Testing for misleading effects in the phylogenetic reconstruction of ancient lineages of hexapods: influence of character dependence and character choice in analyses of 28S rRNA sequences

Abstract

The present analyses employ the almost complete sequence of the 28S rRNA gene to investigate phylogenetic relationships among Pancrustacea, placing special emphasis on the position of basal hexapod lineages. This study utilizes a greater number of characters and taxa of Protura, Collembola and Diplura than previous analyses to focus on conflicts in the reconstruction of the early steps in hexapod evolution. Phylogenetic trees are mainly based on Bayesian approaches, but likewise include analyses with Maximum Likelihood and Maximum Parsimony. Different analyses, including the application of a mixed DNA/RNA substitution model, were performed to narrow possible misleading effects of non-stationarity of nucleotide frequencies, saturation and character independence down to a minimum. This is the first time that a mixed DNA/RNA model is applied to analyse 28S rRNA sequences of basal hexapods. All methods yielded strong support for the monophyly of Collembola, Diplura, Dicondylia and Insecta s.str., as well as for a cluster composed of Diplura and Protura (‘Nonoculata-hypothesis’). However, the last cluster may be an artifact caused by a shared GC bias of the 28S sequences between these orders, in combination with a long branch effect. The instability of the position of the ‘Nonoculata’ within Pancrustacea further bears out the misleading effect of non-stationarity of nucleotide frequencies. Protura and Diplura either form the sister-group to Collembola (Entognatha) or cluster with branchiopod crustaceans. Overall, the phylogenetic signal of the complete sequences of the 28S rRNA gene favours monophyly of Hexapoda over paraphyly. However, further corroboration from independent data is needed to rule out the competing hypothesis of mutually paraphyletic Crustacea and Hexapoda

A morphometrics-based phylogeny of the temperate Gondwanan mite harvestmen (Opiliones, Cyphophthalmi, Pettalidae)

“…For the latter, a common method has been to eliminate or combine correlated characters (Poe and Wiens 2000;Poe 2004;Molina et al 2008;DellÕAmpio et al 2009;Naczi 2009) or at least test which characters are providing the most signal and should be examined more closely for correlations (DeGusta 2004). This follows from a definition of independence that Ôthe state of one character does not predict the state of anotherÕ (Doyle 1997).…”

The spermatogenesis and sperm structure of Acerentomon microrhinus (Protura, Hexapoda) with considerations on the phylogenetic position of the taxon

“…An additional potential synapomorphy of Diplura and Ectognatha is the lack of temporary organs (Koch 1997). Molecular data also support the monophyly of this hexapod taxon (Dell'Ampio et al 2009). Collembola and Protura, in addition to quite diVerent internal anatomies, also have a series of morphological features, which develop quite diVerently (Bitsch and Bitsch 2004).…”

“…Molecular data do not support the monophyletic taxon Entognatha (Protura, Collembola and Diplura), and instead indicate a position for Collembola outside of Insecta (Nardi et al 2003;Kjer 2004;Giribet et al 2004; 123 Regier et al 2004;Carapelli et al 2006), while Protura seem to be related to Diplura (Wheeler et al 2001;Luan et al 2005;Kjer et al 2006;Mallat and Giribet 2006;Dell'Ampio et al 2009) to form the taxon Nonoculata. However, based on embryological results, Fukui and Machida (2006) and Machida (2006) agree that Entognatha are not a monophyletic taxon and that Protura are neither related to Collembola nor to Diplura, but hypothesize instead that they have some aYnity with Myriapoda or Crustacea.…”

“…Recently, however, molecular data have proposed a new scenario, with Collembola outside Insecta (Nardi et al 2003;Giribet et al 2004;Kjer et al 2006;Regier et al 2004) and Diplura closely related to Protura (Giribet et al 2004;Luan et al 2005;Kjer et al 2006;Mallat and Giribet 2006;Dell'Ampio et al 2009). From a spermatological point of view, the earlier data agree with the peculiarities of the collembolan sperm (Dallai et al 2004): the proposal based on molecular data is more diYcult to accept, as Diplura have an insect-type sperm with a 9 + 2 Xagellar axoneme surrounded by 9 accessory microtubules ( Table 1).…”

Phylogenetic analysis of the Australian trans-Bass Strait millipede genus Pogonosternum (Carl, 1912) (Diplopoda, Polydesmida, Paradoxosomatidae) indicates multiple glacial refugia in southeastern Australia

“…Primer pairs 28S D1a (Fw) and 28S D3b (Rv) (Dell’Ampio et al 2009) were used to amplify 1225 bp of the D2 fragment and adjacent areas of D1 and D3 on the nuclear 28S ribosomal RNA gene.…”