Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study

<p>Abstract</p> <p>Background</p> <p>In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis.</p> <p>Results</p> <p>Our trees show broad concordance with previous morphological hypotheses of ditrysian phylogeny, although most relationships among superfamilies are weakly supported. There are also notable surprises, such as a consistently closer relationship of Pyraloidea than of butterflies to most Macrolepidoptera. Monophyly is significantly rejected by one or more character sets for the putative clades Macrolepidoptera as currently defined (<it>P </it>< 0.05) and Macrolepidoptera excluding Noctuoidea and Bombycoidea sensu lato (<it>P </it>≤ 0.005), and nearly so for the superfamily Drepanoidea as currently defined (<it>P </it>< 0.08). Superfamilies are typically recovered or nearly so, but usually without strong support. Relationships within superfamilies and families, however, are often robustly resolved. We provide some of the first strong molecular evidence on deeper splits within Pyraloidea, Tortricoidea, Geometroidea, Noctuoidea and others.</p> <p>Separate analyses of mostly synonymous versus non-synonymous character sets revealed notable differences (though not strong conflict), including a marked influence of compositional heterogeneity on apparent signal in the third codon position (nt3). As available model partitioning methods cannot correct for this variation, we assessed overall phylogeny resolution through separate examination of trees from each character set. Exploration of "tree space" with GARLI, using grid computing, showed that hundreds of searches are typically needed to find the best-feasible phylogeny estimate for these data.</p> <p>Conclusion</p> <p>Our results (a) corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, (b) demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and (c) resolve the majority of family and subfamily relationships within superfamilies as thus far sampled. Much further gene and taxon sampling will be needed, however, to strongly resolve individual deeper nodes.</p

Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?

This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78–85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A “more-genes-only” data set (41 taxa×26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses

Arizona\u27s Vulnerable Populations

Arizona’s vulnerable populations are struggling on a daily basis but usually do so in silence, undetected by traditional radar and rankings, often unaware themselves of their high risk for being pushed or pulled into a full crisis. Ineligible for financial assistance under strict eligibility guidelines, they don’t qualify as poor because vulnerable populations are not yet in full crisis. To be clear, this report is not about the “poor,” at least not in the limited sense of the word. It is about our underemployed wage earners, our single-parent households, our deployed or returning military members, our under-educated and unskilled workforce, our debt-ridden neighbors, our uninsured friends, our family members with no savings for an emergency, much less retirement

Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants

BACKGROUND: Experimental animal data show that protection against severe acute respiratory syndrome coronavirus (SARS-CoV) infection with human monoclonal antibodies (mAbs) is feasible. For an effective immune prophylaxis in humans, broad coverage of different strains of SARS-CoV and control of potential neutralization escape variants will be required. Combinations of virus-neutralizing, noncompeting mAbs may have these properties. METHODS AND FINDINGS: Human mAb CR3014 has been shown to completely prevent lung pathology and abolish pharyngeal shedding of SARS-CoV in infected ferrets. We generated in vitro SARS-CoV variants escaping neutralization by CR3014, which all had a single P462L mutation in the glycoprotein spike (S) of the escape virus. In vitro experiments confirmed that binding of CR3014 to a recombinant S fragment (amino acid residues 318–510) harboring this mutation was abolished. We therefore screened an antibody-phage library derived from blood of a convalescent SARS patient for antibodies complementary to CR3014. A novel mAb, CR3022, was identified that neutralized CR3014 escape viruses, did not compete with CR3014 for binding to recombinant S1 fragments, and bound to S1 fragments derived from the civet cat SARS-CoV-like strain SZ3. No escape variants could be generated with CR3022. The mixture of both mAbs showed neutralization of SARS-CoV in a synergistic fashion by recognizing different epitopes on the receptor-binding domain. Dose reduction indices of 4.5 and 20.5 were observed for CR3014 and CR3022, respectively, at 100% neutralization. Because enhancement of SARS-CoV infection by subneutralizing antibody concentrations is of concern, we show here that anti-SARS-CoV antibodies do not convert the abortive infection of primary human macrophages by SARS-CoV into a productive one. CONCLUSIONS: The combination of two noncompeting human mAbs CR3014 and CR3022 potentially controls immune escape and extends the breadth of protection. At the same time, synergy between CR3014 and CR3022 may allow for a lower total antibody dose to be administered for passive immune prophylaxis of SARS-CoV infection

A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

<div><p>Background</p><p>Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.</p><p>Methodology / Principal Findings</p><p>483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity.</p><p>Conclusions / Significance</p><p>Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.</p></div

A further assessment of the effectiveness of the GARLI heuristic bootstrap search by instituting a huge increase in the number of search replicates performed per individual bootstrap pseudoreplicate in an analysis of 505 483-taxon, 19-gene, <i>nt123_degen1</i>, bootstrapped data sets.^*

<p>A further assessment of the effectiveness of the GARLI heuristic bootstrap search by instituting a huge increase in the number of search replicates performed per individual bootstrap pseudoreplicate in an analysis of 505 483-taxon, 19-gene, <i>nt123_degen1</i>, bootstrapped data sets.^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#nt103" target="_blank">*</a>}</p

Previous hypotheses of deep-level relationships in Lepidoptera.

<p>A. Composite working hypothesis based on morphology <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#pone.0058568-Kristensen1" target="_blank">[7]</a>. B. Ditrysian-only relationships (rooted on Tineoidea) inferred from <i>degen1</i> ML analysis of 123 taxa sequenced either for 5 or 26 gene segments, with bootstrap values ≥50% displayed for nodes at the superfamily level and above <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#pone.0058568-Cho1" target="_blank">[6]</a>. C. Lepidopteran relationships (rooted on Micropterigoidea) inferred from ML analysis of 350 taxa, using nucleotides from the first and second codon positions (+ third codon position for EF-1α only) of 8 gene segments, with bootstrap values >50% displayed for nodes at the superfamily level and above <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#pone.0058568-Mutanen1" target="_blank">[5]</a>. Numbers in parentheses after taxon names are numbers of exemplars sampled.</p

Assessing the effectiveness of the GARLI heuristic bootstrap search by varying the number of search replicates performed per individual bootstrap pseudoreplicate in an analysis of 500 483-taxon, 19-gene, <i>nt123</i>, bootstrapped data sets.^*

<p>Assessing the effectiveness of the GARLI heuristic bootstrap search by varying the number of search replicates performed per individual bootstrap pseudoreplicate in an analysis of 500 483-taxon, 19-gene, <i>nt123</i>, bootstrapped data sets.^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#nt102" target="_blank">*</a>}</p

Summary of phylogenetic analyses based on taxon (sub)sampling of Tineoidea.

<p>Summary phylogenetic trees are displayed with corresponding bootstrap percentages for analysis of <i>nt123</i> and <i>nt123_degen1</i> data sets based on different taxon subsamples for Tineoidea. For ease and focus of presentation, only relationships among strongly supported, higher-level groupings are shown (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#pone-0058568-g003" target="_blank">Figure 3</a>). These groupings are: <i>Tine</i>: Tineidae – <i>Eudarcia</i> (20 taxa total); <i>Psych</i>  =  Psychidae (9 taxa total); <i>Eudarcia</i> (currently classified within Tineidae, 1 taxon); <i>Compsoctena</i> (currently classified within Eriocottidae; 1 taxon); <i>NTD</i>: non-tineoid Ditrysia (27 taxa total); and the non-ditrysian outgroup (not shown), which consist of Palaephatidae + Tischeriidae (5 taxa total).</p

Summary of three phylogenetic analyses of 483 taxa and 19 genes.

<p>Bootstrap percentages derived from GARLI analysis of three data sets -- <i>nt123_degen1</i>, <i>nt123, and nt123_partition</i> -- are displayed in that order above internal branches of a condensed, higher-level-only portion of the <i>nt123_degen1</i> ML topology (see numbers in black). Selected nodes are arbitrarily numbered for convenient reference (see numbers in blue). The full <i>nt123_degen1</i> and <i>nt123</i> topologies are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#pone.0058568.s001" target="_blank">Figure S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#pone.0058568.s002" target="_blank">S2</a>, respectively. A bracket indicates that the node displayed was not recovered in the ML analysis of that data set. A dash indicates that the bootstrap value is <50%. The number of exemplars is listed in parentheses after the family or subfamily name. The region of the topology that includes Tineoidea has blue-colored branches, and its favored alternative topology, based on analysis of <i>nt123</i>, is also displayed (see lower boxed area). Throughout this report, we have subsumed all tineoid taxa traditionally identified as Acrolophidae under Tineidae, all tineoid taxa traditionally identified as Arrhenophanidae under Psychidae, and Crinopterygidae under Incurvariidae, following van Nieukerken et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058568#pone.0058568-vanNieukerken1" target="_blank">[1]</a>. <i>BP</i>, bootstrap percentage.</p