4 ms·

A flip side of constraint is constrained diversity. Does a tree always work? Where are the genomes in ILS? Those will be very interesting regions.

inciampati 3y ago
From the abstract: "However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineage sorting and historical hybridization." So it can't be avoided, and the solution of making more trees from different stuff is somewhat unsatisfying. They have to work with the methods they have today.
- f6v 3y ago
  They used maximum likelihood tree building. In Bayesian approach it’s possible to sample from a distribution of trees which can help with the uncertainty. Anyway, I only have very limited knowledge on this from my evolutionary biology course.
  - runeblaze 3y ago
    Reading the paper I think they used both SVDquartets (coalescence-based explicitly for ILS) and concatenation + maximum likelihood, which is a very sane combination for the analysis. Not contradicting you here, but at their scale it is unlikely any Bayesian approach will converge, so they had to settle with whatever they had to quantify uncertainty (branch supports and others). Edit: and also the Bayesian approaches might have model mismatch, for example I am not sure what's an accurate Bayesian method that models hybridization and ILS
sandworm101 3y ago
Trees are tricky. They assume solid splits between species. While that may work well across millions/billions of years it does not work well when describing the specifics of split points. There is no bright line when one generation is suddenly a different species than the last. Genetics describes the slow accumulation of changes. Translating that into a tree of lines connected by points will always require compromise.

4 ms·

A flip side of constraint is constrained diversity. Does a tree always work? Where are the genomes in ILS? Those will be very interesting regions.

by inciampati 3y ago

inciampati 3y ago
From the abstract: "However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineage sorting and historical hybridization." So it can't be avoided, and the solution of making more trees from different stuff is somewhat unsatisfying. They have to work with the methods they have today.
- f6v 3y ago
  They used maximum likelihood tree building. In Bayesian approach it’s possible to sample from a distribution of trees which can help with the uncertainty. Anyway, I only have very limited knowledge on this from my evolutionary biology course.
  - runeblaze 3y ago
    Reading the paper I think they used both SVDquartets (coalescence-based explicitly for ILS) and concatenation + maximum likelihood, which is a very sane combination for the analysis. Not contradicting you here, but at their scale it is unlikely any Bayesian approach will converge, so they had to settle with whatever they had to quantify uncertainty (branch supports and others). Edit: and also the Bayesian approaches might have model mismatch, for example I am not sure what's an accurate Bayesian method that models hybridization and ILS
sandworm101 3y ago
Trees are tricky. They assume solid splits between species. While that may work well across millions/billions of years it does not work well when describing the specifics of split points. There is no bright line when one generation is suddenly a different species than the last. Genetics describes the slow accumulation of changes. Translating that into a tree of lines connected by points will always require compromise.