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Accuracy of ancestral state reconstruction for non-neutral traits

Citation

Holland, BR and Ketelaar-Jones, S and O'Mara, AR and Woodhams, MD and Jordan, GJ, Accuracy of ancestral state reconstruction for non-neutral traits, Scientific Reports, 10, (1) Article 7644. ISSN 2045-2322 (2020) [Refereed Article]


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Copyright 2020 The Authors. Licensed under Creative Commons Attribution 4.0 International (CC BY 4.0) https://creativecommons.org/licenses/by/4.0/

DOI: doi:10.1038/s41598-020-64647-4

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.

Item Details

Item Type:Refereed Article
Keywords:ancestral state reconstruction, phylogeny, trait dependent speciation and extinction
Research Division:Biological Sciences
Research Group:Evolutionary biology
Research Field:Phylogeny and comparative analysis
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the biological sciences
UTAS Author:Holland, BR (Professor Barbara Holland)
UTAS Author:Ketelaar-Jones, S (Ms Saan Ketelaar-Jones)
UTAS Author:O'Mara, AR (Mr Aidan O'Mara)
UTAS Author:Woodhams, MD (Dr Michael Woodhams)
UTAS Author:Jordan, GJ (Professor Greg Jordan)
ID Code:141852
Year Published:2020
Funding Support:Australian Research Council (DP160100809)
Deposited By:Mathematics
Deposited On:2020-11-26
Last Modified:2020-12-10
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