RNA-based processes traceable to the Last Universal Common Ancestor.

<p>Universal Rfam families that show evidence of vertical inheritance (Table S1 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752.s008" target="_blank">Text S1</a>) are all associated with the processes of translation (rRNAs, tRNAs, RNase P) and protein export (SRP RNA). A previous study examining the antiquity of protein coding genes <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Harris1" target="_blank">[21]</a> identified only 37 universally distributed proteins which show evidence of vertical inheritance. The majority of these vertically inherited proteins are associated with translation and protein export; numbers of such proteins associated with each of the depicted processes is given in grey (original data are from Harris <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Harris1" target="_blank">[21]</a>). The proteins associated with RNase P are not universally conserved, with archaeal and eukaryotic RNase P proteins being unrelated to their bacterial counterparts <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Hartmann1" target="_blank">[72]</a>. While tRNA synthetases are universal, they have undergone ancient horizontal gene transfer events <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Fournier1" target="_blank">[73]</a>, which complicates establishing the timing of their origin.</p

Reconstruction of broadly distributed RNA repertoires for each domain, plus interdomain RNA families.

<p>Colored bars at far right indicate normalized taxonomic abundance of each Rfam for major taxonomic groupings within each domain. Horizontal traces (see text, Table S1 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752.s008" target="_blank">Text S1</a>) for interdomain families, are depicted as follows: general transfer patterns are given by dashed arrows; proposed HGT patterns for individual families are depicted by number (inset). For Rfam families present in more than one domain (far left and inset), bars indicate normalized taxonomic abundance by domain (color scheme at bottom left). Asterisks indicate additional broadly-distributed bacterial candidates identified using GEBA tree topology <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Wu1" target="_blank">[56]</a> (see text). Note that the Rfam rRNA families in Rfam 10.0 are based on conserved subsequences, and are not as comprehensive as other resources (see main text) and are included here for consistency. The universally-distributed rRNAs are the small subunit (16/18S) rRNA, large subunit (23/28S) rRNA and 5S rRNA (see Table S1 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752.s008" target="_blank">Text S1</a>). The 5.8S rRNA of eukaryotes is known to be homologous to the 5′ end of bacterial and archaeal 23S rRNA <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Jacq1" target="_blank">[74]</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Lafontaine1" target="_blank">[75]</a>, so its inclusion as a eukaryote-specific family in Rfam is in this respect artefactual.</p

Venn diagram of RNA family distribution.

<p>Taxonomic information attached to EMBL-derived Rfam annotations reveals that the majority (99%) of RNA families are domain-specific, with only seven RNA families universally conserved (across the three domains of life plus viruses; Table S1 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752.s008" target="_blank">Text S1</a>). Numbers within dashed circles indicate viral RNA families.</p

Rfam-based functional classification of RNA families.

<p>The tree depicts classification of the higher level data structures within Rfam, and is not a phylogeny. Numbers of sequences and families in Rfam 10 that fall into each functional classification are shown as bar charts. Domain-level taxonomic distribution for each functional category is shown by black (present) and white (absent) boxes, right. The grey box indicates that H/ACA family RNAs are known from archaea <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Tang1" target="_blank">[47]</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002752#pcbi.1002752-Muller1" target="_blank">[48]</a>, but are not in Rfam 10.</p

Potential energies and number of hydrogen bonds between different components of simulated p19 systems.

<p>Systems comprise wild-type and all <i>permissible</i> mutations of p19 alone or in complex with the siRNA. (A) Average potential energies (<i>E</i>_pot) of the interaction between the two protein subunits making up the p19 dimer (prot:prot). (B) Average potential energies (<i>E</i>_pot) of the interaction between the protein dimer and the RNA (prot;RNA). (C) Average potential energies (<i>E</i>_pot) of the complete protein/RNA complex (prot+RNA). The electrostatic and van der Waals contributions are shown separately alongside the total potential energy, as indicated above the graphs. (D) Average number of hydrogen bonds during the entire simulation between the two protein subunits making up the p19 dimer. (E) Average number of hydrogen bonds during the entire simulation between the protein dimer and the RNA. Solid bars correspond to simulations with RNA included, and empty bars to simulations without RNA present. Averages were calculated from the first 50 ns of simulation, after 10 ns equilibration, so that the averages calculated from the simulations of p19 with RNA bound (200 ns) are comparable to those of the simulations without RNA bound (50 ns). The error bars correspond to the standard deviation in all cases.</p

Alignment of amino acid sequences of p19 from 11 different tombusvirus species.

<p>The single-letter residue codes are coloured according to the nature of the amino acid side chain: (red) negatively-charged (D,E); (dark blue) aromatic (F,Y); (blue) positively-charged (K, R); (cyan) large polar amide-containing (Q,N); (orange) small polar hydroxyl-containing (S,T); (yellow) sulfur-containing (C,M); (grey) small aliphatic (A,G); (green) medium aliphatic (I,V,L); (purple-blue) imidazole (H); (violet) indole (W); (pink-brown) cyclised secondary amine (P). Sites identified as being under positive selection by all four analyses are highlighted in pale green. The secondary structure elements are indicated above the sequences: (barrels) α-helices; (arrows) β-strands. Viral species and NCBI accession numbers are as follows: CIR (Carnation italian ringspot virus, NC003500), TBS (Tomato bushy stunt virus, NC001554), AMC (Artichoke mottle crinkle virus, NC001339), LNV (Lisianthus necrosis virus, NC007983), PLV (Pear latent virus, NC004723), PNV (Pelagornium necrotic streak virus, NC005285), CNV (Cucumber necrosis virus, NC001469), GAL (Grapevine algerian latent virus, AY830918), CRV (Cymbidium ringspot virus, NC003532), CBL (Cucumber bulgarian latent virus, NC004725), MNV (Maize necrotic streak virus, NC007729).</p

Residues identified as being under positive selection.

<p>See text for details of each of the four analyses. Light green indicates residues that only some of the analyses identified as being under positive selection. Dark green indicates residues found to be under positive selection in all four analyses. Note that some residues predicted to be under positive selection by HyPhy FEL2 (36, 43, 67, 107, 145) actually show no variation (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147619#pone.0147619.g002" target="_blank">Fig 2</a>).</p

Human-Assisted Spread of a Maladaptive Behavior in a Critically Endangered Bird

<div><p>Conservation management often focuses on counteracting the adverse effects of human activities on threatened populations. However, conservation measures may unintentionally relax selection by allowing the ‘survival of the not-so-fit’, increasing the risk of fixation of maladaptive traits. Here, we report such a case in the critically-endangered Chatham Island black robin (<i>Petroica traversi</i>) which, in 1980, was reduced to a single breeding pair. Following this bottleneck, some females were observed to lay eggs on the rims of their nests. Rim eggs left in place always failed to hatch. To expedite population recovery, rim eggs were repositioned inside nests, yielding viable hatchlings. Repositioning resulted in rapid growth of the black robin population, but by 1989 over 50% of all females were laying rim eggs. We used an exceptional, species-wide pedigree to consider both recessive and dominant models of inheritance over all plausible founder genotype combinations at a biallelic and possibly sex-linked locus. The pattern of rim laying is best fitted as an autosomal dominant Mendelian trait. Using a phenotype permutation test we could also reject the null hypothesis of non-heritability for this trait in favour of our best-fitting model of heritability. Data collected after intervention ceased shows that the frequency of rim laying has strongly declined, and that this trait is maladaptive. This episode yields an important lesson for conservation biology: fixation of maladaptive traits could render small threatened populations completely dependent on humans for reproduction, irreversibly compromising the long term viability of populations humanity seeks to conserve.</p></div

Fitness consequences of rim laying behavior.

<p>Data from 2007–11 (during which rim eggs were not repositioned) shows that females that laid rim eggs had a significantly reduced clutch size (i.e. number of eggs laid inside nests that were incubated), and decreased hatching and breeding success compared to normal-laying females. We obtain p-values from likelihood ratio tests with generalized linear mixed models of data with sample size <i>n</i>.</p

Inferred trajectories of allele A under the simple dominant model (model No. 4 in Table 2) between 1980 and 1989.

<p>The mean trajectory is shown by black line and the 50% and 95% confidence sets of the trajectories are shown in decreasing shades of grey. Twice the population size (total number of alleles) is shown by the dashed and dotted line.</p