Hexapod Origins: Monophyletic or Paraphyletic?

Nardi, Francesco; Spinsanti, Giacomo; Boore, Jeffrey L.; Carapelli, Antonio; Dallai, Romano; Frati, Francesco

doi:10.1126/science.1078607

Cited by 346 publications

(252 citation statements)

References 19 publications

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“…The support for the monophyly of Crustacea plus Hexapoda, which came most emphatically from the evidence of a shared mitochondrial genome rearrangement, has been bolstered by numerous subsequent molecular phylogenetic analyses (Friedrich & Tautz 1995;Hwang et al 2001;Delsuc et al 2003;Nardi et al 2003;Regier et al 2005). Consideration of various aspects of morphology, in particular of nervous system ontogeny and structure, gives further weight to the integrity of this clade.…”

Section: The Position Of the Hexapoda Within The Pancrustaceamentioning

confidence: 99%

“…While rRNA and nuclear coding gene phylogenies recover the expected monophyly of the hexapods (Insecta, Diplura, Protura and Collembola), analyses using complete mitochondrial genomes recover a diphyletic Hexapoda with the Insecta separated from the Collembola ( Nardi et al 2003); sequences for Diplura and Protura were not available. The basis of this result has been questioned by subsequent authors Figure 3.…”

Section: The Position Of the Hexapoda Within The Pancrustaceamentioning

confidence: 99%

See 1 more Smart Citation

The evolution of the Ecdysozoa

Telford

Bourlat

Economou

et al. 2008

Phil. Trans. R. Soc. B

192

121

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Ecdysozoa is a clade composed of eight phyla: the arthropods, tardigrades and onychophorans that share segmentation and appendages and the nematodes, nematomorphs, priapulids, kinorhynchs and loriciferans, which are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species and there is a great diversity of body plans among both living and fossil members. The monophyly of the clade has been called into question by some workers based on analyses of whole genome datasets. We review the evidence that now conclusively supports the unique origin of these phyla. Relationships within Ecdysozoa are also controversial and we discuss the molecular and morphological evidence for a number of monophyletic groups within this superphylum.

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Section: The Position Of the Hexapoda Within The Pancrustaceamentioning

confidence: 99%

Section: The Position Of the Hexapoda Within The Pancrustaceamentioning

confidence: 99%

The evolution of the Ecdysozoa

Telford

Bourlat

Economou

et al. 2008

Phil. Trans. R. Soc. B

192

121

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“…This rate has several shortcomings: (1) it was estimated from eight arthropod examples only; (2) comparisons were only made at the intraspecific level or between closely related species; (3) the sequences used were short, representing only a small fraction of the mitochondrial genome (partial cox1, cox2, rrnS and rrnL sequences) and (4) genetic distances were calculated from restriction site polymorphisms, DNA-levels. The analysis of full mitochondrial genomes has been established as a powerful approach to elucidate deeper-level relationships among vertebrates (e.g., Zardoya and Meyer, 1996;Meyer and Zardoya, 2003;Murata et al, 2003) and also among Arthropods (e.g., Nardi et al, 2003;Masta et al, 2009). Recent studies have explored the utility of applying mitochondrial genome data to resolve phylogenetic relationships at the intraordinal level of insects with promising results, as for the Diptera (Cameron et al, 2007), Orthoptera (Fenn et al, 2008) and Hymenoptera (Dowton et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

Pons

Ribera

Bertranpetit

et al. 2010

Molecular Phylogenetics and Evolution

149

120

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The ages of cladogenetic events in Coleoptera are frequently estimated with mitochondrial protein coding genes (MPCGs) and the -standard‖ mitochondrial nucleotide substitution rate for arthropods. This rate has been used for different mitochondrial gene combinations and time scales despite it was estimated on short mitochondrial sequences from few comparisons of close related species. These shortcomings may cause greater impact at deep phylogenetic levels as errors in rates and ages increase with branch lengths. We use the full set of MPCGs of 15 species of beetles (two of them newly sequenced here) to estimate the nucleotide evolutionary rates in a reconstructed phylogeny among suborders, paying special attention to the effect of data partitioning and model choices on these estimations. The optimal strategy for nucleotide data, as measured with Bayes factors, was partitioning by codon position. This retrieved Adephaga as a sister group to Myxophaga with strong support (expected likelihood weights test 0.94-1) and both sisters to Polyphaga, in contradiction with the most currently accepted views. The hypothesis of Archostermata being sister to the remaining Coleoptera, which is in agreement with morphology, was increasingly supported when third codon sites were recoded or completely removed, sequences were analyzed as AA, and heterogeneous models were implemented but the support levels remained low. Nucleotide substitution rates were strongly affected by the choice of data partitioning (codon position versus individual genes), with up to sixfold levels of variation, whereas differences in the molecular clock algorithm produced changes of only about 20%. The global mitochondrial protein coding rate using codon partitioning and an estimated age of 250 million years (MY) for the origin of the Coleoptera was 1.34% per branch per MY, which closely matches the ‗standard' clock of 1.15% per MY. The estimation of the rates on alternative topologies gave similar results. Using local molecular clocks, the evolutionary rate in the Polyphaga and Archostemata was estimated to be nearly twice as fast as in the Adephaga and Myxophaga (1.03% versus 0.53% per MY). Rates across individual genes varied from 0.55% to 8.61% per MY. Our results suggest that cox1 might not be an optimal gene for implementing molecular clocks in deep phylogenies for beetles because it shows relatively slow rates at first and second codon positions but very fast rates at third ones. In contrast, nad5, nad4 and nad2 perform better, as they exhibit more homogeneous rates among codon positions.

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“…Mitochondrial genome analyses, both on gene order and nucleotide analyses of the brachiopod Terebratulina retusa convincingly support a protostome relationship with an affiliation to the spiral cleaving molluscs and annelids (Stechmann and Schlegel, 1999). However, some results on the analysis of mitochondrial genome comparisons challenge classical evidence, such as the monophyly of insects (Nardi et al, 2003).…”

Section: Metazoan Phylogeny From Mitochondrial Genomesmentioning

confidence: 48%

Alignments of mitochondrial genome arrangements: Applications to metazoan phylogeny

Fritzsch

Schlegel

Stadler

2006

Journal of Theoretical Biology

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Mitochondrial genomes provide a valuable dataset for phylogenetic studies in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combined pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements.

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Hexapod Origins: Monophyletic or Paraphyletic?

Cited by 346 publications

References 19 publications

The evolution of the Ecdysozoa

The evolution of the Ecdysozoa

Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera

Alignments of mitochondrial genome arrangements: Applications to metazoan phylogeny

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