Abstract
The assumptions underpinning ancestral state reconstruction are violated in many evolutionary systems, especially for traits under directional selection. However, the accuracy of ancestral state reconstruction for non-neutral traits is poorly understood. To investigate the accuracy of ancestral state reconstruction methods, trees and binary characters were simulated under the BiSSE (Binary State Speciation and Extinction) model using a wide range of character-state-dependent rates of speciation, extinction and character-state transition. We used maximum parsimony (MP), BiSSE and two-state Markov (Mk2) models to reconstruct ancestral states. Under each method, error rates increased with node depth, true number of state transitions, and rates of state transition and extinction; exceeding 30% for the deepest 10% of nodes and highest rates of extinction and character-state transition. Where rates of character-state transition were asymmetrical, error rates were greater when the rate away from the ancestral state was largest. Preferential extinction of species with the ancestral character state also led to higher error rates. BiSSE outperformed Mk2 in all scenarios where either speciation or extinction was state dependent and outperformed MP under most conditions. MP outperformed Mk2 in most scenarios except when the rates of character-state transition and/or extinction were highly asymmetrical and the ancestral state was unfavoured.
Highlights
The assumptions underpinning ancestral state reconstruction are violated in many evolutionary systems, especially for traits under directional selection
We address the questions: (1) How much does accuracy of ancestral state reconstruction decrease with increasing rates of character-state transition and increasing node depth? (2) Does accuracy decrease with increasing rates of extinction? (3) Is accuracy lower when the ancestral state is unfavoured compared to otherwise comparable scenarios in which the ancestral state is favoured? This hypothesis is addressed by assessing the impacts of preferential extinction of species carrying the ancestral state, preferential transition from the ancestral to the derived state and preferential speciation of the derived state
For each of the maximum parsimony (MP), Mk2 and Binary State Speciation and Extinction (BiSSE) reconstruction methods, ancestral state reconstruction performed worst for deep nodes in trees evolved under the highest rate of extinction of species with the ancestral state (μ0 = 0.8), and the highest rate of character-state transition from the ancestral to derived state (i.e. q01 = 0.1) (Figs. 1 and 2)
Summary
The assumptions underpinning ancestral state reconstruction are violated in many evolutionary systems, especially for traits under directional selection. Most methods of ancestral state reconstruction assume that the character under consideration is neutral, and that the evolutionary process has not changed across the phylogenetic tree These assumptions make data analysis more straight-forward, they can impact on the accuracy and biological validity of findings[6,7,8]. Known sources of bias in both phylogenetic tree construction and ancestral state reconstruction include changes in rates and processes of evolution across the tree[1,9,10,11,12], dependence between the state of a character and the likelihood of lineage extinction or speciation[13,14], evolutionary convergence[15,16,17] and hemiplasy[18]. Numerous traits have been proposed to influence diversification[26,27], this has potential to bias ancestral state reconstruction
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