FYI, we run PSMCs against self-Masurca assemblies of Illumina reads, as well as against our reference genome. Clermontia spp. are rather poorly divergent which makes the reference genome approach OK, so long as coverage OK. Mapping Cyanea, Delissea and Brighamia to Clermontia not advisable ;)

Will be happy to talk shop w you about other findings we have .. trees, PCAs, F3 analyses, NeighborNet (all of these just complementary w each other and ADMIXTURE) .. but also PSMCs

Here’s the other - needs some manual adjustments tho. This work done by expert PhD student Michaela Richter 😀

Here’s one haplotype .. 14 chrs

Still working on it! We just generated two new assemblies - phased haplotypes - using HifiAsm with the ONT flag plus our HiC reads. Such a big step means we need to re-call our SNPs .. on both haplotypes, independently

The Droseraceae issue arises if one wants a monophyletic Drosera

The NeighborNet doesn’t help much to discern admixture vs other sources of homoplasy; it’s a summary of all splits that may imply any source incongruence. It does reflect the admixture graph in this case. Also in the Stachys/Hawaiian mint case I posted