- Research article
- Open Access
Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships
BMC Evolutionary Biology volume 9, Article number: 119 (2009)
Whenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes.
We analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear.
Analyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.
Most recent studies that focused on the reconstruction of ancient splits in animals, have relied on 18S and/or 28S rRNA sequences, e.g. . These data sets strongly contributed to our knowledge of relationships, however, several nodes remain that are suspected of being artifacts caused by peculiar evolutionary rates which may be lineage specific. Particular unorthodox nodes were discussed as long branch artifacts, others were held to be clusters caused by non-stationary evolutionary processes as indicated by differences in nucleotide composition among the terminals. The reconstruction of ancient splits seems to be especially dependent on taxon sampling and character choice, since in single lineages the signal-to-noise ratio is consistently marginal in allowing a reasonable resolution. Thus, quality assessment of data via e.g. secondary structure guided alignments, discarding of randomly similar aligned positions or heterogeneity of the data set prior to analysis is a crucial step to obtain reliable results. Arthropod phylogeny is especially suitable as a case study, since their ancient and variable phylogenetic history, which may have included intermittent phases of fast radiation, impedes phylogenetic reconstruction.
Major arthropod relationships
While currently there is wide agreement about the monophyly of Arthropoda, relationships among the four major subgroups (Chelicerata, Myriapoda, Crustacea, Hexapoda) remain contested, even the monophyly of each of the subgroups has come under question. The best supported relationship among these subgroups seems to be the clade comprising all crustaceans and hexapods. This clade, named Pancrustacea , or Tetraconata , is supported by most molecular analyses, e.g. [1, 4–14]. Likewise, the clade has increasingly found support from morphological data [3, 15–18], especially when malacostracans are directly compared with insects. Most of these studies reveal that crustaceans are paraphyletic with respect to a monophyletic Hexapoda. However, most analyses of mitochondrial genes question hexapod monophyly [19–22]. Additionally, various crustacean subgroups are discussed as potential hexapod sister groups. Fanenbruck et al.  favored a derivation of Hexapoda from a common ancestor with Malacostraca + Remipedia based on neuroanatomical data. In recent molecular studies, either Branchiopoda  or Copepoda [1, 11, 23] emerged as the sister group of Hexapoda. The Pancrustacea hypothesis implies that Atelocerata (Myriapoda + Hexapoda) is not monophyletic. In most of the above mentioned molecular studies, the Myriapoda appear at the base of the clade Mandibulata or as the sistergroup to Chelicerata. The combination of Chelicerata + Myriapoda [1, 7, 13, 14, 24] was coined Paradoxopoda  or Myriochelata . It seems that this grouping can be partly explained by signal erosion , and likewise is dependent on outgroup choice . In addition, the most recent morphological data is consistent with the monophyly of Mandibulata , but not of Myriochelata. Almost no morphological data corroborate Myriochelata except for a reported correspondence in neurogenesis ; this however alternatively may reflect the plesiomorphic state within Arthropoda [29, 30]. Within Hexapoda, relationships among insect orders are far from being resolved [31–35]. Open questions concern the earliest splits within Hexapoda, e.g. the monophyly or paraphyly of Entognatha (Protura + Diplura + Collembola) [9, 19, 22, 32, 34, 36–45].
Goals and methodological background
The aim of the present study is to optimize the phylogenetic signal contained in 18S and 28S rRNA sequences for the reconstruction of relationships among the major arthropod lineages. A total of 148 arthropod taxa representing all major arthropod clades including onychophorans and tardigrades (the latter as outgroup taxa) were sampled to minimize long-branch artifacts . A new alignment procedure that takes secondary structure into account is meant to corroborate the underlying hypotheses of positional homology as accurately as possible. A new tool for quality control optimizes the signal-to-noise ratio for the final analyses. In the final step, we try to improve the analyses by fitting biologically realistic mixed DNA/RNA substitution models to the rRNA data. Time-heterogeneous runs were performed to allow for lineage specific variation of the model of evolution.
The use of secondary structure information both corroborates hypotheses of positional homology in the course of sequence alignment, as well as helps to avoid misleading effects of character dependence due to covariation among sites. It was demonstrated that ignoring correlated variance may mislead tree reconstructions biased by an overemphasis of changes in paired sites [34, 46, 47]. Evolutionary constraints on rRNA molecules are well known, for example constraints resulting from secondary structure interactions. The accuracy of rRNA comparative structure models [48–50] has been confirmed by crystallographic analyses [51, 52]. Based on this background knowledge, rRNA sequences are an ideal test case to study the effect of biologically realistic substitution models on tree reconstructions.
Recent studies of genome scale data revealed that a careful choice of biologically realistic substitution models and model fitting are of particular importance in phylogenetic reconstructions [53–55]. The extent, however, to which biological processes can/should be modeled in detail is still unclear. The analyses of rRNA sequences can still deliver new insights in this direction, since the relatively comprehensive background knowledge allows to better separate different aspects of the substitution processes. In order to model covariation in rRNA sequences, we estimated secondary structure interactions by applying a new approach implemented in the software RNAsalsa  (download available from http://rnasalsa.zfmk.de/), which helps to accommodate inadequate modeling (e.g. missing covariotide effects) of rRNA substitution processes in deep phylogenetic inference [34, 57]. Essentially, this approach combines prior knowledge of conserved site interactions modeled in a canonical eukaryote secondary structure consensus model with the estimation of alternative and/or additional site interactions supported by the specific data. Inferred site covariation patterns were used then to guide the application of mixed substitution models in subsequent phylogenetic analyses.
Finally, we accounted for inhomogeneous base composition across taxa, a frequently observed phenomenon indicating non-stationary substitution processes [58–60]. Non-stationary processes, if present, clearly violate assumptions of stationarity regularly assumed in phylogenetic analyses [60–62]. Thus, we modeled non-stationary processes combined with the application of mixed DNA/RNA substitution models in a Bayesian approach using the PHASE-2.0 software package  to provide a better fit to our data than standard substitution models [60, 64]. In PHASE-2.0 a nonhomogeneous substitution model is implemented [...] "by introducing a reversible jump Markov chain Monte Carlo method for efficient Bayesian inference of the model order along with other phylogenetic parameters of interest" .
Application of a new hierarchical prior leads to more reasonable results when only a small number of lineages share a particular substitution process. Additionally PHASE-2.0 includes specialized substitution models for RNA genes with conserved secondary structure .
We contributed 103 new and nearly complete 18S or 28S rRNA sequences and analyzed sequences for 148 taxa (Additional file 1), of which 145 are Arthropoda sensu stricto, two onychophorans and Milnesium sp. (Tardigrada). The alignment of the 18S rRNA sequences comprised 3503 positions, and the 28S rRNA alignment 8184. The final secondary consensus structures included 794 paired positions in the 18S and 1326 paired positions in the 28S. The consensus structures contained all paired sites that in 60% or more sequences were detected after folding (default s3 = 0.6 in RNAsalsa). ALISCORE scored 1873 positions as randomly similar (negative scoring values in the consensus profile) to the 18S and 5712 positions of the 28S alignment (Figure 1).
Alignment filtering and concatenation of data
After the exclusion of randomly similar sections identified by ALISCORE, 1630 (originally 3503) of the 18S rRNA and 2472 (originally 8184) positions of the 28S rRNA remained. Filtered alignments were concatenated and used for analyses in PHASE-2.0. The concatenated alignment comprised 4102 positions.
Split supporting patterns
The neighbornet graph, which results from a split decomposition based on uncorrected p-distances (Figure 2) and LogDet correction plus invariant sites model (see Additional file 2) pictured a dense network, which hardly resembles a tree-like topology. This indicates the presence of some problems typical in studies of deep phylogeny: a) Some taxa like Diptera (which do not cluster with ectognathous insects), Diplura, Protura and Collembola each appear in a different part of the network with Diplura and Protura seperated from other hexapods, Lepisma saccharina (clearly separated from the second zygentoman Ctenolepisma that is nested within Ectognatha), Symphyla, Pauropoda, as well as Remipedia and Cephalocarida have very long branches. Consequently the taxa may be misplaced due to signal erosion or occurrence of homoplasies, and their placement in trees must be discussed critically . The usage of the LogDet distance adjusts the length of some branches but does not decrease the amount of conflicts in deep divergence splits. b) The inner part of the network shows little treeness, which indicates a high degree of conflicting signal.
A remarkable observation seen in both phylogenetic networks is that some taxa have long stem-lineages, which means that the species share distinct nucleotide patterns not present in other taxa. Such well separated groups are Copepoda, Branchiopoda, Cirripedia, Symphyla, Collembola, Diplura, Protura and Diptera, while e.g. Myriapoda partim, Chelicerata and the Ectognatha (bristletails, silverfish/firebrats and pterygote insects) excluding Diptera share weaker patterns.
Compositional heterogeneity of base frequency
We excluded in PAUP 4.0b10  parsimony uninformative positions explicitely for the base compositional heterogeneity test. Randomly similar alignment blocks identified by ALISCORE were excluded for both, the base compositional heterogeneity test and phylogenetic recontructions. 901 characters of the 18S rRNA and 1152 characters of the 28S rRNA were separately checked for inhomogeneous base frequencies. Results led to a rejection of the null hypothesis (H0), which assumes homogeneous base composition among taxa (18S: χ2 = 1168.94, df = 441, P = 0.00; 28S: χ2 = 1279.98, df = 441, P = 0.00). Thus, base frequencies significantly differed across taxa in both 18S and 28S data sets.
A data partition into stems and loops revealed 477 unpaired positions and 424 paired positions in the 18S, and 515 unpaired and 637 paired positions in the 28S. Separate analyses of all four partitions confirmed heterogeneity of base frequencies across taxa in all sets (P = 0.00 in all four partitions).
We repeated the homogeneity test for partitions as used in tree reconstruction, if base pairs were disrupted by the identification of the corresponding partner as randomly similar (ALISCORE), remaining formerly paired positions were treated as unpaired. Hence, 1848 characters of the concatenated alignment (18S: 706; 28S: 1142) were treated as paired in all analyses. Again the test revealed heterogeneity in unpaired characters of both the 18S and 28S (P = 0.00 for both genes; 18S: 506 characters; 28S: 567 characters). Examination at paired positions also rejected the null hypothesis H0 (18S, 395 characters included: P < 0.0003, 28S, 585 characters included: P = 0.00). Since non-stationary processes in all tests were strongly indicated, we chose to apply time-heterogeneous models to account for lineage-specific substitution patterns. To fix the number of "free base frequency sub-models" in time-heterogeneous analyses, we identified the minimal exclusive set of sequence groups. Based on χ2-tests the dataset could be divided into three groups for both rRNA genes. In both genes Diptera are characterized by a high A/T content and Diplura by a low A/T content. Exclusion of only one of the groups was not sufficient to retain a homogeneous data set (18S: excluding Diptera: χ2 = 972.91, df = 423, P = 0.00, excluding Diplura: χ2 = 532.13, df = 423, P < 0.0003; 28S: excluding Diptera: χ2 = 986.72, df = 423, P = 0.00, excluding Diplura: χ2 = 813.8, df = 423, P = 0.00). Simultaneous exclusion of both groups led to acceptance of H0 for 18S sequences (χ2 = 342.22, df = 405, P = 0.99). For the 28S, after exclusion of both groups, H0 was still rejected (χ2 = 524.98, df = 405, P < 0.0001). After sorting taxa according to base frequencies in ascending order, additional exclusion of Peripatus sp. and Sinentomon erythranum resulted in a homogeneous base composition for the 28S gene (H0: χ2 = 434.99, df = 399, P = 0.1), likewise indicating that three sub-models are suffucient to cover the taxon set. We repeated the homogeneity-test for stem and loop regions of each gene seperately. The exclusion of Diplura was sufficient to obtain homogeneity in the loop regions for both genes (18S: 474 characters, P = 0.9757; 28S: 541 characters, P = 0.0684). For stem regions in the 18S it likewise was sufficient to exclude either Diptera (378 characters, P = 0.6635) or Diplura (385 characters, P = 0.99). These partitions would make two sub-models sufficient to cover the data set. However, in the stem regions of the 28S homogeneity was received only after the exclusion of both Diptera and Diplura (547 characters, P = 0.99). Since PHASE-2.0 does not allow to vary the number of chosen sub-models among partitions, we applied and fitted three sub-models to each data partition.
Three combinations of mixed DNA/RNA models (REV + Γ & RNA16I + Γ, TN93 + Γ & RNA16J + Γ and HKY85 + Γ & RNA16K + Γ) were compared to select the best model set. Overall model ln likelihoods converged for all tested mixed models after a burn-in of 250,499 generations in an initial pre-run of 500,000 generations. However, most parameters did not converge for the combined REV + Γ & RNA16I + Γ models, consequently, this set up was excluded from further analyses. For each of the remaining two sets a chain was initiated for 3 million generations, with a burn-in set to 299,999 generations. The applied Bayes Factor Test [[67, 68], BFT], favored the TN93 + Γ & RNA16J + Γ model combination (2lnB10 = 425.39, harmonic mean lnL0(TN93 + Γ & RNA16J + Γ) = 79791.08; harmonic mean lnL1(HKY85 + Γ & RNA16K + Γ) = 80003.78). For each approach (Aditional file 3) all chains which passed a threshold value in a BFT were assembled to a metachain. Each resulting extended majority rule consensus tree was rooted with Milnesium. Node support values for clades were deduced from 56,000 sampled trees for the time-heterogeneous set (Figure 3) and from 18,000 sampled trees for the time-homogeneous set (Figure 4), detailed support values are shown in Additional file 3. Harmonic means of the ln likelihoods of included time-heterogeneous chains were compared against all ln likelihoods of included time-homogeneous chains (burn-in discarded) in a final BFT: the time-heterogeneous model was strongly favored (2lnB10 = 1362.13).
Representatives of Symphyla and Pauropoda, already identified in the neighbornet graph as taxa with conspicuously long branches (Figure 2), assumed unorthodox positions in both trees which are clearly incongruent with morphological evidence and results obtained from other genes. Symphyla formed the sister group of all remaining arthropod clades, and Pauropoda clustered with Onychophora. Consequently, myriapods always appeared polyphyletic in both analyses. We consider these results as highly unlikely, since they contradict all independent evidence from morphology, development, and partly from other genes. In the following, we focus on major clades and point out differences between time-heterogeneous tree (Figure 3) and time-homogeneous tree (Figure 4) without considering the position of Symphyla and Pauropoda. Possible causes for the misplacement of these groups, however, will be treated in the discussion. Both analyses supported a monophyletic Chelicerata (pP 0.91 in the time-heterogeneous tree and maximal support in the time-homogeneous tree) with Pycnogonida (sea spiders) as sister group to remaining chelicerates. Pycnogonida received maximal support in both analyses. Euchelicerata received highest support in the time-homogeneous approach while this clade in the time-heterogeneous approach received a support of only pP 0.89. Limulus polyphemus (horseshoe crab) clustered within arachnids, but some internal relationships within Euchelicerata received only low support. Chilopoda always formed the sister group of a monophyletic Diplopoda in both analyses with high support. Within the latter the most ancient split lied between Penicillata and Helminthomorpha. This myriapod assemblage – Myriapoda partim – formed the sister group of Chelicerata, thus giving support to the Myriochelata hypothesis, respectively Myriochelata partim, when the long-branch clades Symphyla and Pauropoda are disregarded.
Pancrustacea showed always maximal support. The monophyly of Malacostraca and Branchiopoda received highest support in both approaches while their position varied. Branchiopoda was the sister group of the clade consisting of Copepoda + Hexapoda in the homogeneous tree (Figure 4), however the cephalocarid Hutchinsoniella nested within hexapods. Among hexapods, monophyly was unambiguously supported for Protura, Diplura, Collembola, Archaeognatha, Odonata, Ephemeroptera, Phasmatodea, Mantophasmatodea, Mantodea, Plecoptera, Hemiptera, Coleoptera, Hymenoptera, Lepidoptera and Diptera. Diplura clustered with Protura, and gave support to a monophyletic Nonoculata. Pterygota occurred in both topologies, well supported in the non-stationary tree (pP 0.97) and with moderate support (pP 0.94) in stationary tree. Within the winged insects, both analyses resolved Odonata as the sister group to a well supported monophyletic clade Ephemeroptera + Neoptera (heterogeneous: pP 0.96; homogeneous: pP 0.97), known as the "Chiastomyaria" clade [32, 34, 35, 69]. Blattodea were always paraphyletic with respect to the isopteran representative. This assemblage formed a sister group relationship with Mantodea, thus giving support to a monophyletic Blattopteroidea or Dictyoptera while the position of Dictyoptera among hemimetabolan insects differed. Dermaptera always clustered with Plecoptera. Hemiptera (Heteroptera + Homoptera) in both approaches formed a clade with the remaining orthopterans + ((Acheta + Mantophamsmatodea)Phasmatodea) with low statistical support. Caused by Acheta orthopteran insects appeared always polyphyletic. Within the monophyletic Holometabola (pP 1.0), Hymenoptera formed the sister group of the remaining taxa.
While the time-heterogeneous and time-homogeneous trees corresponded in overall topologies, they differed in a number of remarkable details.
1) Hexapoda, Entognatha, Ectognatha and Dicondylia were only reconstructed in the time-heterogeneous approach. 2) The cephalocarid Hutchinsoniella clustered among crustaceans as sister group to the Branchiopoda only in the heterogeneous approach, this clade formed the sister group to (Copepoda + Hexapoda) although with low support. 3) The time-homogeneous runs revealed highly supported (Malacostraca + Ostracoda) as the sister group to a clade ((Mystacocarida + Pentastomida) + (Branchiura + Cirripedia)). In contrast, in the time-heterogeneous analysis more terminal positioned Malacostraca are the sister group of a clade (Pentastomida((Cephalocarida + Branchiopoda) + (Copepoda + Hexapoda))). The altered postition of Pentastomida was only low supported in this tree. 4) In the homogeneous tree Hutchinsoniella emerged as sister taxon to Lepisma with low support (pP 0.72), and this cluster was positioned within the remaining hexapods (Figure 4). Hexapoda were monophyletic only in the time-heterogeneous approach, well supported (pP 0.96, Figure 3), with Copepoda as sister group, latter with low support (pP 0.69). 5) In the time-homogeneous tree (Figure 4), Copepoda emerged as sister group, again with a low support value (pP 0.70) of ((Lepisma + Hutchinsoniella) + "Hexapoda"). 6) Entognatha (pP 0.98), and Ectognatha (pP 1.0) and Dicondylia (pP 0.99) were monophyletic only in the time-heterogeneous tree. 7) The time-heterogeneous tree showed the expected paraphyly of primarily wing-less insects with Archaeognatha as sister group to Zygentoma + Pterygota. 8) Within pterygote insects (Dermaptera + Plecoptera) emerged as sister group of Dictyoptera in the non-stationary tree, contrary as sister group of Holometabola in the stationary tree, both scenarios with negligible support.
Among arthropods 18S and 28S rRNA genes have the densest coverage of known sequences. Apart of some exceptions most studies on phylogenetic relationships at least partly rely on rRNA data. Often, however, only one of the genes was used, sometimes even just fragments of a gene [23, 32, 34, 40, 42, 44, 70–72], while only few studies used nearly complete 18S and 28S rRNA sequences [1, 11, 73]. Despite this wide usage, the reliability of reconstructions based on rRNA markers is still debated (for contradicting views see [34, 74, 75]. A major cause of concern is the pronounced site heterogeneity of evolutionary rates, the non-stationarity of base composition among taxa and rate variation in time. All three phenomena quickly lead to the erosion of phylogenetic signal . On the one hand, our understanding of the molecular structure of other markers and about taxon-dependent processes of molecular evolution remains poor. On the other hand, our vast background knowledge regarding rRNA molecules offers a unique opportunity to study the effects of selection and application of substitution models in greater detail.
Quality check and character choice in alignments
Phylogenetic signal in sequence data can get noisy due to (i) multiple substitution processes (saturation) and (ii) erroneous homology hypotheses caused by ambiguous sequence alignment. Both effects correspond in that they result in random similarity of alignment regions. Such noisy sections potentially bias tree reconstructions in several ways which have been appreciated for years but only recently been applied, that allow to account for these problems [25, 54, 77, 78]. Exclusion of these ambiguously aligned or saturated regions can help to reduce noise, see e.g. . If this topic is addressed at all, the majority of studies include a manual alignment check for untrustworthy regions [1, 4, 22, 32, 34, 39, 44, 71–73]. Only some recent publications addressing arthropod relationships have used automated tools, e.g. [14, 79, 80].
To identify alignment sections of random similarity prior to tree reconstructions, we used ALISCORE, which, compared to the commonly used Gblocks , is not dependent on the specification of an arbitrary threshold . To improve the signal-to-noise ratio we restricted our character choice to alignment sections which contained nucleotide patterns that differ from randomized patterns.
Phylogenetic reconstruction methods
Arthropod phylogenies have been inferred with reconstruction methods like Maximum Parsimony, Maximum Likelihood and Bayesian approaches. We tried to implement knowledge about the evolution of rRNA in two ways: (i) the use of mixed DNA/RNA models is meant to account for known instances of character dependence due to compensatory mutations in stem regions, (ii) the application of time-heterogeneous models accounts for non-stationary processes that occurred in arthropod lineages. The consensus secondary structure of our dataset, generated with RNAsalsa, can be understood as a model parameter that defines site interactions and thus character dependence due to compensatory mutations [34, 82, 83]. Neglect of character dependence surely results in unrealistic support values. In single low supported nodes, where the signal-to-noise ratio is at the edge of resolution, such a neglect theoretically can even turn the balance between two competing hypotheses. Additionally a consensus secondary structure is necessary to apply a mixed model approach, since it determines whether the evolution of a given site is modeled by the DNA-model, or as part of a base-pair by the RNA-model. Within the mixed model approach, we opted for DNA-corresponding 16-state RNA models . It can certainly be argued that the choice of 16-state models is problematic because it is difficult to fit these models to real data due to their parameter richness and heavy computational costs. However, even the best choice of a consensus secondary structure can only capture the predominantly conserved structural features among the sequences. This implies that the applied RNA models must be able to cope with mismatches in base-pairing. Less complex RNA models like those of the 6 and 7-state families either ignore mismatches completely or pool these mismatches into a single character state which produces artificial synapomorphies. Additionally, according to Schöninger and v. Haeseler , it is more likely that co-variation is a multiple step process which allows for the intermediate existence of instable (non Watson-Crick) pairs. These intermediate states are only described in 16-state RNA models.
Concerning rRNA-genes of arthropods, shifts in base composition are mentioned for Diptera, Diplura, Protura and Symphyla [1, 23, 34, 44, 73, 85]. Since base compositional heterogeneity within a dataset can mislead phylogenetic reconstruction [61, 86, 87] and , some of these studies discussed observed but not incorporated non-stationary processes as possible explanations for misplacements of some taxa [11, 23, 24, 44, 73]. The selective exclusion of these taxa to test for misleading effects on the remaining topology, however, is not appropriate to test whether non-stationarity really fits as the causal explanation of the placement incongruent with other analyses. LogDet methods have been applied to compensate for variations of base frequencies [1, 11, 44], which leads to some independence of non-stationarity, but among site rate variation (ASRV) cannot be handled efficiently. After detecting compositional base frequency heterogeneity in our data, we chose a non-stationary approach implemented in PHASE-2.0. Because no previous study of arthropod phylogeny has used a time-heterogeneous approach including mixed DNA/RNA models, we compared this approach with a "classical" time-homogeneous setup. Our results prove that the time-heterogeneous approach produces improved likelihood values with improved branch lengths estimates and more realistic, though not perfect (see below), topology estimates. Since modeling of general time-heterogeneous processes is in its infancy and since its behavioural effect on real data is relatively unknown [60, 61], we favored a set up accounting for the three different "submodels" corresponding to three base frequency categories in our dataset (Additional file 4). The application of the three submodels to individual branches in a tree by the MCMC process was not further constrained. This scheme allowed for a maximum of flexibility without losing the proper mix of parameters.
Conflicting phylogenetic hypotheses and non-stationary processes of rRNA evolution
The comparison of our time-homogeneous approach to our time-heterogeneous one was not only meant to show improvements in the application of more realistic models, but also to indicate which incongruities of analyses of rRNA genes may be causally explained by non-stationary processes during the evolution of these genes.
In our time-homogeneous approach, the crustacean Hutchinsoniella (Cephalocarida) clustered with Lepisma (Zygentoma, Hexapoda) within enthognathans as sister group to Nonoculata (Protura + Diplura), (see Figure 4). This led to the polyphyly or paraphyly of several major groups (e.g. Hexapoda, Entognatha, Ectognatha, Dicondylia). In our time-heterogeneous analysis, Cephalocarida clustered as sister group to Branchiopoda. This result, although marginal supported, is congruent, at least, with some morphological data . Most recent molecular studies have not included Cephalocarida, e.g. [1, 11]. Regier et al.  reconstructed a sister group relationship of Remipedia and Cephalocarida (likewise represented by Hutchinsoniella), but his result also received only moderate bootstrap support. The same clade was presented in Giribet et al.  based on morphological and molecular data.
Independent of the sister group relationship of Cephalocarida within crustaceans, the correction of the misplacement of Hutchinsoniella, by allowing for non-stationary processes, has a major effect on the heuristic value of our analyses. Not only is the monophyletic status of Hexapoda, Entognatha, Ectognatha, Dicondylia supported after the correction, but likewise a causal explanation is given for the misplacement in the time-homogeneous approach, which cannot be accomplished by alternatively excluding the taxon. Our time-heterogeneous analyses resulted in a sister group relationship of Diplura and Protura, which lends support to a monophyletic Nonoculata within a monophyletic Entognatha. This result is congruent with trees published by Kjer , Luan et al. , Mallat and Giribet , and Dell'Ampio et al. . Following Luan et al.  Dell'Ampio et al.  cautioned that Nonoculata may be an artificial cluster caused by a shared nucleotide bias and long branch attraction. Since this node is recovered with high support by our non-stationary approach, Nonoculata cannot be suspected of being an artificial group based on shared compositional biases alone. However, one must keep in mind that Protura and Diplura have longer branches than Ectognatha and Collembola (Figure 3 and 4), and long-branch effects may still be present. Thus monophyly of a clade Nonoculata still awaits support from a data set independent from rRNA sequences.
Clades not affected by non-stationary processes
Symphyla and Pauropoda
Although we tried to break down long branches by a dense taxon sampling, some long-branch problems persisted. We cannot clearly address the reason but, due to the symptoms, assume that saturation by multiple substitution caused signal erosion (class II effect, ). To evaluate the impact on the topology of the very likely incorrect positions of Symphyla and Pauropoda, we repeated the time-heterogeneous analysis using a reduced dataset excluding these taxa. We limited the analysis to ten chains with 7, 000, 000 generations each (2, 000, 000 burn-in). Differences occurring in the inferred consensus topology (not shown) of the final three chains (15, 000, 000 generations) show that some nodes are still sensitive to taxon sampling, since e.g. Pycnogonida clustered with (Chilopoda + Diplopoda) after exclusion of pauropod and symphylan sequences. Also the crustacean topology changed, remaining long branch taxa Hutchinsoniella and Speleonectes clustered together in the reduced dataset, forming a clade with (Branchiura + Cirripedia).
Mandibulata versus Myriochelata
Analyses of rRNA sequences up till now were held to favor Myriochelata (Myriapoda + Chelicerata) over Mandibulata [1, 4, 11]. Our analyses provide no final conclusion with respect to this conflict, since the position of Pauropoda and Symphyla is unusual, it results in polyphyletic myriapods. The exact reconstruction of the position of myriapods within the Euarthropoda thus demands e.g. the application of new markers and suitable phylogenetic strategies.
Phylogenetic position of Malacostraca and Pentastomida
The position of Malacostraca differs among molecular studies. Often, Malacostraca emerge as nested within the remaining crustacean groups, e.g. [5, 89]. Complete mitochondrial genomes place Malacostraca close to insects [90, 91]. However, studies of rRNA sequences recover this group as the sister group to all remaining crustaceans [1, 11, 92]. Since in our stationary tree monophyletic Malacostraca branched off at a more basal split within crustaceans [88, 93], forming a sister group relationship to Ostracoda and contrary they branched off at a more terminal split in the non-stationary tree we cannot draw a final conclusion about the placement of Malacostraca. Unfortunately the position of the Pentastomida remains ambiguous in our analyses, we argue that low pP values might be induced by conflicting phylogenetic signal.
Sister group of Hexapoda
The sister group of Hexapoda is still disputed. Most molecular studies support paraphyly of crustaceans with respect to hexapods. A sister group relationship between Branchiopoda and Hexapoda was proposed for the first time by Regier and Shultz , yet with low support. Shultz and Regier  and Regier et al.  corroborated this relationship, which is likewise favored by authors of rRNA-based studies [1, 11], despite their result that Cyclopidae (Copepoda) is the sister group of Hexapoda. Our denser taxon sampling further supports Copepoda as the sister group to Hexapoda, but the low support value might indicate conflicting signal. This clade up till now, however, lacks any support from morphological studies.
Ancient splits within pterygote insects
We find that the rRNA data cannot robustly resolve the most ancient splits within Pterygota. Nonetheless, rRNA data, when analyzed under more realistic models favour Chiastomyaria as the most likely hypothesis. Since all three possible arrangements of Odonata, Ephemeroptera and Neoptera likewise receive morphological support, we agree with Whitfield and Kjer  that the ambiguity can best be explained by early 'explosive radiation' within Pterygota.
We conclude that the implementation of biologically realistic model parameters, such as site interaction (mixed DNA/RNA models) and compositional heterogeneity of base frequency, is fundamental to robustly reconstruct phylogenies. The most conspicuous examples comparing our tress are a) the position of Hutchinsoniella (Crustacea), although a low pP value of 0.59 in the non-stationary tree prohibits conclusions about its internal crustacean relationship and b) the well supported position of Ctenolepisma and Lepisma (Zygentoma). As a consequence, the monophyly of Hexapoda, Entognatha and Ectognatha and Dicondylia received support only in the time-heterogeneous approach. Several artificial clades remain in our analyses which cannot be causally explained unambiguously. However, the examples given here clearly demonstrate that the probability to causally explain some incongruities between different data sets, as well as the correction of certain obvious misplacements, is enhanced by using more complex but realistic models. The present study aimed to incorporate background knowledge on the evolution of molecular sequences in general and ribosomal RNA-genes in special into various steps of data processing. For all steps fully automated methods were used, including an automated secondary structure guided alignment approach, a software that enables to distinguish random similarity from putative phylogenetic signal, mixed models that avoid artefacts due to co-variation among sites, and analyses that account for variation of evolutionary rates among lineages. The resolution of many relationships among arthropods, and the minimization of obvious misplacements demonstrate that the increased computational effort pays off.
Our taxon sampling was designed to represent a taxonomically even collection of specimens across arthropod groups. In particular, we took care to include taxa which do not differ too widely from the hypothetical morphological ground-pattern of the represented group, when possible [53, 78]. In total we included 148 concatenated 18S and 28S rRNA sequences in the analysis (Additional file 1). Of these, we contributed 103 new sequences, 41 for the 18S and 62 for the 28S rRNA gene, respectively. Only sequences which span at least 1500 bp for the 18S and 3000 bp for the 28S were included. For 29 taxa we had to construct chimeran concatenated sequences of 18S and 28S rRNA sequences of different species, marked with an asterisk. Details are listed in Additional file 5, we chose species as closely related as possible depending on it's availability in GenBank. The outgroup included the concatenated 18S and 28S rRNA sequences of Milnesium sp. (Tardigrada).
Collected material was preserved in 94 – 99% ethanol or liquid nitrogen. Samples were stored at temperatures ranging from -20°C to -80°C. DNA extraction of complete specimens or tissue followed different standard protocols. We used phenol-chloroform isoamyl extraction , standard column DNA extraction kits DNeasy Blood & Tissue Kit (Qiagen) and NucleoSpin Tissue Kit (Machery-Nagel) following the manual. Single specimens were macerated for extraction, only specimens of Ctenocephalides felis were pooled. Manufacturer protocols were modified for all crustaceans, some apterygote hexapods and myriapods (overnight incubation and adding 8 μl RNAse [10 mg/ml] after lysis). Extracted genomic DNA was amplified with the Illustra GenomiPhi V2 DNA Amplification Kit (GE Healthcare) for tiny, rare or hard to collect specimens.
Partly published rRNA primer sets were used, they were designed in part for specific groups (Additional file 6 and 7). The 18S of crustaceans was amplified in one PCR product and sequenced using four primer combinations. The 18S of apterygotes was amplified in three or four fragments (Additional file 8). The 28S of crustaceans and basal hexapods was amplified in nine overlapping fragments starting approximately in the middle of the rRNA 5.8S to the nearly end of the D12 of 28S rRNA (Additional file 9). The 28S of odonats was amplified in seven or eight, the 28S of ephemeropterans and neopterans in eight overlapping fragments (Additional file 10). Primers were ordered from Metabion, Biomers or Sigma-Genosys. PCR products were purified using following kits: NucleoSpin ExtractionII (Machery-Nagel), QIAquick PCR purification kit (Qiagen), peqGOLD Gel Extraction Kit (peqLab Biotechnologie GmbH), MultiScreen PCR Plate (Millipore) and ExoI (Biolabs Inc.)/SAP (Promega). Some samples were purified using a NHAc [4 mol] based ethanol precipitation. In case of multiple bands fragments with the expected size were cut from 1% – 1.5% agarose gel and purified according to manufacturer protocols.
Cycle sequencing and sequence analyses took place on different thermocyclers and sequencers. Cycle sequencing products were purified and sequenced double stranded. Several amplified and purified PCR products were sequenced by Macrogen (Inc.), Korea. Sequencing of the 28S fragment 28V – D10b.PAUR of the Pauropodidae sp. (Myriapoda) was only successful via cloning. Fragments of the 28S rRNA of the diplopod Monographis sp. (Myriapoda) were processed following Mallatt et al.  and Luan et al. . Please refer to the electronic supplement (Additional file 11) for detailed information about PCR-conditions, applied temperature profiles (Additional file 12), primer combinations, used chemicals (Additional file 13) and settings to amplify DNA fragments. Sequence electropherograms were analyzed and assembled to consensus sequences applying the software SeqMan (DNAStar Lasergene) or BioEdit 7.0 . All sequences or composed fragments were blasted in NCBI using BLASTN, mega BLAST or "BLAST 2 SEQUENCES"  to exclude contaminations.
Alignments and alignment evaluation
Secondary structures of rRNA genes were considered (as advocated in [98–101] to improve sequence alignment. Structural features are the targets of natural selection, thus the primary sequence may vary, as long as the functional domains are structurally retained. Alignments and their preparation for analyses were executed for each gene separately. We prealigned sequences using MUSCLE v3.6 . Sequences of 24 taxa of Pterygota were additionally added applying a profile-profile alignment . The 28S sequences of Hutchinsoniella macracantha (Cephalocarida), Speleonectes tulumensis (Remipedia), Raillietiella sp. (Pentastomida), Eosentomon sp. (Protura) and Lepisma saccharina (Zygentoma) were incomplete. Apart from L. saccharina, prealignments of these taxa had to be corrected manually. We used the "BLAST 2 SEQUENCES" tool to identify the correct position of sequence fragments in the multiple sequence alignment (MSA) for these incomplete sequences.
The software RNAsalsa  is a new approach to align structural RNA sequences based on existing knowledge about structure patterns, adapted constraint directed thermodynamic folding algorithms and comparative evidence methods. It automatically and simultaneously generates both individual secondary structure predictions within a set of homologous RNA genes and a consensus structure for the data set. Successively sequence and structure information is taken into account as part of the alignment's scoring function. Thus, functional properties of the investigated molecule are incorporated and corroborate homology hypotheses for individual sequence positions. The program employs a progressive multiple alignment method which includes dynamic programming and affine gap penalties, a description of the exact algorithm of RNAsalsa will be presented elsewhere.
As a constraint, we used the 28S + 5.8S (U53879) and 18S (V01335) sequences and the corresponding secondary structures of Saccharomyces cerevisae extracted from the European Ribosomal Database [104–106]. Structure strings were converted into dot-bracket-format using Perl-scripts. Folding interactions between 28S and 5.8S [74, 107, 108] required the inclusion of the 5.8S in the constraint to avoid artificial stems. Alignment sections presumably involved in the formation of pseudoknots were locked from folding to avoid artifacts. Pseudoknots in Saccharomyces cerevisae are known for the 18S (stem 1 and stem 20, V4-region: stem E23 9, E23 10, E23 11 and E23 13) while they are lacking in the 28S secondary structure. Prealignments and constraints served as input, and RNAsalsa was run with default parameters. We constructed manually chimeran 18S sequences of Speleonectes tulumensis (EU370431, present study and L81936) and 28S sequences of Raillietiella sp. (EU370448, present study and AY744894). Concerning the 18S of Speleonectes tulumensis we combined positions 1–1644 of L81936 and positions 1645–3436 of sequence EU370043. Regarding the 28S of Raillietiella we combined positions 1–3331 of AY744894 with positions 3332–7838 of sequence EU370448. Position numbers refer to aligned positions.
RNAsalsa alignments were checked with ALISCORE. ALISCORE generates profiles of randomness using a sliding window approach. Sequences within this window are assumed to be unrelated if the observed score does not exceed 95% of scores of random sequences of similar window size and character composition generated by a Monte Carlo resampling process. ALISCORE generates a list of all putative randomly similar sections. No distinction is made between random similarity caused by mutational saturation and alignment ambiguity. A sliding window size (w = 6) was used, and gaps were treated as ambiguities (- N option).
The maximum number of possible random pairwise comparisons (- r: 10,878) was analyzed. After the exclusion of putative random sections and uninformative positions using PAUP 4.0b10, alignments were checked for compositional base heterogeneity using the χ2-test. Additionally, for each sequence the heterogeneity-test was performed for paired and unpaired sites separately. Further heterogeneity-tests were applied to determine the minimal number of base frequency groups.
RNAsalsa generated consensus structure strings for 18S and 28S rRNA sequences, subsequently implemented in the MSA. Randomly similar sections identified by ALISCORE were excluded using a Perl-script. ALISCORE currently ignores base pairings. If ambiguously aligned positions within stems are discarded the corresponding positions will be handled as an unpaired character in the tree reconstruction. The cleaned 18S and 28S alignments were concatenated.
To analyze information content of raw data SplitsTree4 was used to calculate phylogenetic networks (see Huson and Bryant  for a review of applications). We compared the network structure based on the neighbornet algorithm  and applying the LogDet transformation, e.g. [111, 112]. LogDet is a distance transformation that corrects for biases in base composition. The network graph gives a first indication of signal-like patterns and conflict present in the alignments. We used the alignment after filtering of random-like patterns with ALISCORE.
Mixed DNA/RNA substitution models were chosen, in which sequence partitions corresponding to loop regions were governed by DNA models and partitions corresponding to stem regions by RNA models that consider co-variation. Among site rate variation  was implemented in both types of substitution models. Base frequency tests indicated that base composition was inhomogeneous among taxa (see results), suggesting non-stationary processes of sequence evolution. To take such processes into account the analyses were performed in PHASE-2.0  to accommodate this compositional heterogeneity to minimize bias in tree reconstruction. Base compositional heterogeneity is implemented in PHASE-2.0 according to the ideas developed by Foster .
We limited the number of candidate models to the REV + Γ, TN93 + Γ and the HKY85 + Γ models for loop regions and the corresponding RNA16I + Γ, RNA16J + Γ and RNA16K + Γ models for stem regions. Site heterogeneity was modeled by a discrete gamma distribution  with six categories. The extent of invariant characters was not estimated since it was shown to correlate strongly with the estimation of the shape parameter of the gamma distribution [113, 115–117]. The data was partitioned into four units representing loop and stem regions of 18S rRNA and loop and stem regions of 28S rRNA. DNA and RNA substitution model parameters were independently estimated for each partition. Substitution models were selected based on results of time-homogeneous setups. We tested three different combinations of substitution models, REV + Γ & RNA16I + Γ, TN93 + Γ & RNA16J + Γ and HKY85 + Γ & RNA16K + Γ. We used Dirichlet distribution for priors, proposal distribution and Dirichlet priors and proposals for a set of exchangeability parameters (Additional file 14) described in Gowri-Shankar and Rattray .
Appropriate visiting of the parameter space according to the posterior density function  was checked by plotting values of each parameter and monitoring their convergence. This was calculated for all combinations after 500,000 generations (sampling period: 150 generations). We discarded models in which values of several parameters did not converge. For models which displayed convergence of nearly all parameter values, we re-run MCMC processes with 3,000,000 generations and a sampling period of 150 generations. Prior to comparison of the harmonic means of lnL values, 299,999 generations were discarded as burn-in. After a second check for convergence the model with the best fitness was selected applying a Bayes Factor Test (BFT) to the positive values of the harmonic means calculated from lnL values [67, 68]. The favored model (2lnB10 > 10) was used for final phylogenetic reconstructions.
To compare results of time-homogeneous and time-heterogeneous models, 14 independent chains of 7,000,000 generations and two chains of 10 million generations for both setups were run on Linux clusters (Pentium 4, 3.0 GHz, 2 Gb RAM, and AMD Opteron Dual Core, 64 bit systems, 32 Gb RAM). For each chain the first two million generations were discarded as burn-in (sampling period of 1000). The setup for the time-homogeneous approach was identical to the pre-run except for number of generations, sampling period and burn-in. The setting for the time-heterogeneous approach differed (Additional file 4). We followed the method of Foster  and Gowri-Shankar and Rattray  in the non-homogeneous setup whereby only a limited number of composition vectors can be shared by different branches in the tree. Exchangeability parameters (average substitution rate ratio values, rate ratios and alpha shape parameter) were fixed as input values. Values for these parameters were computed from results of the preliminary time-homogeneous pre-run (3,000,000 generations). A consensus tree was inferred in PHASE mcmcsummarize using the output of the pre-run. This consensus tree topology and the model file of this run served as input for a ML estimation of parameters in PHASE optimizer. Estimated values of exchangeability parameters from the resulting optimizer output file and estimated start values for base frequencies were fed into mcmcphase for the time-heterogeneous analysis. Values of exchangeability parameters remained fixed during the analysis. The number of allowed base frequency categories (models) along the tree was also fixed. The number of base frequency groups was set to three "submodels"), reflecting base frequency heterogeneity.
Harmonic means of lnL values of these 16 independent chains were again compared with a BFT to identify possible local optima in which a single chain might have been trapped. We only merged sample data of chains with a 2lnB10-value < 10  using a Perl-script to construct a "metachain" . Finally we included ten time-heterogeneous chains and three time-homogeneous chains. The assembled meta-chains included 56 million generations for the non-stationary approach (Additional file 15) and 18 million generations for the time-homogeneous approach (Additional file 16), burn-ins were discarded. Consensus trees and posterior probability values were inferred using mcmcsummarize. Branch lengths of the time-homogeneous and time-heterogeneous consensus tree were estimated using three mcmcphase chains (4 million generations, sampling period 500, topology changes turned off, starting tree = consensus tree, burn-in: 1 million generations) from different initial states with a Gowri-Shankar modified PHASE version. To infer mean branch lengths we combined data with the described branch lengths and mcmcsummarize. These mean branch lengths were used to redraw the consensus tree (Additional file 4).
Localities of sampled specimen used for amplication are listed in Additional file 17.
polymerase chain reaction
degree of freedom
species epithet not known
- ln natural logarithm or log:
Bayes Factor Test.
Mallatt J, Giribet G: Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol Phylogenet Evol. 2006, 40 (3): 772-794. 10.1016/j.ympev.2006.04.021.
Zrzavý J, Štys P: The basic body plan of arthropods: insights from evolutionary morphology and developmental biology. J Evol Biol. 1997, 10 (3): 653-367. 10.1007/s000360050029.
Dohle W: Are the insects terrestrial crustaceans? A discussion of some new facts and arguments and the proposal of the proper name "Tetraconata" for the monophyletic unit Crustacea + Hexapoda. Ann Soc Entomol Fr (New Series). 2001, 37 (3): 85-103.
Friedrich M, Tautz D: Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature. 1995, 376 (6536): 165-167. 10.1038/376165a0.
Shultz JW, Regier JC: Phylogenetic analysis of arthropods using two nuclear protein-encoding gene ssupports a crustacean + hexapod clade. Proc Biol Sci. 2000, 267 (1447): 1011-1019. 10.1098/rspb.2000.1104.
Friedrich M, Tautz D: Arthropod rDNA phylogeny revisited: A consistency analysis using Monte Carlo simulation. Ann Soc Entomol Fr (New Series). 2001, 37 (1–2): 21-40.
Hwang UW, Friedrich M, Tautz D, Park CJ, Kim W: Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature. 2001, 413 (6852): 154-157. 10.1038/35093090.
Regier JC, Shultz JW: Elongation factor-2: A useful gene for arthropod phylogenetics. Mol Phylogenet Evol. 2001, 20: 136-148. 10.1006/mpev.2001.0956.
Giribet G, Edgecombe GD, Wheeler WC: Arthropod phylogeny based on eight molecular loci and morphology. Nature. 2001, 413 (6852): 157-161. 10.1038/35093097.
Pisani D, Poling L, Lyons-Weiler M, Hedges SB: The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol. 2004, 2: 1-10.1186/1741-7007-2-1.
Mallatt JM, Garey JR, Shultz JW: Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol Phylogenet Evol. 2004, 31: 178-191. 10.1016/j.ympev.2003.07.013.
Regier JC, Shultz JW, Kambic RE: Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc Biol Sci. 2005, 272 (1561): 395-401. 10.1098/rspb.2004.2917.
Hassanin A: Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol Phylogenet Evol. 2006, 38: 100-16. 10.1016/j.ympev.2005.09.012.
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sorensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G: Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008, 452 (7188): 745-749. 10.1038/nature06614.
Fanenbruck M, Harzsch S, Wägele JW: The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships. Proc Natl Acad Sci USA. 2004, 101 (11): 3868-3873. 10.1073/pnas.0306212101.
Harzsch S, Müller CHG, Wolf H: From variable to constant cell numbers: cellular characteristics of the arthropod nervous system argue against a sister-group relationship of Chelicerata and "Myriapoda" but favour the Mandibulata concept. Dev Genes Evol. 2005, 215 (2): 53-68. 10.1007/s00427-004-0451-z.
Harzsch S: Neurophylogeny: Architecture of the nervous system and a fresh view on arthropod phyologeny. Integr Comp Biol. 2006, 46 (2): 162-194. 10.1093/icb/icj011.
Ungerer P, Scholtz G: Filling the gap between identified neuroblasts and neurons in crustaceans adds new support for Tetraconata. Proc Biol Sci. 2008, 275 (1633): 369-376. 10.1098/rspb.2007.1391.
Nardi F, Spinsanti G, Boore JL, Carapelli A, Dallai R, Frati F: Hexapod origins: monophyletic or paraphyletic?. Science. 2003, 299 (5614): 1887-1889. 10.1126/science.1078607.
Cameron SL, Miller KB, D'Haese CA, Whiting MF, Barker SC: Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda). Cladistics. 2004, 20 (6): 534-557. 10.1111/j.1096-0031.2004.00040.x.
Cook CE, Yue Q, Akam M: Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc Biol Sci. 2005, 272 (1569): 1295-1304. 10.1098/rspb.2004.3042.
Carapelli A, Liò P, Nardi F, Wath van der E, Frati F: Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea. BMC Evol Biol. 2007, S8-10.1186/1471-2148-7-S2-S8. Suppl 2
Dell'Ampio E, Szucsich NU, Carapelli A, Frati F, Steiner G, Steinacher A, Pass G: 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. Zool Scr. 2009, 38 (2): 155-170. 10.1111/j.1463-6409.2008.00368.x.
Hassanin A, Léger N, Deutsch J: Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst Biol. 2005, 54 (2): 277-298. 10.1080/10635150590947843.
Wägele JW, Mayer C: Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol Biol. 2007, 7: 147-10.1186/1471-2148-7-147.
Rota-Stabelli O, Telford ML: A multi criterion approach for the selection of optimal outgroups in phylogeny: Recovering some support for Mandibulata over Myriochelata using mitogenomics. Mol Phylogenet Evol. 2008, 48: 103-111. 10.1016/j.ympev.2008.03.033.
Bäcker H, Fanenbruck M, Wägele JW: A forgotten homology supporting the monophyly of Tracheata: The subcoxa of insects and myriapods re-visited. Zool Anz. 2008, 247 (3): 185-207. 10.1016/j.jcz.2007.11.002.
Kadner D, Stollewerk A: Neurogenesis in the chilopod Lithobius forficatus suggests more similarities to chelicerates than to insects. Dev Genes Evol. 2004, 214 (8): 367-379. 10.1007/s00427-004-0419-z.
Stollewerk A, Simpson P: Evolution of early development of the nervous system: a comparison between arthropods. Bioessays. 2005, 27 (9): 874-883. 10.1002/bies.20276.
Stollewerk A, Chipman AD: Neurogenesis in myriapods and chelicerates and its importance for understanding arthropod relationships. Integr Comp Biol. 2006, 46 (2): 195-206. 10.1093/icb/icj020.
Ogden TH, Whiting MF: The problem with "the Paleoptera Problem": sense and sensitivity. Cladistics. 2003, 19 (5): 432-442.
Kjer KM: Aligned 18S and insect phylogeny. Syst Biol. 2004, 53 (3): 506-514. 10.1080/10635150490445922.
Kukalová-Peck J, Lawrence JF: Relationships among coleopteran suborders and major endoneopteran lineages: Evidence from hind wing characters. Eur J Entomol. 2004, 101: 95-144.
Misof B, Niehuis O, Bischoff I, Rickert A, Erpenbeck D, Staniczek A: Towards an 18S phylogeny of hexapods: Accounting for group-specific character covariance in optimized mixed nucleotide/doublet models. Zoology (Jena). 2007, 110 (5): 409-429.
Whitfield JB, Kjer KM: Ancient rapid radiations of insects: Challenges for phylogenetic analysis. Annu Rev Entomol. 2008, 53: 449-472. 10.1146/annurev.ento.53.103106.093304.
Koch M: Monophyly and phylogenetic position of the Diplura (Hexapoda). Pedobiologia (Jena). 1997, 41 (9): 9-12.
Kristensen NP: The groundplan and basal diversification of the hexapods. Arthropod Relationships. London: Chapman and Hall, 281-293.
Carapelli A, Frati F, Nardi F, Dallai R, Simon C: Molecular phylogeny of the apterygotan insects based on nuclear and mitochondrial genes. Pedobiologia (Jena). 2000, 44 (3–4): 361-373. 10.1078/S0031-4056(04)70055-4.
Carapelli A, Nardi F, Dallai R, Boore JL, Liò P, Frati F: Relationships between hexapods and crustaceans based on four mitochondrial genes. Crustacean and Arthropod Relationships, Volume 16 of Crustacean Issues. Edited by: Koenemann S, Jenner RA. 2005, CRC Press, 295-306.
D'Haese CA: Were the first springtails semi-aquatic? A phylogenetic approach by means of 28S rDNA and optimization alignment. Proc Biol Sci. 2002, 269 (1496): 1143-1151. 10.1098/rspb.2002.1981.
Luan Yx, Zhang Y, Qiaoyun Y, Pang J, Xie R, Yin W: Ribosomal DNA gene and phylogenetic relationships of Diplura and lower hexapods. Sci China C Life Sci. 2003, 46: 67-76. 10.1360/03yc9008.
Giribet G, Edgecombe GD, Carpenter JM, D'Haese CA, Wheeler WC: Is Ellipura monophyletic? A combined analysis of basal hexapod relationships with emphasis on the origin of insects. Org Divers Evol. 2004, 4 (4): 319-340. 10.1016/j.ode.2004.05.001.
Regier JC, Shultz JW, Kambic RE: Phylogeny of basal hexapod lineages and estimates of divergence times. Ann Entomol Soc Am. 2004, 97 (9): 411-419. 10.1603/0013-8746(2004)097[0411:POBHLA]2.0.CO;2.
Luan Yx, Mallatt JM, Xie Rd, Yang Ym, Yin Wy: The phylogenetic positions of three basal-hexapod groups (Protura, Diplura, and Collembola) based on on ribosomal RNA gene sequences. Mol Biol Evol. 2005, 22 (7): 1579-1592. 10.1093/molbev/msi148.
Szucsich NU, Pass G: Incongruent phylogenetic hypotheses and character conflicts in morphology: The root and early branches of the hexapodan tree. Mitt Dtsch Ges Allg Angew Entomol. 2008, 16: 415-429.
Jow H, Hudelot C, Rattray M, Higgs PG: Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol Biol Evol. 2002, 19 (9): 1591-1601.
Galtier N: Sampling properties of the bootstrap support in molecular phylogeny: Influence of nonindependence among sites. Syst Biol. 2004, 53: 38-46. 10.1080/10635150490264680.
Fox GE, Woese CR: The architecture of 5S rRNA and its relation to function. J Mol Evol. 1975, 6: 61-76. 10.1007/BF01732674.
Wuyts J, De Rijk P, Peer Van de Y, Pison G, Rousseeuw P, De Wachter R: Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res. 2000, 28 (23): 4698-4708. 10.1093/nar/28.23.4698.
Gutell JC, Robin R, Lee , Cannone JJ: The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol. 2002, 12 (3): 301-310. 10.1016/S0959-440X(02)00339-1.
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA: The complete atomic structure of the large ribosomal subunit at 2.4 Å Resolution. Science. 2000, 289 (5481): 905-920. 10.1126/science.289.5481.905.
Noller HF: RNA structure: reading the ribosome. Science. 2005, 309 (5740): 1508-1514. 10.1126/science.1111771.
Lartillot N, Philippe H: Improvement of molecular phylogenetic inference and the phylogeny of Bilateria. Philos Trans R Soc Lond B Biol Sci. 2008, 363 (1496): 1463-1472. 10.1098/rstb.2007.2236.
Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H: Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol. 2007, 56 (3): 389-399. 10.1080/10635150701397643.
Philippe H, Germot A, Moreira D: The new phylogeny of eukaryotes. Curr Opin Genet Dev. 2000, 10 (6): 596-601. 10.1016/S0959-437X(00)00137-4.
Stocsits RR, Letsch H, Hertel J, Misof B, Stadler PF: RNAsalsa. Version 0.7.3, current versions. 2008, Zoologisches Forschungsmuseum A. Koenig, Bonn, [http://rnasalsa.zfmk.de]
Brown JM, Lemmon AR: The importance of data partitioning and the utility of bayes factors in bayesian phylogenetics. Syst Biol. 2007, 56 (4): 643-655. 10.1080/10635150701546249.
Galtier N, Gouy M: Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci USA. 1995, 92 (24): 11317-11321. 10.1073/pnas.92.24.11317.
Tarrío R, Rodríguez-Trelles F, Ayala FJ: Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae. Mol Biol Evol. 2001, 18 (8): 1464-1473.
Gowri-Shankar V, Rattray M: A reversible jump method for bayesian phylogenetic inference with a nonhomogeneous substitution model. Mol Biol Evol. 2007, 24 (6): 1286-1299. 10.1093/molbev/msm046.
Blanquart S, Lartillot N: A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution. Mol Biol Evol. 2006, 23 (11): 2058-2071. 10.1093/molbev/msl091.
Gowri-Shankar V, Rattray M: On the correlation between composition and site-specific evolutionary rate: Implications for phylogenetic inference. Mol Biol Evol. 2006, 23 (2): 352-364. 10.1093/molbev/msj040.
Gowri-Shankar V, Jow H: PHASE: a software package for Phylogenetics And Sequence Evolution. 2.0. 2006, University of Manchester
Telford MJ, Wise MJ, Gowri-Shankar V: Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: Examples from the Bilateria. Mol Biol Evol. 2005, 22 (4): 1129-1136. 10.1093/molbev/msi099.
Misof B, Misof K: A Monte Carlo approach successfully identifies randomness in multiple sequence alignments: a more objective means of data exclusion. Syst Biol. 2009, 58: syp006-
Swofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. 2003, Sinauer Associates, Sunderland, Massachusetts
Kaas RE, Raftery AE: Bayes Factors. Journal of the American Statistical Association. 1995, 90 (430): 773-795. 10.2307/2291091.
Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL: Bayesian phylogenetic analysis of combined data. Syst Biol. 2004, 53 (21): 47-67. 10.1080/10635150490264699.
Boudreaux BH: Arthropod phylogeny: with special reference to insects. 1979, John Wiley & Sons Inc
Edgecombe GD, Giribet G: Myriapod phylogeny and the relationships of Chilopoda. Biodiversidad, Taxonomía y Biogeografia de Artrópodos de México: Hacia una Síntesis de su Conocimiento. Edited by: Bousquets JL, Morrone J, Aula-Verlag. 2002, III: 143-168.
Kjer KM, Carle FL, Litman J, Ware J: A Molecular Phylogeny of Hexapoda. Arthropod Systematics & Phylogeny. 2006, 64: 35-44.
Yamaguchi S, Endo K: Molecular phylogeny of Ostracoda (Crustacea) inferred from 18S ribosomal DNA sequences: implication for its origin and diversification. Mar Biol. 2003, 143: 23-38. 10.1007/s00227-003-1062-3.
Gai YH, Song DX, Sun HY, Zhou KY: Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences. Zool Sci. 2006, 23 (12): 1101-1108. 10.2108/zsj.23.1101.
Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR: Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. Insect Mol Biol. 2005, 15 (5): 657-686. 10.1111/j.1365-2583.2006.00689.x.
Jordal B, Gillespie JJ, Cognato AI: Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae). Zool Scr. 2008, 37: 43-56.
Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT: Incorporating Molecular Evolution into Phylogenetic Analysis, and a New Compilation of Conserved Polymerase Chain Reaction Primers for Animal Mitochondrial DNA. Annu Rev Ecol Evol Syst. 2006, 37: 545-579. 10.1146/annurev.ecolsys.37.091305.110018.
Susko E, Spencer M, Roger AJ: Biases in phylogenetic estimation can be caused by random sequence segments. J Mol Evol. 2005, 61 (3): 351-359. 10.1007/s00239-004-0352-9.
Philippe H, Delsuc F, Brinkmann H, Lartillot N: Phylogenomics. Annual Review of Ecology, Evolution, and Systematics. 2005, 36: 541-562. 10.1146/annurev.ecolsys.35.112202.130205.
Roeding F, Hagner-Holler S, Ruhberg H, Ebersberger I, von Haeseler Arndt, Kube M, Reinhardt R, Burmester T: EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol Phylogenet Evol. 2007, 45 (3): 942-951.
Podsiadlowski L, Kohlhagen H, Koch M: The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla. Mol Phylogenet Evol. 2007, 45: 251-260. 10.1016/j.ympev.2007.07.017.
Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17 (4): 540-552.
Hancock JM, Tautz D, Dover GA: Evolution of the secondary structures and compensatory mutations of the ribosomal RNAs of Drosophila melanogaster . Mol Biol Evol. 1988, 5 (4): 393-414.
Stephan W: The rate of compensatory evolution. Genetics. 1996, 144: 419-426.
Schöninger M, von Haeseler A: A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol. 1994, 3 (3): 240-247. 10.1006/mpev.1994.1026.
Friedrich M, Tautz D: An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera. Mol Biol Evol. 1997, 14 (6): 644-653.
Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD: The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst Biol. 2004, 53 (4): 638-643. 10.1080/10635150490468648.
Foster PG: Modeling compositional heterogeneity. Syst Biol. 2004, 53 (3): 485-495. 10.1080/10635150490445779.
Walossek D: On the Cambrian diversity of Crustacea. Crustaceans and the Biodiversity Crisis, Proceedings of the Fourth International Crustacean Congress, Amsterdam, The Netherlands, July 20–24, 1998. Edited by: von Vaupel Klein FRSJC. 1998, Brill Academic Publishers, Leiden, 1: 3-27.
Edgecombe GD, Wilson GDF, Colgan DJ, Gray MR, Cassis G: Arthropod Cladistics: Combined analysis of histone H3 and U2 snRNA sequences and morphology. Cladistics. 2000, 16 (2): 155-203. 10.1111/j.1096-0031.2000.tb00352.x.
Lim JT, Hwang UW: The complete mitochondrial genome of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia): non-monophylies of Maxillopoda and Crustacea. Mol Cells. 2006, 22 (3): 314-322.
Wilson K, Cahill V, Ballment E, Benzie J: The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: Are malacostracan crustaceans more closely related to insects than to branchiopods?. Mol Biol Evol. 2000, 17 (6): 863-874.
Glenner H, Thomsen PF, Hebsgaard MB, Sørensen MV, Willerslev E: Evolution: The origin of insects. Science. 2006, 314 (5807): 1883-1884. 10.1126/science.1129844.
Zhang Xg, Siveter DJ, Waloszek D, Maas A: An epipodite-bearing crown-group crustacean from the Lower Cambrian. Nature. 2007, 449 (7162): 595-598. 10.1038/nature06138.
Regier JC, Shultz JW: Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Mol Biol Evol. 1997, 14 (9): 902-913.
Schierwater B, Hadrys H: Environmental factors and metagenesis in the hydroid Eleutheria dichotoma . Invertebr Reprod Dev. 1998, 34 (2–3): 139-148.
Hall TA: BioEdit: a user-friendly biological alignment sequence EDITOR and analysis program for Windows95/98/NT. Nucleic Acids Symp Ser. 1999, 41 (2–3): 95-98.
Tatusova TA, Madden TL: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett. 1999, 174 (2): 247-250. 10.1111/j.1574-6968.1999.tb13575.x.
Kjer KM: Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Mol Phylogenet Evol. 1995, 4 (3): 314-330. 10.1006/mpev.1995.1028.
Hickson RE, Simon C, Perrey SW: The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol Biol Evol. 2000, 17 (4): 530-539.
Buckley TR, Simon C, Chambers GK: Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst Biol. 2001, 50: 67-86. 10.1080/106351501750107495.
Misof B, Niehuis O, Bischoff I, Rickert A, Erpenbeck D, Staniczek A: A hexapod nuclear SSU rRNA secondary-structure model and catalog of taxon-specific structural variation. J Exp Zool B Mol Dev Evol. 2006, 306B: 70-88. 10.1002/jez.b.21040.
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797. 10.1093/nar/gkh340.
Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004, 5: 113-10.1186/1471-2105-5-113.
Peer Van de Y, De Rijk P, Wuyts J, Winkelmans T, De Wachter R: The European Small Subunit Ribosomal RNA database. Nucleic Acids Res. 2000, 28: 175-176. 10.1093/nar/28.1.175.
Wuyts J, Peer Van de Y, Winkelmans T, De Wachter R: The European database on small subunit ribosomal RNA. Nucleic Acids Res. 2002, 30: 183-185. 10.1093/nar/30.1.183.
Wuyts J, Perrière G, Peer Van de Y: The European ribosomal RNA database. Nucleic Acids Res. 2004, 32 (Suppl 1, Database): D101-103. 10.1093/nar/gkh065.
Michot B, Bachellerie JP, Raynal F: Structure of mouse rRNA precursors. Complete sequence and potential folding of the spacer regions between 18S and 28S rRNA. Nucleic Acids Res. 1983, 11 (10): 3375-3391. 10.1093/nar/11.10.3375.
Gillespie JJ, Munro JB, Heraty JM, Yoder MJ, Owen AK, Carmichael AE: A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera: Chalcidoidea). Mol Biol Evol. 2005, 22 (7): 1593-1608. 10.1093/molbev/msi152.
Huson DH, Bryant D: Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006, 23 (2): 254-267. 10.1093/molbev/msj030.
Bryant D, Moulton V: Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Mol Biol Evol. 2004, 21 (2): 255-265. 10.1093/molbev/msh018.
Penny D, Lockhart PJ, Steel MA, Hendy MD: The role of models in reconstructing evolutionary trees. Models in phylogeny reconstruction, The Systematics Association Special Volume Series. Edited by: Scotland RW, Diebert DJ, Williams DM. 1994, Oxford University Press, 211-230.
Steel M, Huson D, Lockhart PJ: Invariable sites models and their use in phylogeny reconstruction. Syst Biol. 2000, 49 (2): 225-232. 10.1093/sysbio/49.2.225.
Yang Z: Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol (Amst.). 1996, 11 (9): 367-372. 10.1016/0169-5347(96)10041-0.
Yang Z: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 1994, 39 (3): 306-314. 10.1007/BF00160154.
Kelchner SA, Thomas MA: Model use in phylogenetics: nine key questions. Trends Ecol Evol (Amst.). 2007, 22 (2): 87-94. 10.1016/j.tree.2006.10.004.
Sullivan J, Swofford DL: Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?. Syst Biol. 2001, 50 (5): 723-729. 10.1080/106351501753328848.
Waddell PJ, Penny D, Moore T: Hadamard conjugations and modeling sequence evolution with unequal rates across sites. Mol Phylogenet Evol. 1997, 8: 33-50. 10.1006/mpev.1997.0405.
Zwickl DJ, Holder MT: Model parameterization, prior distributions, and the general time-reversible model in bayesian phylogenetics. Syst Biol. 2004, 53 (6): 877-888. 10.1080/10635150490522584.
Beiko RG, Keith JM, Harlow TJ, Ragan MA: Searching for convergence in phylogenetic Markov Chain Monte Carlo. Syst Biol. 2006, 55 (4): 553-565. 10.1080/10635150600812544.
We thank Matty Berg, Anke Braband, Antonio Carapelli, Erhard Christian, Romano Dallai, Johannes Dambach, Wolfram Dunger, Erich Eder, Christian Epe, Pietro Paolo Fanciulli, Makiko Fikui, Francesco Frati, Peter Frenzel, Yan Gao, Max Hable, Bernhard Huber, Herbert Kliebhan, Stefan Koenemann, Franz Krabb, Ryuichiro Machida, Albert Melber, Wolfgang Moser, Reinhard Predel, Michael Raupach, Sven Sagasser, Kaoru Sekiya, Marc Sztatecsny, Dieter Waloßek, Manfred Walzl and Yi-ming Yang for help in collecting specimens, for providing tissue or other DNA-samples or for laboratory help. Thanks also go to Andreas Wißkirchen, Theory Department, Physikalisches Institut, University of Bonn for using their computational power. We thank Berit Ullrich, Oliver Niehuis and Patrick Kück for providing Perl-Scripts and Thomas Stamm for suggestions on the discussion structure. Special thanks go to John Plant for linguistic help. This work was supported by the German Science Foundation (DFG) in the priority program SPP 1174 "Deep Metazoan Phylogeny" http://www.deep-phylogeny.org. Work by JWW, BMvR is supported by the DFG grant WA 530/34; BM, KM are funded by the DFG grant MI 649/6, HH and SS are supported by the DFG grant HA 1947/5. NUS, ED, DB and GP are funded by the Austrian Science Foundation (FWF) grant P 20497-B17.
BMvR, KM and BM conceived the study, designed the setup and performed all analyses. VG complemented PHASE-2.0 and contributed to PHASE-2.0 analyses setup. RRS, HOL, BM provided RNAsalsa and software support. JWW allocated the neighbornet-analysis. BMvR, KM, ED, SS, HOL, DB and YL contributed sequence data and designed primers. BMvR, KM, BM, NUS and JWW wrote the paper with comments and revisions from ED, VG, RRS, DB, SS, GP, HH and YL. All authors read and approved the final manuscript.
Electronic supplementary material
Additional file 1: Taxa list. Taxa list of sampled sequences. * indicates concatenated 18S and 28S rRNA sequences from different species. For combinations of genes to construct concatenated sequences of chimeran taxa, see Table S1. ** contributed sequences in the present study (author of sequences). (XLS 123 KB)
Additional file 2: . LogDet corrected network plus invariant site models (30.79% invariant sites) using SplitsTree4 based on the concatenated 18S and 28S rRNA alignment after exclusion of randomly similar sections evaluated with ALISCORE. (PDF 53 KB)
Additional file 3: Bayesian support values for selected clades. List of Baysian support values (posterior probability, pP) for selected clades of the time-heterogeneous and time-homogeneous tree. (XLS 78 KB)
Additional file 4: . Options used in PHASE-2.0 are italicized above the arrows and are followed by input files. Black arrows represent general flows of the analysis procedure, green arrows show that results or parameter values after single steps were inserted or accessed in a further process. Red block-arrows mark the final run of the time-heterogeneous and time-homogeneous approach with 16 chains each (2 × 118,000,000 generations). First row: I.) We prepared 3 control files (control.mcmc) for mcmcphase using three different mixed models. This "pre-run" was used for a first model selection (500,000 generations for each setting). We excluded model (C) based on non-convergence of parameter values. II.) We repeated step one (I.) with 3,000,000 generations using similar control files (different number of generations and random seeds) of the two remaining model settings. Calculated ln likelihoods values of both chains were compared in a BFT resulting in the exclusion of mixed model (A). Parameter values of the remaining model (B) were implemented in the time-heterogeneous setting. III.) We started the final analysis (final run) using sixteen chains for both the time-homogeneous and the time-heterogeneous approach. In the final time-homogeneous approach, the control files were similar to step II.) except for a different number of generations and random seeds. Second row: Additional steps were necessary prior to the computation of the final time-heterogeneous chains. We applied mcmcsummarize for the selected mixed model (B) to calculate a consensus tree. Optimizer was executed to conduct a ML estimation for each parameter value (opt.mod) based on the inferred consensus tree and optimized parameter-values (mcmc-best.mod), a data file delivered by mcmcphase. Estimated values were implemented in an initial.mod file. The initial.mod file and its parameter values were accessed by the control files of the final time-heterogeneous chains (only topology and base frequencies estimated). Third row: Trees were reconstructed separately for the time-homogeneous and time-heterogeneous setting. All chains of each approach were tested in a BFT against the chain with the best lnL. We only included chains with a 2lnB10-value > 10. From these chains we constructed a metachain for each setting using Perl and applied mcmcsummarize to infer the consensus topology. To estimate branch lengths properly we ran mcmcphase, resulting branch lengths were implemented in the consensus trees. Finally, both trees were optimized using graphic programs (Dendroscope, Adobe Illustrator CS II). (PDF 447 KB)
Additional file 8: . Primers used for hexapods or myriapods are shown in the upper part, primers for crustaceans in the lower part. Positions of forward primers are marked with green arrows, those of reverse primers with red arrows. When different primers with identical position were used, all primer labels are given at the single arrow for the specific position. Primers and their combinations are given in Additional file 6 and 11. (PDF 529 KB)
Additional file 9: . Positions of forward primers are tagged with green arrows, those of reverse primers with red arrows. When different primers with identical position were used, all primer labels are given at the single arrow for the specific position. Primers and their combinations are given in Additional file 7 and 11. (PDF 577 KB)
Additional file 10: . Positions of forward primers are assigned by green arrows, those of reverse primers with red arrows. When different primers with identical position were used, all primer labels are given at the single arrow for the specific position. Primers and their combinations are given in Additional file 7 and 11. (PDF 565 KB)
Additional file 11: Supplementary Information. Supplementary information for lab work (amplificaion, purification and sequencing of PCR products). (PDF 83 KB)
Additional file 14: . Listed settings of exchangeability parameters used in pre-runs in PHASE-2.0. (XLS 48 KB)
Additional file 15: . Number of chains, generations per chain, harmonic means (lnL) and 2lnB10-values included to infer the time-heterogeneous consensus tree. (XLS 55 KB)
Additional file 16: . Number of chains, generations per chain, harmonic means (lnL) and 2lnB10-values included to infer the time-homogeneous consensus tree. (XLS 54 KB)
About this article
Cite this article
von Reumont, B.M., Meusemann, K., Szucsich, N.U. et al. Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships. BMC Evol Biol 9, 119 (2009). https://doi.org/10.1186/1471-2148-9-119
- Sister Group
- Base Frequency
- Tree Reconstruction
- Sister Group Relationship
- Consensus Secondary Structure