Sources of signal in 62 protein-coding nuclear genes for higher-level phylogenetics of arthropods.

Jerome C Regier,Andreas Zwick

doi:10.1371/journal.pone.0023408

Abstract

BackgroundThis study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions.Methodology/Principal FindingsThe current study analyzes DNA sequences from 68 gene segments of 62 distinct protein-coding nuclear genes for 80 species. Gene segments analyzed individually support numerous nodes recovered in combined-gene analyses, but few of the higher-level nodes of greatest current interest. However, neither is there support for conflicting alternatives to these higher-level nodes. Gene segments with higher rates of nonsynonymous change tend to be more informative overall, but those with lower rates tend to provide stronger support for deeper nodes. Higher-level nodes with bootstrap values in the 80% – 99% range for the complete data matrix are markedly more sensitive to substantial drops in their bootstrap percentages after character subsampling than those with 100% bootstrap, suggesting that these nodes are likely not to have been strongly supported with many fewer data than in the full matrix. Data set partitioning of total data by (mostly) synonymous and (mostly) nonsynonymous change improves overall node support, but the result remains much inferior to analysis of (unpartitioned) nonsynonymous change alone. Clusters of genes with similar nonsynonymous rate properties (e.g., faster vs. slower) show some distinct patterns of node support but few conflicts. Synonymous change is shown to contribute little, if any, phylogenetic signal to the support of higher-level nodes, but it does contribute nonphylogenetic signal, probably through its underlying heterogeneous nucleotide composition. Analysis of seemingly conservative indels does not prove useful.ConclusionsGenerating a robust molecular higher-level phylogeny of Arthropoda is currently possible with large amounts of data and an exclusive reliance on nonsynonymous change.

Highlights

The robust resolution of higher-level arthropod phylogeny has been a challenging problem, as evidenced by numerous publications with alternative proposals of relationships [1,2,3,4,5,6,7,8,9,10]
Generating a robust molecular higher-level phylogeny of Arthropoda is currently possible with large amounts of data and an exclusive reliance on nonsynonymous change
The apparent success of this study is likely due to its relatively broad taxon sample (75 arthropod spp. from all major lineages +5-10 diverse outgroup spp.), large data matrix, and focus on appropriate methodologies

Summary

Introduction

The robust resolution of higher-level arthropod phylogeny has been a challenging problem, as evidenced by numerous publications with alternative proposals of relationships [1,2,3,4,5,6,7,8,9,10]. A recent molecular report [11] describes fully resolved relationships within and among four all-inclusive, extant arthropod clades -Pancrustacea, Myriapoda, Euchelicerata, and Pycnogonida -- with generally high levels of node support, with some exceptions, inside Euchelicerata (redrawn in Figure 1 of this report; see Table 1 and Materials & Methods for character set definitions used in this and previous reports). Codons, and amino acids all recover these seven groups in their maximum likelihood topologies, analysis of amino acids is unique in that support for six of the seven is significantly lower than with other approaches, in which bootstrap support is always strong. This study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions

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Results

Discussion

Conclusion