Illustrations of calibrating fossils. All illustrations reproduced with permission. Scale bars equal 1 mm. 1, Cretaholocompsa montsecana Martinez-Delclos, 1993 (in Martinez-Delclos, 1993, figure 8). 2, Cariblattoides labandeirai Vršanský, Vidlička, Čiampor, Jr. and Marsh 2012 (in Vršanský et al., 2012, figure 12). 3, Ectobius kohlsi Vršanský, Vidlička, and Labandeira 2014 (in Vršanský et al., 2014, figure 3).
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Soil‐burrowing cockroaches (Blaberidae: Geoscapheinae) are large insects endemic to Australia. Originally thought to represent a monophyletic group, these enigmatic species have in fact evolved burrowing behaviour, associated fossorial morphological modifications, and dietary transitions to dry leaf litter feeding multiple times from the wood‐feeding Panesthiinae in a striking example of parallel evolution. However, various relationships within these two subfamilies remain unresolved or poorly understood, notably the apparent paraphyly of Panesthiinae with respect to Geoscapheinae, the position and diversification of certain species within major clades, and several aspects of the overall group's biogeography and morphological evolution. Here, we investigate the phylogeny of Australian members of these two subfamilies using whole mitochondrial genomes paired with nuclear ribosomal markers and highly conserved genes from the bacterial endosymbiont Blattabacterium. Using the resulting robust, fossil‐calibrated phylogeny from these three sources we confirm the nonmonophyly of both subfamilies and recover Geoscapheinae as polyphyletic within a paraphyletic Panesthiinae. The nonmonophyly of natural groups, at all levels from subfamily to species, has been driven by repeated, independent acquisitions of burrowing forms in Geoscapheinae from panesthiine ancestors that colonized the continent on two separate occasions during the Miocene. We additionally find morphological variation within Geoscapheinae itself is correlated with species distributions. Older soil‐burrowing clades living in comparatively arid environments have additional morphological reductions beyond obvious fossorial adaptations compared to those in younger burrowing clades from more temperate habitats. Ultimately, the results presented here demonstrate connections among phylogeny, biogeography and morphology throughout Australian representatives of these two subfamilies, factors that could not be previously consolidated using existing phylogenetic frameworks. Given the discordance between molecular data implemented here and the existing taxonomic classification, we find no support for retaining Geoscapheinae as a discrete taxonomic grouping. In closing, we discuss the taxonomic implications of these results and present a roadmap for future research on Geoscapheinae and their panesthiine relatives.
Time and again, over hundreds of millions of years, environmental disturbances have caused mass extinctions of animals ranging from reptiles to corals. The anthropogenic loss of species diversity happening now is often discussed as the ‘sixth mass extinction’ in light of the ‘Big Five’ mass extinctions in the fossil record. But insects, whose taxonomic diversity now appears to be threatened by human activity, have a unique extinction history. Prehistoric losses of insect diversity at the levels of order and family appear to have been driven by competition among insect lineages, with biotic replacement ensuring minimal net losses in taxonomic diversity. The end-Permian extinction, the ‘mother of mass extinctions’ in the seas, was more of a faunal turnover than a mass extinction for insects. Insects’ current biotic crisis has been measured in terms of the loss of abundance and biomass (rather than the loss of species, genera, or families) and these are essentially impossible to measure in the fossil record. However, should the ongoing loss of insect abundance and biomass cause the demise of many insect families, the current extinction event may well be the first sudden loss of higher-level insect diversity in our planet’s history. This is not insects’ sixth mass extinction—in fact, it may become their first.
Phylogenomics seeks to use next‐generation data to robustly infer an organism's evolutionary history. Yet, the practical caveats of phylogenomics motivate investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in Blaberoidea. We examine locus substitution rate, saturation, evolutionary divergence, rate heterogeneity, stabilizing selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species. Loci with high substitution rate, low saturation, low sequence distance, low rate heterogeneity, and strong stabilizing selection derive more support for phylogenetic relationships. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori. We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction, improved statistical support, and potential 4‐6x improvements to computation time. Supported by phylogenetic and morphological evidence, we erect three newly named clades (Anallactinae Evangelista & Wipfler subfam. nov., Orkrasomeria tax. nov. Evangelista, Wipfler, & Béthoux and Hemithyrsocerini Evangelista tribe nov.) and propose other taxonomic modifications. The diagnosis of Pseudophyllodromiidae Grandcolas, 1996 is modified to accommodate Anallactinae and Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel morphological characters.
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.
Members of the class Armophorea occur in microaerophilic and anaerobic habitats, including the digestive tract of invertebrates and vertebrates. Phylogenetic kinships of metopid and clevelandellid armophoreans conflict with traditional morphology‐based classifications. To reconcile their relationships and understand their morphological evolution and diversification, we utilized the molecular clock theory as well as information contained in the estimated time trees and morphology of extant taxa. The radiation of the last common ancestor of metopids and clevelandellids very likely occurred during the Paleozoic and crown diversification of the endosymbiotic clevelandellids dates back to the Mesozoic. According to diversification analyses, endosymbiotic clevelandellids have higher net diversification rates than predominantly free‐living metopids. Their cladogenic success was very likely associated with sharply isolated ecological niches constituted by their hosts. Conflicts between traditional classifications and molecular phylogenies of metopids and clevelandellids very likely come from processes, leading to further diversification without extinction of ancestral lineages as well as from morphological plesiomorphies incorrectly classified as apomorphies. Our study thus suggests that diversification processes and reconstruction of ancestral morphologies improve the understanding of paraphyly which occurs in groups of organisms with an apparently long evolutionary history and when speciation prevails over extinction. This article is protected by copyright. All rights reserved.
Cockroaches are among the most recognizable of all insects. In addition to their role as pests, they play a key ecological role as decomposers. Despite numerous studies of cockroach phylogeny in recent decades, relationships among most major lineages are yet to be resolved. Here we examine phylogenetic relationships among cockroaches based on five genes (mitochondrial 12S rRNA, 16S rRNA, COII; nuclear 28S rRNA and histone H3), and infer divergence times on the basis of 8 fossils. We included in our analyses sequences from 52 new species collected in China, representing 7 families. These were combined with data from a recent study that examined these same genes from 49 species, resulting in a significant increase in taxa analysed. Three major lineages, Corydioidea, Blaberoidea, and Blattoidea were recovered, the latter comprising Blattidae, Tryonicidae, Lamproblattidae, Anaplectidae, Cryptocercidae and Isoptera. The estimated age of the split between Mantodea and Blattodea ranged from 204.3 Ma to 289.1 Ma. Corydioidea was estimated to have diverged 209.7 Ma (180.5–244.3 Ma 95% confidence interval [CI]) from the remaining Blattodea. The clade Blattoidea diverged from their sister group, Blaberoidea, around 198.3 Ma (173.1–229.1 Ma). The addition of the extra taxa in this study has resulted in significantly higher levels of support for a number of previously recognized groupings.