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Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny

Author:
Evangelista, Dominic, Thouzé, France, Kohli, Manpreet Kaur, Lopez, Philippe, Legendre, Frédéric
Source:
Molecular phylogenetics and evolution 2018 v.128 pp. 112-122
ISSN:
1055-7903
Subject:
Bayesian theory, Blattodea, Isoptera, data quality, genetic markers, loci, phylogeny, probability, qualitative analysis, topology, trees
Abstract:
Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied. Here we argue that a single qualitative analysis is insufficient to assess support of a phylogenetic hypothesis and relate data quality to tree quality. We use six molecular markers to infer the phylogeny of Blattodea and apply various tests to assess relationship support, locus quality, and the relationship between the two. We use internode-certainty calculations in conjunction with bootstrap scores, alignment permutations, and an approximately unbiased (AU) test to assess if the molecular data unambiguously support the phylogenetic relationships found. Our results show higher support for the position of Lamproblattidae, high support for the termite phylogeny, and low support for the position of Anaplectidae, Corydioidea and phylogeny of Blaberoidea. We use Lento plots in conjunction with mutation-saturation plots, calculations of locus homoplasy to assess locus quality, identify long branch attraction, and decide if the tree’s relationships are the result of data biases. We conclude that multiple tests and metrics need to be taken into account to assess tree support and data robustness.
Agid:
6124972