13: Characters and Diversification Rates
Many evolutionary models postulate a link between species characteristics and speciation, extinction, or both. These hypotheses can be tested using state-dependent diversification models, which explicitly consider the possibility that species’ characters affect their diversification rates. State-dependent models as currently implemented have some potential problems, but there are methods to deal with these critiques. The overall ability of state-dependent models to explain broad patterns of evolutionary change remains to be determined, but represents a promising avenue for future research.
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- 13.1: The Evolution of Self-Incompatibility
- Some species of angiosperms can avoid self-fertilization through self-incompatibility. In plants with self-incompatibility, the process by which the sperm meets the egg is interrupted at some stage if pollen grains have a genotype that is the same as the parent. This prevents self-fertilization – and also prevents sexual reproduction with plants that have the same genotype(s) at loci involved in the process.
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- 13.2: A State-Dependent Model of Diversification
- The models that we will consider in this chapter include trait evolution and associated lineage diversification. In the simplest case, we can consider a model where the character has two states, 0 and 1, and diversification rates depend on those states. We need to model the transitions among these states, which we can do in an identical way to what we did previously with a continuous-time Markov model.
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- 13.3: Calculating Likelihoods for State-Dependent Diversification Models
- To calculate likelihoods for state-dependent diversification models we use a pruning algorithm with calculations that progress back through the tree from the tips to the root. We have already used this approach to derive likelihoods for constant rate birth-death models on trees and this derivation is similar.
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- 13.4: ML and Bayesian Tests for State-Dependent Diversification
- Now that we can calculate the likelihood for state-dependent diversification models, formulating ML and Bayesian tests follows the same pattern we have encountered before. For ML, some comparisons are nested and so you can use likelihood ratio tests.
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- 13.5: Potential Pitfalls and How to Avoid Them
- The most serious limitation of state-dependent models as currently implemented is that they consider only a relatively small set of possible models. In particular, the approach we describe above compares two models: first, a model where birth and death rates are constant and do not depend on the state of the character; and second, a model where birth and death rates depend only on the character state.