road (assuming my lineage lasts that long).
If you then compared these two genes (my son vs evolutionarily-distant descendant) using Britten's sequence-divergence strategy, you would then come to the conclusion that I am more closely related to my 51-million-years-down-the-road descendant than I am to my own son (at least at that locus). Multiple such deletions across the genome would make it even harder.
So, if you're talking just about
genetic similarity (as I assume you are), then skepticfaith's estimate is probably closer. But, if you're talking about
evolutionary relatedness (which is closer to the topic of this thread), skepticfaith's estimate is an inflation of the distinction between us and chimps.
Signed,
Nobody Important (just Bluejay)