search

ropensci / canaper

Categorical Anaysis of Neo- and Paleo-endemism in R
https://docs.ropensci.org/canaper/
Other
7 stars 3 forks source link

Can this package calculate biogeographical graves besides cradle and museum? #14

Closed Otoliths closed 1 year ago

Otoliths commented 1 year ago

Hi, @joelnitta

This package is fantastic! As Rangel et al.(2018) define them here, “cradles” are about speciation, “museums” about persistence, and “graves” about extinctions. In other words, locations with unusually high rates of speciation as “cradles” of diversity, and to locations with unusually low rates of extinction as “museums.”, and “graves”—locations with unusually high extinction rates. In addition to biogeographical cradle (Neo-endemism) and museum (Paleo-endemism), can this package calculate biogeographical graves?

joelnitta commented 1 year ago

Thanks for the comment @Otoliths!

I think the definition of cradles, museums, and graves may be a bit different from what canaper measures, which is phylogenetic endemism. For cradles, museums, and graves, I think you want to look at speciation rate, not degree of phylogenetic endemism. canaper does not measure speciation rate. One popular (but somewhat controversial) package to do that is BAMMtools; the MiSSE method available in hisse is another more recently developed alternative (Ref 1). Once you have an estimation of tip rates, you would need to somehow characterize regional speciation rates, then determine if any are significantly high or low. I think various studies have done this (e.g. Ref 2), but I am not aware of a standard (widely accepted) method.

So I think this is an interesting idea, but the estimation of speciation rates in the first place is not straightforward, and is beyond the scope of canaper. As such I am closing this issue, but feel free to continue the discussion in this issue if you have any more comments.

Ref 1: Vasconcelos, T., O’Meara, B.C. and Beaulieu, J.M. (2022) ‘A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios’, Evolution, p. evo.14517. Available at: https://doi.org/10.1111/evo.14517.

Ref 2: Igea, J. and Tanentzap, A.J. (2019) ‘Multiple macroevolutionary routes to becoming a biodiversity hotspot’, Science Advances, 5(2), p. eaau8067. Available at: https://doi.org/10/ghppj2.