The resolution of the Insect Tree of Life has recently improved using phylogenomic data. Here, new data sets resolved the origin of hexapods (Pancrustacea = “Crustacea” + Hexapoda) (Regier et al. 2008
; Meusemann et al. 2010
; Regier et al. 2010
; von Reumont et al. 2012
), the sistergroup relationship of Hymenoptera to remaining Holometabola (Savard et al. 2006
; Zdobnov and Bork 2007
; Simon et al. 2009
; Meusemann et al. 2010
) and the intra-ordinal relationships within some holometabolan orders; for example, in Hymenoptera (Sharanowski et al. 2010
), or in Coleoptera (Hughes et al. 2006
). Despite this increase in resolution, several ambiguities within the Insect Tree exist. Recent discussions center around 1) the phylogenetic relationships of the three wingless entognathous orders (Collembola, Protura, and Diplura), 2) the basal pterygote divergence (“Palaeoptera Problem”), 3) the polyneopteran relationships (unresolved polytomy), and 4) the monophyly of Paraneoptera and their position within Neoptera (for review see also Trautwein et al. 2012
; Yeates et al. 2012
One major problem in resolving insect relationships using phylogenomic data is the lack and/or overlap of genomic and/or transcriptomic data. There are more than one million described insect species (Foottit and Adler 2009
) but only 172 insect genomes have been sequenced or are in progress (http://www.ncbi.nlm.nih.gov/genome
; last accessed April 2012). In addition, 151 of these projects are conducted on the single most derived lineage of Neoptera: Holometabola. For Polyneoptera, comprising 11 orders and representing presumably the earliest splits of the neopteran lineage, no genome project is available.
The polyneopteran lineage still appears in an unresolved polytomy within the Insect Tree and even its monophyly is disputed. Herein, especially the phylogenetic position of Plecoptera (Zwick 2009
) and Zoraptera (Yoshizawa 2007
) is far from settled (). Both of them belong to the most phylogenetically ambiguous insect orders and even their placement within the polyneopteran lineage is still under discussion.
Existing Phylogenetic Hypotheses within the Polyneopteran Lineages
To further clarify this most controversial problem among the higher systematics of insects, in this study we provide the first transcriptomic data (derived from 454 expressed sequence tag [EST] data) for three representatives of hitherto unsampled polyneopteran orders: Zoraptera (Zorotypus gurneyi?), Plecoptera (Nemurella pitetii), and Dermaptera (Forficula auricularia).
In addition to addressing these phylogenetic questions with new genomic information, we further address several mechanistic problems relevant to phylogenetic reconstruction. These problems include missing data, phylogenetic resolution, and taxon and gene sampling, all of which contribute to the underlying data quality and consequently the resolution of a certain phylogenetic question (Philippe et al. 2005
; Baurain et al. 2007
). For example, following a previous study (Simon et al. 2009
) that has shown how biological function of the genes might have an impact on data quality, we extended this approach in the current study using dense taxon sampling across the diverse insect lineages. The difficulty inherent in insect systematics and the existence of competing phylogenetic hypotheses offers a great opportunity to explore the source of incongruence in phylogenomic studies more generally. Here, we test several phylogenetic hypotheses within the Insect Tree and explore how support for these hypotheses might be influenced by missing data, matrix selection, gene and taxa number/choice, and the biological function of the genes. Different approaches to reduce missing data and to select an optimal data set to infer the species evolution were compared. We further characterized the strength of support for the concatenated phylogenetic hypotheses using a newly developed approach, RADICAL (Narechania et al. 2012
), which allows us to identify the problematic nodes within the Insect Tree and quantify their relative weakness. In sum, this study 1) provides new insights into the evolution of three ambiguous insect orders, 2) highlights the problems in insect systematics despite the use of numerous characters even in the context of this phylogenomic data set, and 3) demonstrates which factors might influence the phylogenetic inference.