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Abstract Detail

Modeling the processes that mediate speciation and extinction rates across plants

Martinez-Gomez, Jesus [1], Song, Michael [2], Tribble, Carrie [3], Freyman, William [4], Höhna, Sebastian [5], Specht, Chelsea [6], Rothfels, Carl [7].

A comparison of different Bayesian methods for estimating branch-specific shifts in diversification rates.

Diversification parameters (the rates at which lineages speciate and go extinct) can be estimated from time-calibrated phylogenies. Identifying where on a phylogeny shifts in diversification rates occur is of interest to evolutionary biologists as such events may coincide with key evolutionary events, such as the evolution of novel morphological features or dispersal to a new habitat. Multiple methods exist to calculate diversification rates and identify shifts, however their accuracy is hotly debated. Here we test whether four Bayesian methods produce comparable results: Bayesian Analysis of Macroevolutionary Mixtures (BAMM), Lineage-Specific Birth-Death-Shift (LSBDS; implemented in Revbayes), the approximate Multi-Type Birth-Death model (MTBD; implemented in BEAST2), and the cladoge-netic diversification rate shift model (CLaDS2; implemented in Julia). We apply each of these methods to a set of 75 chronograms compiled by Henao Diaz et al. (2019) and compare inferences of speciation rate, extinction rate, and net diversification ate. We find that the four methods generally infer comparable rates of speciation (with the exception of CLaDS2), but strongly differing rates of extinction; inferences of net diversification rate are thus also strongly method-dependent. We discuss how empirical biologists may make informed decisions on which method to choose for analyzing their data.

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1 - Cornell University , Section of Plant Biology and L. H. Bailey Horitorium
2 - University of California Berkeley, Integrative Biology
3 - University Of Hawaii At Manoa, Department Of Biology, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI, 96822, United States
4 - Boise State University, Snake River Plains Herbaria, , Boise, Idaho, 83725, USA
5 - Ludwig-Maximilians-Universität
6 - Cornell University, Section of Plant Biology & the L.H. Bailey Hortorium, 502 Mann Library, Ithaca, NY, 14853, United States
7 - University Of California Berkeley, Berkeley, 94720.0, United States

divergence time estimation
Comparative Phylogenetics

Presentation Type: Colloquium Presentations
Session: C01, Modeling the processes that mediate speciation and extinction rates across plants
Location: /
Date: Monday, July 19th, 2021
Time: 11:00 AM(EDT)
Number: C01004
Abstract ID:959
Candidate for Awards:None

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