Comment on "The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia"

Abstract

Brucker and Bordenstein (Reports, 9 August 2013, p. 667) claim that adaptive codivergence of gut bacteria with hosts contributes to hybrid lethality. Yet, they provide no evidence for coadaptation of bacteria and Nasonia hosts. Their data on hybrid viability suggest that bacteria contribute to inviability only because intrinsic hybrid dysfunction increases susceptibility to free-living bacteria. Hologenomic speciation remains testable speculation without experimental support.

Fig. 1. Bootstrapped clustering using the UniFrac distance metric

Raw sequences were obtained from the Dryad Digital Repository, doi:10.5061/dryad.5r09q. The data were processed following the recommendations of the QIIME tutorial (http://qiime.org/tutorials/tutorial.html) except that OTUs were formed using the 95% similarity threshold [following the method described in the supplemental material of (1)]. The details of our analyses are provided at http://figshare.com/articles/Hologenomic_speculation_on_Nasonia_speciation/1084395. Any sequences classified as Wolbachia or chloroplasts or that could not be classified as bacteria were removed from the dataset. To obtain bootstrapped replicates, data were subsampled to 206 reads (75% of smallest library size; again as recommended by the QIIME/UniFrac developers [(9) and http://qiime.org/tutorials/tutorial.html]. Support values represent the proportion of 100 subsampled trees supporting each node of the consensus topology. Note that the clustering algorithms employed (UPGMA and neighbor joining) produce rooted trees, no outgroup is selected a priori. The results provide weak support for the “phylosymbiosis” prediction that the bacterial communities recapitulate the host's phylogeny: S. bullata in not consistently identified as the outgroup with N. giraulti and N. longicornis as sister species. We used neighbor joining in addition to the QIIME default of UPGMA, because there is no reason to assume equal rates of divergence along different branches. (A) Unweighted UniFrac, UPGMA clustering; (B) Weighed UniFrac, UPGMA clustering; (C) Unweighted UniFrac, neighbor-joining clustering; (D) Weighted UniFrac, neighbor-joining clustering.

Fig. 2. Bootstrapped clustering using the Bray-Curtis distance metric

Data were processed as in Fig. 1, but an alternative metric (the default from QIIME) was used to quantify bacterial community differences. Other abundance-based beta-diversity metrics (Chi-squared, Chord, Euclidian, Hellinger, Kulczynski, Manhattan, Morisita-Horn, and Pearson) find the same topologies and similar support values (data not shown), again providing little support for phylosymbiosis. (A) UPGMA clustering, (B) Neighbor-joining clustering.