Arsenophonus, an emerging clade of intracellular symbionts with a broad host distribution

Abstract

Background: The genus Arsenophonus is a group of symbiotic, mainly insect-associated bacteria with rapidly increasing number of records. It is known from a broad spectrum of hosts and symbiotic relationships varying from parasitic son-killers to coevolving mutualists.The present study extends the currently known diversity with 34 samples retrieved mainly from hippoboscid (Diptera: Hippoboscidae) and nycteribiid (Diptera: Nycteribiidae) hosts, and investigates phylogenetic relationships within the genus.

Results: The analysis of 110 Arsenophonus sequences (incl. Riesia and Phlomobacter), provides a robust monophyletic clade, characterized by unique molecular synapomorphies. On the other hand, unstable inner topology indicates that complete understanding of Arsenophonus evolution cannot be achieved with 16S rDNA. Moreover, taxonomically restricted Sampling matrices prove sensitivity of the phylogenetic signal to sampling; in some cases, Arsenophonus monophyly is disrupted by other symbiotic bacteria. Two contrasting coevolutionary patterns occur throughout the tree: parallel host-symbiont evolution and the haphazard association of the symbionts with distant hosts. A further conspicuous feature of the topology is the occurrence of monophyletic symbiont lineages associated with monophyletic groups of hosts without a co-speciation pattern. We suggest that part of this incongruence could be caused by methodological artifacts, such as intragenomic variability.

Conclusion: The sample of currently available molecular data presents the genus Arsenophonus as one of the richest and most widespread clusters of insect symbiotic bacteria. The analysis of its phylogenetic lineages indicates a complex evolution and apparent ecological versatility with switches between entirely different life styles. Due to these properties, the genus should play an important role in the studies of evolutionary trends in insect intracellular symbionts. However, under the current practice, relying exclusively on 16S rRNA sequences, the phylogenetic analyses are sensitive to various methodological artifacts that may even lead to description of new Arsenophonus lineages as independent genera (e.g. Riesia and Phlomobacter). The resolution of the evolutionary questions encountered within the Arsenophonus clade will thus require identification of new molecular markers suitable for the low-level phylogenetics.

Figure 1

An increase of records on Arsenophonus bacteria from various insect groups. The bars show cumulative numbers of sequences deposited into GenBank; dark tops represent new records added in the given year. The sequences are identified with the following accession numbers: 1991 – M90801; 1997 – U91786; 2000 – AF263561, AF263562, AF286129, AB038366; 2001 – AF400474, AF400480, AF400481, AF400478, AY057392; 2002 – AY136168, AY136153, AY136142; 2003 – AY265341–AY265348, Y264663–AY264673, AY264677; 2004 – AY587141, AY587142, AY587140; 2005 – DQ068928, DQ314770–DQ314774, DQ314777, DQ314768, DQ115536; 2006 – DQ538372–DQ538379, DQ508171–DQ508186, DQ517447, DQ508193, DQ837612, DQ837613; 2007 – EU039464, EU043378, EF110573, EF110574, DQ076660, DQ076659, EF110572, EF647590, AB263104.

Figure 2

Phylogenetic tree derived from the Basic matrix (1222 positions) under ML criterion. Names of the taxa clustering within the Arsenophonus clade are printed in colour: red for the long-branched taxa, dark orange for the short-branched taxa. The arrows point to the new sequences obtained in our study. Different types of sequences determined from the specimens of O. avicularia are designated by the numbers with asterisks. The type species A. nasoniae is designated by the orange asterisk. Solid circles on branches label the clusters strictly concordant with the host phylogenies. Open circles designate host-specific lineages without coevolutionary signal. Solid vertical lines indicate reciprocally monophyletic groups of symbionts and hosts. Dashed lines show paraphyletic symbiont clades restricted to monophyletic host groups. Names in the brackets indicate host taxa. "Symb-" in the taxon designation stands for "Symbiotic bacteria of". Bars represent GC content of each taxa. Complete information on the sequences is provided in the Additional file 5.

Figure 3

Topologies derived from Sampling3 matrix (851 positions). A) consensus of the trees and two tree examples A1 and A2, obtained under the MP criterion with Tv/Ts ratio set to 1:1 B) consensus of the trees obtained under the MP criterion with Tv/Ts ratio set to 1:3. The type species A. nasoniae is designated by the orange asterisk.

Figure 4

Tree consensus derived from Sampling5 (936 positions) matrix under the MP criterion. Transversion/transition ratio was set to 1:1. The type species A. nasoniae is designated by the orange asterisk.

Figure 5

Topologies derived from the Basic matrix (1222 positions). A) consensus of the trees obtained under the MP criterion with transversion/transition ratio set to 1:3 and the ML criterion; B) consensus of the MP trees obtained with the transversion/transition ratio 1:1. The type species A. nasoniae is designated by the orange asterisk.

Figure 6

Phylogenetic tree derived from Basic matrix (1222 positions) using Bayesian analysis. Names of the taxa clustering within the Arsenophonus clade are printed in colour: red for the long-branched taxa, dark orange for the short-branched taxa. Names in the brackets designate the host family. Numbers represent Bayesian posterior probability for each node. The type species A. nasoniae is designated by the orange asterisk.