Effects of 16S rDNA sampling on estimates of endosymbiont lineages in sucking lice
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Abstract
Co-evolution between insects and their endosymbiotic bacteria can be detected by constructing and comparing their phylogenetic trees. Even though taxon sampling can greatly affect phylogenetic and co-evolutionary inference, most hypotheses of endosymbiont relationships and estimates of the number of endosymbiont lineages within a host group have used only a small percentage of available bacterial sequences. Here we examined how different sampling strategies of Gammaproteobacteria sequences affect estimates of the number of endosymbiont lineages in parasitic sucking lice (Insecta: Phthirapatera: Anoplura). We estimated the number of louse endosymbiont lineages using both newly obtained and previously sequenced 16S rDNA bacterial sequences and more than 42,000 16S rDNA sequences from other Gammaproteobacteria. We also performed parametric and nonparametric bootstrapping experiments to examine the effects of phylogenetic error and uncertainty on these estimates. We found that sampling of 16S rDNA sequences affected the estimates of endosymbiont diversity in sucking lice until we reached a threshold of genetic diversity. Sampling by maximizing the diversity of 16S rDNA sequences was more efficient than simply randomly sampling available 16S rDNA sequences. Although simulation results support the finding of multiple endosymbiont lineages in sucking lice, the bootstrap results suggest that there is still uncertainty in estimates of the number of endosymbiont origins inferred from 16S rDNA alone.
Cite this as
2015. Effects of 16S rDNA sampling on estimates of endosymbiont lineages in sucking lice. PeerJ PrePrints 3:e1457v1 https://doi.org/10.7287/peerj.preprints.1457v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Julie M Allen conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
J Gordon Burleigh conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Jessica E Light conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
David L Reed conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
DNA sequences will be submitted upon publication. I have attached the sequences and the alignment to the article documents.
Data Deposition
The following information was supplied regarding data availability:
The alignment and resulting trees will be submitted to DRYAD upon acceptance. They have all been uploaded with the manuscript.
Funding
This work was funded in part by grants from the National Science Foundation to DLR (DEB 0717165 and DEB 0845392) and JEL (DEB 0308878 and DEB 0717165). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
