Fig 5.A: meaning of horizontal lines
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I'm confused by the horizontal line in fig 5A between nodes B and C. Since E only inherits from B, should there not just be a direct line from B to E (like we have from B to A)?
I think we should have a quick explanation for the difference between horizontal and vertical lines. Or perhaps make one type dashed and the other full, to emphasise that they are qualitatively different?
I've made horizontal lines dotted and adjusted the caption. What do you think? I think that we should have the line in the pedigree between B and C, because those dotted lines mean "parents of", which is conceptually different than "contributed genome to".
This is good, thanks. I am still slightly confused by C being a parent of E, but not contributing any genome though... Am I just being too literal about the meaning of 'parent'?
I have re-made these figures: the resulting tree sequence has one more tree, but now this could be the result of diploids mating (and I have said so in the caption). I could cut out A if you think that would help?
The result also no longer has multiple chunks of ancestry coming together from different places into a single coalescent event at the top, which was a nice complicated bit about the previous example; but, simpler is better here.
Yes, I follow it now! Changing to explicitly talking about diploids makes this much easier to understand I think. This is a great figure; it really makes the forwards-time model totally clear.
Minor issues:
- "D and E were parents to F ," -> should be G?
- "(C) Simplified for I,J:" -> should read J, K
I haven't gone through the edges and trees in full detail yet, but I'll do it at some point.
whoops; yes. fixed.