12: Beyond Birth-Death models
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In this chapter I discussed models that go beyond constant rate birth-death models. We can fit models where speciation rate varies across clades or through time (or both). In some cases, very different models predict the same pattern in phylogenetic trees, warranting some caution until direct fossil data can be incorporated. I also described a model of protracted speciation, where speciation takes some time to complete. This latter model is potentially better connected to microevolutionary models of speciation, and could point towards fruitful directions for the field. We know that simple birth-death models do not capture the richness of speciation and extinction across the tree of life, so these models that range beyond birth and death are critical to the growth of comparative methods.
- 12.1: Capturing Variable Evolution
- Simple, constant-rate birth-death models are not adequate to capture the complexity and dynamics of speciation and extinction across the tree of life. Speciation and extinction rates vary through time, across clades, and among geographic regions. We can sometimes predict this variation based on what we know about the mechanisms that lead to speciation and/or extinction. This chapter explores some extensions to birth-death models that allow us to explore diversification in more detail.
- 12.2: Variation in Diversification Rates across Clades
- We know from analyses of tree balance that the tree of life is more imbalanced than birth-death models predict. We can explore this variation in diversification rates by allowing birth and death models to vary along branches in phylogenetic trees. The simplest scenario is when one has a particular prediction about diversification rates to test. For example, we might wonder if diversification rates in one clade are higher than in the rest of the phylogenetic tree.
- 12.3: Variation in Diversification Rates through Time
- In addition to considering rate variation across clades, we might also wonder whether birth and/or death rates have changed through time. For example, perhaps we think our clade is an adaptive radiation that experienced rapid diversification upon arrival to an island archipelago and slowed as this new adaptive zone got filled. This hypothesis is an example of density-dependent diversification, where diversification rate depends on the number of lineages that are present
- 12.4: Diversity-Dependent Models
- Time-dependent models in the previous section are often used as a proxy to capture processes like key innovations or adaptive radiations. Many of these theories suggest that diversification rates should depend on the number of species alive in a certain time or place, rather than time . Therefore, we might want to define speciation rate in a truly diversity dependent manner rather than using time as a proxy.
- 12.5: Protracted Speciation
- In all of the diversification models that we have considered so far, speciation happens instantly; one moment we have a single species, and then immediately two. But this is not biologically plausible. Speciation takes time, as evidenced by the increasing numbers of partially distinct populations that biologists have identified in the natural world. Furthermore, the fact that speciation takes time can have a profound impact on the shapes of phylogenetic trees.