...years

``Unlike that of physics, the fundamental paradigm of evolutionary biology has not changed in over a century, and it is sometimes depressing to think that we may be forever sweeping up behind the Darwinian elephant.cite --Jerry Coyne coyne.

...above

As an aside, the problem in the previous example can be framed as one of coalescence times-- the time at which the genealogy of the present-day alleles ``coalesces" into a common ancestor. One way to think of this is through identity by descent. Imagine extending a pedigree backwards in time. Every generation back, two alleles could either be identical by descent or not with respect to the previous generation. Eventually, if you go back far enough, they will be IBD, and the two lineages will ``coalesce" into one. Coalescent theory, which uses probability-based models of population processes to guide the reconstruction of these unknown lineages, has proved to be an extremely flexible and useful way to look at DNA sequence evolution. For some early reviews, see Hudson[7], Tavare[13]. For some applications, see any issue of the journal Genetics in the last 10 years.)

...used

In animals. Plant mitochondrial genomes are quite different, having very low rates of point mutation, and very high rates of recombination and large-scale genome rearrangement.

...neutral

Later expanded to include ``nearly neutral" mutations (for review, see Ohta[10]).

...diploid

Their mitochondria, on the other hand, are haploid.

...frequencies

Alternatively, from a coalescent perspective, we could say that each offspring chooses its parent randomly from the previous generation

...hemoglobin

In the interest of historical accuracy, it should be pointed out that the neutral theory was proposed in part to account for such observations, rather than the other way around.

...equation)

Again, many of the key results from this approach have been re-derived, with considerably more ease, using coalescent theory.

Simon Cawley
Tue May 12 11:50:21 PDT 1998