`Chromosome painting' with tree sequences

Hello, thanks for the excellent software! This is a request for a feature rather than an `issue’.

It would be really useful to be able to track the local ancestry of each leaf along a chromosome so that the simulated chromosomes can be ‘painted’ according to their population of origin. Ie. traverse back up the tree from a leaf until you get to the ancestor at the time of the relevant admixture, but at every tree and every sequence.

[gtsambos]

Blast from the past! 🕰

[gtsambos]

Hi @jeromekelleher and @gdurif - thanks for your comments and thoughtful engagement with this! I am about to fly to New Zealand and will be computer-less for a few days, but will engage with this properly next week when my brain is back in work mode.

Just quickly though:

Thanks for the feature request @gtsambos — we’re actually thinking about something pretty similar at the moment where we want to compute for every node in the tree sequence, the mean fraction of samples descending from that node that are from each population. So, suppose we had node in a tree that had 100 samples from p1 below it and 100 samples from p2 below it (and these we only have two populations, p1 and p2). Then the fractions would be 0.5 and 0.5.

Is this similar to what you’re thinking about?

I was thinking about this at the more de-aggregated level of individual leaf nodes, like @gdurif is describing. Say the two admixing populations are labelled X and Y, and you’re using msprime to generate sequences from admixed descendants of these populations. Then for any specific tree in a TreeSequence, every leaf node should descend from exactly one of those populations, and thus have ancestry with that population. Say your TreeSequence has 3 trees spanning the intervals [0,1], [1,2] and [2,3]; then a sample might have ancestry X on [0,1], Y on [1,2] and X on [2,3] for example.

Will write more when I’m back from holidays!