Recovering speciation and extinction dynamics based on phylogenies

Abstract

Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic tree shapes (i.e. trees without branch length information) allowing us to test for speciation rate variation and (ii) methods using the phylogenetic trees with branch length information allowing us to quantify speciation and extinction rates. I end the article with an overview on limitations, open questions and challenges of the reviewed methodology.

Five palaeobiological laws needed to understand the evolution of the living biota

“…While there has been a dramatic increase in the number of integrated palaeontological and neontological studies [1][2][3][4] , from a palaeobiological perspective, the field of biology has not yet fully assimilated the fundamental findings from the fossil record. Here I summarize these findings in the context of their relevance to our understanding of the living biota.…”

“…While the notion of immortality at the level of individuals has been rejected for millennia, it was not until around 1800 that the idea that species could become extinct was established through the discovery of fossils that could not be ascribed to any living species 5 . More formally, the first law can be expressed in terms of the probability that clade will ultimately go extinct, P e : P e = 1, when λ < μ (1) P e = (μ/λ), when λ > μ (2) Five palaeobiological laws needed to understand the evolution of the living biota…”

“…Note that without a fossil record, or some other independent way of testing inferred divergence times, it may be hard to know which prior gives the more accurate answer. Fortunately, in the past few years there has been an increase in the development and use of methods that allow for time varying origination and extinction rates 2,3 , but these methods still need more extensive testing with groups that have good fossil records to determine how well they are able to capture the trajectories and magnitudes of past origination and extinction rates. And as noted above, we also need to bear in mind the possibility that phylogenetic data from only living taxa might simply be insufficient to reliably infer past origination and extinction rates 36 .…”

“…The prevalence of extinction also makes it difficult to determine a clade's true diversity dynamics 2,3,26 . For example, analysis of lineage through time (LTT) plots derived from molecular phylogenies are often used to conclude that living groups are in the midst of ongoing radiations, especially if they show steady or increasing rates of diversification (Fig.…”

“…We are seeing a much deeper appreciation for the magnitude of extinction, its role in shaping the living biota, and the development of tools for incorporating it into the analysis of molecular phylogenies 2,3 . Nonetheless, the palaeontological insights encapsulated by the laws described above have not yet become part of the foundational thinking in evolutionary biology.…”