In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

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Science  27 Apr 2012:
Vol. 336, Issue 6080, pp. 462-466
DOI: 10.1126/science.1218389

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  1. Fig. 1

    Leptospirillum group II genotype distribution shows dispersal across the Richmond Mine and type III strain turnover at the C75 location. (A) Richmond Mine schematic map, with pie charts indicating genotype proportions in 24 samples, estimated on the basis of read recruitment (figs. S5 and S9). (B) Acid mine drainage flow rate (measured at the mine entrance) and community composition at the C75 location, measured by fluorescence in situ hybridization (Arc, Archaea; L3, Leptospirillum group III; L2, Leptospirillum group II). Leptospirillum group II, type III strain transitions, revealed by SNP analysis, are indicated by an asterisk inside the Leptospirillum group II FISH data. (C) Flow data, 2001 to 2011. Shading indicates period displayed in (B).

  2. Fig. 2

    Reconstruction of the recent evolutionary history of Leptospirillum group II. (A) The outer circle plots the counts of peptides unique to the type I (red) and type VI (blue) reference genomes at each protein locus (dots) for the C75 type III population [proteomics-inferred genotyping (PIGT); data from (15)]. Inner circles show Illumina read recruitment to the reference genomes, revealing the prevalence of type III, IV, IVa, V, and VI recombinants. (B) Correspondence of PIGT and recruitment data, highlighting the identical recombination point in genotypes III to V. (C) Evolutionary history of the sampled genotypes, based on the variant loci (table S7), inferred using the maximum parsimony method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches. Dotted arrows indicate recombination events; circle schematics represent the regions affected. The timeline indicates the calculated time ranges of recombination events (table S3) as well as historical events (fig. S2) (18, 21). Branch D* is presented as two strains, each assigned half the total number of UBA 06/05 SNPs, because low incidence of SNPs precluded their linkage. BP, years before the present.

  3. Fig. 3

    Overview of the Leptospirillum group II high-frequency variants, based on read recruitment to the C75 June 2006 type III genotype. Dots indicate variant nucleotides relative to the last common ancestor of types III to VI. Functional categories (table S6) are indicated only for nonsynonymous substitutions and only for the first occurrence, starting from the most recent genotype (outside circle). Shading in inner circles indicates regions that were excluded for SNP analysis in a particular genotype because of recombination or indel events.

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