... genes.¹

In certain cases it may make sense to talk about a phylogeny of populations within species, but in many cases it doesn't. We'll discuss this further when we get to phylogeography in a couple of weeks.

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... tenuous.²

One way of justifying a strict parsimony approach to cladistics is by arguing (a) that by minimizing character state changes on a tree you're merely trying to find a pattern of character changes as consistent as possible with the data you've gathered and (b) that evolutionary processes should be invoked only to explain that pattern, not to construct it.

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... expressed.³

Of course, differences in expression must ultimately be the result of a DNA sequence difference somewhere, e.g., in a promoter sequence or the locus encoding a promotor or repressor protein, if it is a genetic difference or the result of an epigenetic modification of the sequence, e.g., by methylation.

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... out'',⁴

See below for a description of some of these repetitive seqeuences.

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... loci.⁵

Classical Mendelian genetics, and quantitative genetics too for that matter, depend on genetic variation in traits to identify the presence of a gene.

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... inbreeding.⁶

To be fair, it is possible to distinguish heterozygotes from homozyotes with AFLPs, if you are very careful with your PCR technique [5]. That being said, few people are careful enough with their PCR to be able to score AFLPs reliably as codominant markers, and I am unaware of anyone who has done so outside of a controlled breeding program.

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... time.⁷

By now you should realize that when I write that somethin is ``fairly simple'', I mean that it's fairly simple to someone who's comfortable with mathematics.

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....⁸

The factor 2 is there because $\lambda t$ substitutions are expected on each branch. In fact you will usually see the equation for $q_t$ written as $q_t = 1 - (3/4)\left(1 - e^{-4\alpha t/3}\right)$, where $\alpha = 2\lambda$. $\alpha$ is also referred to as the substitution rate, but it refers to the rate of substitution between the two sequences, not to the rate of substitution between each sequence and their common ancestor. If mutations are neutral $\lambda$ equals the mutation rate, while $\alpha$ equals twice the mutation rate.

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...fig:asrv).⁹

And, to be honest, because it is mathematically convenient to work with.

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