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State-dependent speciation and extinction
Understanding Diversification Complexity in Large Phylogenies with State-Dependent Speciation and Extinction Models
Sixteen years have passed since Wayne Maddison, Peter Midford, and Sally Otto introduced the binary state speciation and extinction model (BiSSE). BiSSE revolutionized the field of phylogenetic comparative analysis by enabling us to investigate the influence of traits on the tempo of speciation and extinction. However, working with phylogenies presents challenges. The lack of independence between taxa complicates likelihood calculations, and as phylogenies grow, additional factors such as accelerated extinction and unmeasured variables can impact diversification rates.
In this presentation, I will explore recent advancements in state-dependent diversification models using the graphical modeling software RevBayes. I will demonstrate how to incorporate multiple traits and assess their respective contributions to the diversification process. Additionally, I will show how to integrate enhanced extinction histories and conclude by explaining how to measure the significance of diversification based on transition type and not state value within a cladogenetic framework.
How to quantify diversification of real species?
As many biologists, I'm interested in the diversity of species, and the differences in diversity that exist between clades, and I'm thus excited by all the methods that now exist to quantify diversification rates. Indeed, some traits have been proposed to be "key innovations", conferring evolutionary advantages to the lineages in which they evolved. In plants, such traits might be flowers, self-incompatibility, or specialized insect pollination. Although considerable progress has been made in the modelling of diversification rates, the current models remain extremely simple compared to the complex dynamics of diversification in the real world. First, diversification has been shown to be influenced by many intrinsic and extrinsic factors. Second, traits do not act in isolation but are always embedded in the physiological, morphological and ecological context of the species. These are seemingly trivial observations but they have largely faled to be taken into account in diversification research, and I'll explore some of their implications.