Venom insulins of cone snails diversify rapidly and track prey taxa

A specialized insulin was recently found in the venom of a fish-hunting cone snail, Conus geographus. Here we show that many worm-hunting and snail-hunting cones also express venom insulins, and that this novel gene family has diversified explosively. Cone snails express a highly conserved insulin in their nerve ring; presumably this conventional signaling insulin is finely tuned to the Conus insulin receptor, which also evolves very slowly. By contrast, the venom insulins diverge rapidly, apparently in response to biotic interactions with prey and also possibly the cones’ own predators and competitors. Thus, the inwardly directed signaling insulins appear to experience predominantly purifying sele\ction to target an internal receptor that seldom changes, while the outwardly directed venom insulins frequently experience directional selection to target heterospecific insulin receptors in a changing mix of prey, predators and competitors. Prey insulin receptors may often be constrained in ways that prevent their evolutionary escape from targeted venom insulins, if amino-acid substitutions that result in escape also degrade the receptor’s signaling functions

Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution

The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens is due in part to their ability to rapidly adapt to their changing environment and host. Recombination is the fastest way for bacterial genomes to acquire genetic material, but conflicting results about the extent of recombination in the genus Mycobacterium have been reported. We examined a data set comprising 18 distinct strains from 13 named species for evidence of recombination. Genomic regions common to all strains (accounting for 10% to 22% of the full genomes of all examined species) were aligned and concatenated in the chromosomal order of one mycobacterial reference species. The concatenated sequence was screened for evidence of recombination using a variety of statistical methods, with each proposed event evaluated by comparing maximum-likelihood phylogenies of the recombinant section with the non-recombinant portion of the dataset. Incongruent phylogenies were identified by comparing the site-wise log-likelihoods of each tree using multiple tests. We also used a phylogenomic approach to identify genes that may have been acquired through horizontal transfer from non-mycobacterial sources. The most frequent associated lineages (and potential gene transfer partners) in the Mycobacterium lineage-restricted gene trees are other members of suborder Corynebacterinae, but more-distant partners were identified as well. In two examined cases of potentially frequent and habitat-directed transfer ( M. abscessus to Segniliparus and M. smegmatis to Streptomyces ), observed sequence distances were small and consistent with a hypothesis of transfer, while in a third case ( M. vanbaalenii to Streptomyces ) distances were larger. The analyses described here indicate that whereas evidence of recombination in core regions within the genus is relatively sparse, the acquisition of genes from non-mycobacterial lineages is a significant feature of mycobacterial evolution

Accelerated Evolution of Mitochondrial but Not Nuclear Genomes of Hymenoptera: New Evidence from Crabronid Wasps

Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes

Molecular clock analysis of 50 representative taxa from the four major holometabolous insect orders (global molecular clock lnL = −311050, no clock lnL = −309424).

<p>Numbers correspond to significantly different local clock log likelihood values as follows: ΔlnL = 24 df = 2 (branch 1), ΔlnL = 125 df = 3(branch 2), ΔlnL = 170 df = 5 (branch 3), ΔlnL = 172 df = 6 (branch 4), ΔlnL = 263 df = 8 (branch 5), ΔlnL = 817 df = 9 (branch 6), ΔlnL = 2363 df = 19 (branch 7). Branches are color-coded based on order-level taxonomic affiliations (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032826#pone-0032826-g002" target="_blank">Fig. 2</a>).</p

Phylogenetic trees from analyses of four nuclear genes for representative taxa of the four major holometabolous insect orders.

<p>Sequences for the analysis of wingless, PEPCK, and ArgK were obtained from the NCBI database, the 18S dataset represented a reduced dataset from the analysis of Whiting (2002) that was supplemented with some additional taxa of Apidae from the NCBI database. Hymenopteran taxa are highlighted by yellow branches.</p

Principal components analysis of base frequencies among mitochondrial genome sequences.

<p><b>A</b> Plot of the first principal component against the second principal component (explaining 93% and 5% of the variability, respectively). <b>B</b> Boxplot of PC1 according to insect orders. An ANOVA of the first principal component shows that the base composition in Hymenoptera is significantly biased relative to the other orders (<i>P</i><0.01 for all pairwise comparisons involving Hymenoptera), due to very high AT frequencies. Samples are color-coded based on order-level taxonomic affiliations (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032826#pone-0032826-g002" target="_blank">Fig. 2</a>).</p

Maximum likelihood tree inferred from the mitochondrial 12S and 16SrRNA gene sequences of 50 representative taxa from the four major holometabolous insect orders.

<p>Branches are color-coded based on order-level taxonomic affiliations (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032826#pone-0032826-g002" target="_blank">Fig. 2</a>).</p

Comparative analysis of relative substitution rates in hymenopteran and non-hymenopteran taxa for three mitochondrial and four nuclear phylogenies.

(1)<p>significant at <i>P</i><0.01 after Bonferroni correction.</p>(2)<p>all involving <i>Rhopalomyia</i> or <i>Mayetiola.</i></p>(3)<p><i>Orussus</i> vs. <i>Rhopalomyia</i> and <i>Mayetiola.</i></p>(4)<p><i>Cephus</i> vs. <i>Rhopalomyia</i>, <i>Mayetiola</i>, and <i>Pyrocoelia.</i></p>(5)<p>of those 140 involving <i>Rhopalomyia</i> or <i>Mayetiola.</i></p><p>Given are the numbers of significant (after Bonferroni-correction) and non-significant pairwise comparisons of relative rates, as well as the proportion of significant tests (in percent). Comparisons with >50% significant tests are highlighted in bold. To elucidate the origin of elevated substitution rates in Hymenoptera, the results for the basal symphytan taxa are listed individually for the genes for which sequences of these taxa were available. A hemimetabolous species was used as the outgroup for each analysis.</p

Bayesian phylogeny inferred from the 1^st and 2^nd codon positions of the 13 mitochondrial protein-coding genes.

<p>Because most of the maximum likelihood values differed very little from the posterior probabilities, branches are labeled with a single number for reading clarity. Most are maximum likelihood bootstrap proportions (regular text) but are replaced by posterior probabilities (bold italics) for branches with a difference of more than five between the two values. Branches are color-coded based on order-level taxonomic affiliations.</p