Phrasing in first notebook, re alleles

[hyanwong]

You say

The tree consists of nodes, which represent the alleles held by different chromosomes in the history of the sample, and edges, which represent genealogical relationships between the alleles.

But I think it might be read as the nodes representing alleles (which they don't, of course). We normally say that the nodes represent genomes, I think? The genomes can carry mutations, which result in alleles being observed.

[hyanwong]

Similarly for other mentions of "alleles" in that notebook, I would say, e.g. "Suppose we have a sample of 4 alleles" - I think you mean genomes here. I could see the current phrasing as meaning 4 alleles at a single site.

[gtsambos]

Thanks @hyanwong! I'm trying to introduce them first to the idea of a tree at a single point in the genome, would 'nucleotide' be a better choice? (Though I know the sites can be other things, I don't want to introduce that level of abstraction just yet) Then after that I basically say "this single tree might also represent the genealogy at some neighbouring sites, but at some point you'll move along the genome and see a different tree, and that's why it is a tree sequence"

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[hyanwong]

Hmm, well an allele is something different, right? Two sample nodes can contain the same allele at a locus. The node is not an allele itself.

Could you just say " the nodes represent genomes or regions of genomes, here we've picked a short region and so the relationship is just a simple tree" - or something?

[gtsambos]

Yes, I guess I could say "a region spanned by a single nucleotide base"

[hyanwong]

Or "a short region of genome, perhaps just a single base"?