Nooney, C, Barber, S orcid.org/0000-0002-7611-7219, Gusnanto, A et al. (1 more author) (2017) A statistical method for analysing cospeciation in tritrophic ecology using electrical circuit theory. Statistical Applications in Genetics and Molecular Biology, 16 (5-6). pp. 349-365. ISSN 2194-6302
Abstract
We introduce a new method to test efficiently for cospeciation in tritrophic systems. Our method utilises an analogy with electrical circuit theory to reduce higher order systems into bitrophic data sets that retain the information of the original system. We use a sophisticated permutation scheme that weights interactions between two trophic layers based on their connection to the third layer in the system. Our method has several advantages compared to the method of Mramba et al. [Mramba, L. K., S. Barber, K. Hommola, L. A. Dyer, J. S. Wilson, M. L. Forister and W. R. Gilks (2013): “Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology,” Stat. Appl. Genet. Mol. Biol., 12, 679–701.]. We do not require triangular interactions to connect the three phylogenetic trees and an easily interpreted p-value is obtained in one step. Another advantage of our method is the scope for generalisation to higher order systems and phylogenetic networks. The performance of our method is compared to the methods of Hommola et al. [Hommola, K., J. E. Smith, Y. Qiu and W. R. Gilks (2009): “A permutation test of host–parasite cospeciation,” Mol. Biol. Evol., 26, 1457–1468.] and Mramba et al. [Mramba, L. K., S. Barber, K. Hommola, L. A. Dyer, J. S. Wilson, M. L. Forister and W. R. Gilks (2013): “Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology,” Stat. Appl. Genet. Mol. Biol., 12, 679–701.] at the bitrophic and tritrophic level, respectively. This was achieved by evaluating type I error and statistical power. The results show that our method produces unbiased p-values and has comparable power overall at both trophic levels. Our method was successfully applied to a dataset of leaf-mining moths, parasitoid wasps and host plants [Lopez-Vaamonde, C., H. Godfray, S. West, C. Hansson and J. Cook (2005): “The evolution of host use and unusual reproductive strategies in achrysocharoides parasitoid wasps,” J. Evol. Biol., 18, 1029–1041.], at both the bitrophic and tritrophic levels.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2017. Walter de Gruyter GmbH, Berlin/Boston. This paper is published in Statistical Applications in Genetics and Molecular Biology. Reproduced in accordance with the publisher's self-archiving policy. |
Keywords: | cospeciation; electrical circuit; Kirchhoff matrix; tritrophic ecology; weighted permutation test |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Engineering & Physical Sciences (Leeds) > School of Mathematics (Leeds) > Statistics (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 18 Oct 2017 10:32 |
Last Modified: | 21 Oct 2020 07:01 |
Status: | Published |
Publisher: | De Gruyter |
Identification Number: | 10.1515/sagmb-2016-0049 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:122665 |