Hi, Russell. Across taxa/clades, sure: clads (Maliet et al., 2019, https://doi.org/10.1038/s41559-019-0908-0) or MiSSE (Vasconcelos et al., 2022, https://doi.org/10.1111/evo.14517) can do this. They paint different diversification rates on different parts of the tree without requiring a priori assignment.
However, I’d be careful about interpreting rates through time, even with these models. Louca & Pennell (2020, https://www.nature.com/articles/s41586-020-2176-1) show that multiple different rates can be equally likely. You could use clads or MiSSE to paint ancestral nodes into diversification regimes, but I’d worry about how much they actually mean. Best, Brian _________________________________________ Brian O’Meara He/Him Professor, Dept. of Ecology & Evolutionary Biology University of Tennessee, Knoxville From: R-sig-phylo <[email protected]> on behalf of Russell Engelman <[email protected]> Date: Tuesday, July 23, 2024 at 8:42 AM To: mailman, r-sig-phylo <[email protected]> Subject: [R-sig-phylo] Calculating Asymmetry in Speciation Across a Phylogeny Dear R-Sig-Phylo, I was wondering if there was a way to quantitatively examine diversification and speciation rates that is sensitive to the fact that not all clades diversify equally? I have a phylogeny where the overall diversity of the group — particularly in terms of higher level clades — declines at a specific point in time, but the broader pattern is being covered up by a massive burst of speciation at one ecologically stereotyped (and possibly taxonomically oversplit) node on the tree. Raw speciation and extinction rates end up giving a biased view of the pattern because they treat all lineages as equal and can't parse that 6-10 clades are declining while the remaining one is undergoing diversification. This contrasts with older parts of the tree where diversification is more evenly spread across different clades. I had considered calculating a Shannon Diversity Index or Inverse Simpson's Diversity Index at each point on a LTT after dividing the tree up by family to get an idea of the overall balance of alpha diversity across clades over time (i.e., clade X represents a disproportionate contribution to standing alpha diversity as time goes on). However, this relies on dividing the tree into a priori groups based on relatively arbitrary criteria and felt rather hacky. I was wondering if there was a more impartial way of calculating or quantitatively describing the asymmetry in diversification rates across nodes over time? Sincerely, Russell [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
