Testing for phylogenetic signal in species interaction networks
Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks
Recommendation: posted 20 September 2022, validated 05 October 2022
Species are immersed within communities in which they interact mutualistically, as in pollination or seed dispersal, or nonreciprocally, such as in predation or parasitism, with other species and these interactions play a paramount role in shaping biodiversity (Bascompte and Jordano 2013). Researchers have become increasingly interested in the processes that shape these interactions and how these influence community structure and responses to disturbances. Species interactions are often described using bipartite interaction networks and one important question is how the evolutionary history of the species involved influences the network, including whether there is phylogenetic signal in interactions, in other words whether closely related species interact with other closely related species (Bascompte and Jordano 2013, Perez-Lamarque et al. 2022). To address this question different approaches, correlative and model-based, have been developed to test for phylogenetic signal in interactions, although comparative analyses of the performance of these different metrics are lacking. In their article Perez-Lamarque et al. (2022) set out to test the statistical performance of two widely-used methods, Mantel tests and Phylogenetic Bipartite Linear Models (PBLM; Ives and Godfray 2006) using simulations. Phylogenetic signal is measured as the degree to which distance to the nearest common ancestor predicts the observed similarity in trait values among species. In species interaction networks, the data are actually the between-species dissimilarity among interacting species (Perez-Lamarque et al. 2022), and typical approaches to test for phylogenetic signal cannot be used. However, the Mantel test provides a useful means of analyzing the correlation between two distance matrices, the between-species phylogenetic distance and the between-species dissimilarity in interactions. The PBLM approach, on the other hand, assumes that interactions between species are influenced by unobserved traits that evolve along the phylogenies following a given phenotypic evolution model and the parameters of this model are interpreted in terms of phylogenetic signal (Ives and Godfray 2006). Perez-Lamarque et al (2022) found that the model-based PBLM approach has a high type-I error rate, in other words it often detected phylogenetic signal when there was none. The simple Mantel test was found to present a low type-I error rate and moderate statistical power. However, it tended to overestimate the degree to which species interact with dissimilar partners. In addition to the aforementioned analyses, the authors also tested whether the simple Mantel test was able to detect phylogenetic signal in interactions among species within a given clade in the phylogeny, as phylogenetic signal in species interactions may be localized within specific clades. The article concludes with general guidelines for users wishing to test phylogenetic signal in their interaction networks and illustrates them with an example of an orchid-mycorrhizal fungus network from the oceanic island of La Réunion (Martos et al 2012). This broadly accessible article provides a valuable analysis of the performance of tests of phylogenetic signal in interaction networks enabling users to make informed choices of the analytical methods they wish to employ, and provide useful and detailed guidelines. Therefore, the work should be of broad interest to researchers studying species interactions.
Bascompte J, Jordano P (2013) Mutualistic Networks. Princeton University Press. https://doi.org/10.1515/9781400848720
Ives AR, Godfray HCJ (2006) Phylogenetic Analysis of Trophic Associations. The American Naturalist, 168, E1–E14. https://doi.org/10.1086/505157
Martos F, Munoz F, Pailler T, Kottke I, Gonneau C, Selosse M-A (2012) The role of epiphytism in architecture and evolutionary constraint within mycorrhizal networks of tropical orchids. Molecular Ecology, 21, 5098–5109. https://doi.org/10.1111/j.1365-294X.2012.05692.x
Perez-Lamarque B, Maliet O, Pichon B, Selosse M-A, Martos F, Morlon H (2022) Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks. bioRxiv, 2021.08.30.458192, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.08.30.458192
Alejandro Gonzalez Voyer (2022) Testing for phylogenetic signal in species interaction networks. Peer Community in Evolutionary Biology, 100150. https://doi.org/10.24072/pci.evolbiol.100150
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/2021.08.30.458192
Version of the preprint: 4
Author's Reply, 25 Aug 2022
Decision by Alejandro Gonzalez Voyer, posted 22 Aug 2022
I have now received comments from the two expert reviewers who previously provided comments on your preprint. Both are happy with how you addressed their previous comments and think the work is almost ready for recommendation. One reviewer raised to minor points which I think could be relatively easily addressed:
• l.162-184: Although the authors added a new figure that helps summarising the simulations (great job!), a table summarising the different parameters could still be useful (I still need to go back to the methods when reading the results part to find which parameter is which).
• l.431: I am still not sure why the authors used a 10 million arbitrary branch length, is this corresponding to some average speciation time in some other studies? Also on Figure 5, these politomies seem younger than 10 Mya.
I would ask you to address these two minor comments and I will make the final decision without sending the work out for review again.
I would end thanking you for considering PCI Evolutionary Biology for your work and also for the positive responses to the reviewer's comments.
Reviewed by Joaquin Calatayud, 31 Jul 2022
Reviewed by Thomas Guillerme, 21 Aug 2022
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2021.08.30.458192
Version of the preprint: 3
Author's Reply, 18 Jul 2022
Decision by Alejandro Gonzalez Voyer, posted 16 May 2022
I have read with interest the submitted preprint Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks. I think the manuscript is well written and clearly presented in general. I think it could make for a valuable contribution to the field given the meticulous analyses of the perfomance of different metrics to test for phylogenetic signal in interaction networks. The two expert reviewers also agree that the work is well written and could be of interest to evolutionary biologists and evolutionary ecologists. The two reviewers have made a number of excellent suggestions on how to improve the work which should be addressed prior to recommendation. I have very little to add to the thorough reviews by both expert reviewers.
I look forward to receiving a revised version of your manuscript.