HGT turbulence: Confounding phylogenetic influence of duplicative horizontal transfer and differential gene conversion

Abstract

Horizontal gene transfer (HGT) often leads to phylogenetic incongruence. When "duplicative HGT" introduces a second copy of a pre-existing gene, the two copies may then engage in gene conversion, leading to phylogenetically mosiac genes. When duplicative HGT is followed by differential gene conversion among descendant lineages, as under the DH-DC model, phylogenetic analysis is further complicated. To explore the effects of DH-DC on phylogeny reconstruction, we analyzed two sets of sequences: (1) an augmented set of plant mitochondrial atp1 sequences for which we recently published evidence of DH-DC; and (2) a set of simulated sequences for which we varied the extent of chimerism, the number of chimeric genes and nucleotide substitution rates. We show that the phylogenetic behavior of evolutionarily chimeric genes is highly volatile and depends on both the degree of chimerism and the number of differentially chimeric genes present in the analysis. Furthermore, we show that the presence of chimeric genes in gene trees can spuriously affect the phylogenetic position of purely native sequences, especially by attracting these sequences toward basal positions in trees. We propose the term "HGT turbulence" to describe these complex effects of evolutionarily chimeric genes on phylogenetic results.

Figure 1.

Three types of mosaic mitochondrial atp1 genes in Ternstroemia (adapted from ref. 12). The multi-colored boxes represent atp1 genes of the three subclades within Ternstroemia. Black vertical lines represent the 38 nucleotide positions inferred12 to have differed between donor and recipient atp1 genes at the time of atp1 transfer from Vaccinium to a common ancestor of Ternstroemia. Lines at the top of the boxes and red shading indicate sites and regions, respectively, of putatively foreign, Vaccinium ancestry, while bottom lines and blue shading represent native sites and regions. White lines centered within the boxes represent the only two sites that otherwise differ within the Ternstroemia clade. “T-ips” refers to the Ternstroemia subclade containing T. impressa, T. peduncularis and T. stahlii) and “T-glj” to the subclade containing T. gymnanthera, T. longipes and T. japonica (see also Fig. 2A).

Figure 2. Phylogenetic analysis of mosaic mitochondrial atp1 genes. (A) Chronogram showing organismal relationships and divergence times of relevant taxa belonging to the Ericales. As described in reference , the chronogram was constructed by the BEAST program using a Eurya reference fossil calibration of 86 Myr ago. (B-F) Maximum likelihood phylogenies of mitochondrial atp1 genes from the taxa shown in (A), with these analyses varying as to which members of Ternstroemia (shown in red), whose atp1 gene is differentially mosaic, were included. RAxML version 7.0.4 was used to construct all phylogenies with a GTR+Γ+I substitution model. A total of 1000 bootstrap iterations were performed, with all bootstrap values ≥ 50% shown on the trees. Phylogenies were rooted using Fouquieria, Marcgravia and Pentamerista as unshown outgroups (hence the stub branch at the base of each gene tree).

Figure 3. Variable phylogenetic placement of chimeric genes demonstrated by simulations. Artificial sequences were simulated as described in the text. Chimeric sequences were generated by combining the 5′ and 3′ portions of sequences 1 and 9, respectively (both circled in red), with different length ratios (10:90, 30:70 or 50:50) of the two parental sequences. One thousand tree-building iterations were performed. The tree shown in each panel is based (for computational ease) on the concatenated sequences of the first 100 iterations, while the bootstrap support values are from all 1000 trees. All bootstrap values are ≥ 95% except for those shown.

Figure 4. Chimeric sequences increasingly disrupt native-sequence topologies as divergence increases. (A) The same tree as shown in Figure 3D. (B–D) Maximum likelihood analysis of the same simulated sequences, but with increasing branch-length scales across the set of sequences: (B) 2 × the scale in (A); (C) 5 × ; and (D) 10 × . One thousand tree-building iterations were performed. The tree shown in each panel is based (for computational ease) on the concatenated sequences of the first 100 iterations, while the bootstrap support values are from all 1,000 trees. All bootstrap values are ≥ 95% except for those shown.