Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic - Fig 1

<p><b>Phylogenetic trees based on amino acid sequences for (A) Historic full-length Nef, (B) Historic R2, and (C) Modern R2.</b> Each blue triangle represents a full-length Nef sequence or an R2 subsequence where the most stable R2 structure fell into the dominant cluster; each red circle, into the alternative cluster.</p

Dominant (wildtype) secondary structure for R2 and structural variations corresponding to hypothetical mutants.

<p>The green curves enclose codon triplets. The four rectangle insets show local rearrangements of the RNA secondary structures resulting from four mutations. Mutants are labeled in blue and designated M1M2, M3, M4, and M5M6. Major secondary structural changes caused by mutations are shown inside corresponding squares.</p

Mapping of this work’s major results regarding Nef RNA.

<p>Regions (R1, R2, and R3) in red correspond to locations with significant changes in CAF when comparing Historic and Modern HIV-1 Nef sequences. (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163688#pone.0163688.t002" target="_blank">Table 2</a> for exact coordinates.) The green region (sites 186–200) displays significantly reduced stable G4s. The region in black (sites 476–485) showed high diversity (quantified by the Doubly Differenced Relative Entropy ΔΔ<i>I</i>). The grey segment labeled <b>A</b> (segment 123–190) refers to the region coinciding with R1 identified by Westerhout et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163688#pone.0163688.ref034" target="_blank">34</a>]; the gray label <b>B</b> points to segment 416–446, referred to by Peleg et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163688#pone.0163688.ref011" target="_blank">11</a>]. In Fig 3, the term “Sequence and Structural Variations Increasing” refers to the observed simultaneous changes in the GC composition, CFE, and CAF of Modern R3.</p

Measures of diversity and plasticity for Modern, REBT (random) Modern, and Historic R2 sets.

<p>Measures of diversity and plasticity for Modern, REBT (random) Modern, and Historic R2 sets.</p

Features of the Test and Training Datasets of Nef sequences.

<p>Features of the Test and Training Datasets of Nef sequences.</p

Summary of Nef regions with the most significant change in CAF.

<p>Summary of Nef regions with the most significant change in CAF.</p

Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera

<div><p>Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera <em>Annulohypoxylon</em> and <em>Hypoxylon</em>, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of <em>Annulohypoxylon</em> and <em>Hypoxylon</em>. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many <em>Annulohypoxylon</em> and <em>Hypoxylon</em> species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in <em>Annulohypoxylon</em> and <em>Hypoxylon</em>, however. The URL <a href="http://tinyurl.com/spouge-barcode">http://tinyurl.com/spouge-barcode</a> contains computer programs and other supplementary material relevant to this article.</p> </div

PCIs for each of four alignment types and two types of sequence distance.

<p>The error bars indicate 95% confidence intervals, as calculated by the Wilson score interval <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054529#pone.0054529-Wilson1" target="_blank">[46]</a>. The four alignment types used (indicated by different colors at the bottom) were multiple sequence alignment (which imposes an implicit pairwise global alignment on each pair of sequences), and global, semi-global, and local pairwise alignment. The two types of sequence distance used for each alignment method were alignment distance and evolutionary distance. (In fact, for a fixed alignment type and dataset, all evolutionary distances produced the same PCI as p-distance.) The green bars give the value of the barcode gap PCI.</p

Morphological characteristics of <i>Annulohypoxylon</i> and <i>Hypoxylon</i> species found in Thailand.

<p>Stromata (a–p); perithecial structure (q–s); ascospore shapes (t–z); perispore dehiscence (v, y, z). (a) <i>Annulohypoxylon stygium</i> SUT058, (b) <i>A. purpureonitens</i> H125, (c) <i>A. nitens</i> H154, (d) <i>A.</i> aff. <i>nitens</i> H099, (e) <i>Annulohypoxylon</i> sp. H213, (f) <i>Annulohypoxylon</i> sp. H255, (g) <i>Hypoxylon monticulosum</i> H188, (h) <i>H</i>. <i>lenormandii</i> H212, (i) <i>H. investiens</i> H259, (j) <i>H. perforatum</i> SUT218, (k) <i>H. duranii</i> H250, (l) <i>H. haematostroma</i> H114, (m) <i>H. crocopeplum</i> H119, (n) <i>H. pelliculosum</i> H227, (o) <i>H. diatrypeoides</i> H226, (p) <i>H. rubiginosum</i> SUT082, (q) <i>H. fendleri</i> SUT061, (r) <i>H. investiens</i> H259, (s) <i>H. haematostroma</i> H114, (t) <i>H. haematostroma</i> SUT293, (u) <i>A. stygium</i> SUT010, (v) <i>H. duranii</i> SUT284, (w) <i>H. investiens</i> SUT041, (x) <i>A. nitens</i> SUT249, (y) <i>H. monticulosum</i> SUT185 and (z) <i>A. nitens</i> SUT025.</p

Current state-of-the art phylogeny and barcode markers for the main protistan lineages.

<p>(A) A recent phylogeny of eukaryotic life, after <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001419#pbio.1001419-Burki1" target="_blank">[56]</a>. (B) Mean V4 18S rDNA genetic similarity between all congeneric species within each lineage, available in GenBank. (C) Currently used group-specific barcodes. The dashed line indicates the incertitude concerning the position of the root in the tree of eukaryotic life. The unresolved relationships between eukaryotic groups are indicated by polytomies. The names of the three multicellular classical “kingdoms” are highlighted.</p