Technical Comments

Response to Comment on “The hologenomic basis of speciation: Gut bacteria cause hybrid lethality in the genus Nasonia

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Science  29 Aug 2014:
Vol. 345, Issue 6200, pp. 1011
DOI: 10.1126/science.1256708


  • Fig. 1 Evolutionary genomics of hybrid incompatibilities.

    (A) A nuclear-centric model of hybrid incompatibilities in which red arrows indicate potential negative epistasis between N. vitripennis (v/v) and N. giraulti (g/g) genes. (B) Six hologenomic models of hybrid incompatibility evolution in which pie charts reflect microbiota data published in (5). The Providenica taxa in parental v and g encompass several different 16S oligotypes, and Proteus, the dominant microbe in hybrids, is present at low abundance in parental v and g. (i) The v genome negatively interacts with the g microbiome. (ii) The g genome negatively interacts with the v microbiome. (iii) The v, g, and overgrown resident microbiomes interact together. (iv) The v and g microbiomes and derived genomes negatively interact with each other, respectively. (v) A microbiome-microbiome interaction detrimental to the host because the two bacterial genotypes are incompatible with each other (i.e., cytoplasmic incompatibility). (vi) The v and g genomes negatively interact with a new bacterial species (purple); alternatively, the two genomic interactions can abnormally suppress beneficial bacteria and lead to hybrid problems due to the lack of beneficial bacteria, such as an autoimmune response. (C) The predicted rescue of nuclear-centric and hologenomic hybrid incompatibilities in germ-free versus conventional rearing conditions. Portions of this figure are discussed in previous modeling of Bateson-Dobzhansky-Muller models of hybrid incompatibility with and without microbes (6).

  • Fig. 2 Separating the effects of sampling depth and OTU clustering on phylosymbiotic accuracy.

    Weighted UniFrac, unweighted pair group method with arithmetic mean (UPGMA) cluster analyses at 95, 97, and 99.5 percent OTU clusterings, and rarefied sampling depths of 200, 500, and 1000 sequences (75% of smallest sample size, rounded). (A) Weighted UniFrac UPGMA generated using the parameters provided by Chandler and Turelli. (B) Weighted UniFrac UPGMA generated using the parameters specified in (5). (C) Weighted UniFrac UPGMA generated using the parameters specified in (11). (D to I) Weighted UniFrac UPGMA generated with aforementioned parameters under different, rarefied sampling depth (500 sequences ~50% of smallest library and 1000 sequences ~75%) that eliminates the S. bullata host as an inappropriate outgroup. All jackknife support values are calculated in UniFrac based on a midpoint root of the longest branch (black circle). We preferentially draw the dendrograms as unrooted because there is no basis for rooting community cluster dendrograms of microbiomes. Green branches emphasize phylosymbiotic and phylogenetic relationships of Nasonia in which g/g (N. giraulti) and l/l (N. longicornis) are more closely related to each other than to v/v (N. vitripennis).

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