The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding of plant NLR structure and function is limited to the evolutionarily young flowering plant clade. Here, we describe an extended spectrum of NLR diversity across divergent plant lineages and demonstrate the structural and functional similarities of N-terminal domains that trigger immune responses. We show that the broadly distributed coiled-coil (CC) and toll/interleukin-1 receptor (TIR) domain families of non-flowering plants retain immune-related functions through trans-lineage activation of cell death in the angiosperm Nicotiana benthamiana. We further examined a CC subfamily specific to non-flowering lineages and uncovered an essential N-terminal MAEPL motif that is functionally comparable to motifs in resistosome-forming CC-NLRs. Consistent with a conserved role in immunity, the ectopic activation of CCMAEPL in the non-flowering liverwort Marchantia polymorpha led to profound growth inhibition, defense gene activation, and signatures of cell death. Moreover, comparative transcriptomic analyses of CCMAEPL activity delineated a common CC-mediated immune program shared across evolutionarily divergent non-flowering and flowering plants. Collectively, our findings highlight the ancestral nature of NLR-mediated immunity during plant evolution that dates its origin to at least ∼500 million years ago.

Transcriptome data from silica-preserved leaf tissue reveal gene flow patterns in a Caribbean bromeliad

BACKGROUND AND AIMS

Transcriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept in special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from 6-month-old, field-collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genus Pitcairnia (Bromeliaceae) in the Dominican Republic and infer barriers to gene flow.

METHODS

We extracted RNA from silica-dried leaf tissue from 19 Pitcairnia individuals collected across the Dominican Republic. We used a series of macro- and micro-evolutionary approaches to examine the relationships and patterns of gene flow among individuals.

KEY RESULTS

We produced high-quality transcriptomes from silica-dried material and demonstrated that evolutionary relationships on the island match geography more closely than species delimitation methods. A population genetic examination indicates that a combination of ecological and geographical features presents barriers to gene flow in Pitcairnia.

CONCLUSIONS

Transcriptomes can be obtained from silica-preserved tissue. The genetic diversity among Pitcairnia populations does not warrant classification as separate species, but the Dominican Republic contains several barriers to gene flow, notably the Cordillera Central mountain range.

Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants

Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.

Cuticle chemistry drives the development of diffraction gratings on the surface of Hibiscus trionum petals

Plants combine both chemical and structural means to appear colorful. We now have an extensive understanding of the metabolic pathways used by flowering plants to synthesize pigments, but the mechanisms remain obscure whereby cells produce microscopic structures sufficiently regular to interfere with light and create an optical effect. Here, we combine transgenic approaches in a novel model system, Hibiscus trionum, with chemical analyses of the cuticle, both in transgenic lines and in different species of Hibiscus, to investigate the formation of a semi-ordered diffraction grating on the petal surface. We show that regulating both cuticle production and epidermal cell growth is insufficient to determine the type of cuticular pattern produced. Instead, the chemical composition of the cuticle plays a crucial role in restricting the formation of diffraction gratings to the pigmented region of the petal. This suggests that buckling, driven by spatiotemporal regulation of cuticle chemistry, could pattern the petal surface at the nanoscale.

Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway

Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix–loop–helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.

Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets

Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.

Intragenic Conflict in Phylogenomic Data Sets

Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

PREMISE

Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.

METHODS

We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods, and is summarized in a consensus framework.

RESULTS

Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole-genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications.

CONCLUSIONS

We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants

Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a data set in order to resolve recalcitrant relationships and, importantly, identify what the data set is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant data set. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific data set to address deep phylogenetic relationships while also identifying the inferential boundaries of the data set. [Angiosperms; coalescent; gene-tree conflict; genomics; phylogenetics; phylogenomics.]

Characterizing gene tree conflict in plastome-inferred phylogenies

Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

Grow Where You Thrive, or Where Only You Can Survive? An Analysis of Performance Curve Evolution in a Clade with Diverse Habitat Affinities

Performance curves are valuable tools for quantifying the fundamental niches of organisms and testing hypotheses about evolution, life-history trade-offs, and the drivers of variation in species' distribution patterns. Here, we present a novel Bayesian method for characterizing performance curves that facilitates comparisons among species. We then use this model to quantify and compare the hydrological performance curves of 14 different taxa in the genus Lasthenia, an ecologically diverse clade of plants that collectively occupy a variety of habitats with unique hydrological features, including seasonally flooded wetlands called vernal pools. We conducted a growth chamber experiment to measure each taxon's fitness across five hydrological treatments that ranged from severe drought to extended flooding, and we identified differences in hydrological performance curves that explain their associations with vernal pool and terrestrial habitats. Our analysis revealed that the distribution of vernal pool taxa in the field does not reflect their optimal hydrological environments: all taxa, regardless of habitat affinity, have highest fitness under similar hydrological conditions of saturated soil without submergence. We also found that a taxon's relative position across flood gradients within vernal pools is best predicted by the height of its performance curve. These results demonstrate the utility of our approach for generating insights into when and how performance curves evolve among taxa as they diversify into distinct environments. To facilitate its use, the modeling framework has been developed into an R package.

Characterizing gene tree conflict in plastome-inferred phylogenies

Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.

Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

Recent studies have demonstrated that conflict is common among gene trees in phylogenomic studies, and that less than one percent of genes may ultimately drive species tree inference in supermatrix analyses. Herein, we examined two data sets where supermatrix and coalescent-based species trees conflict. We identified two highly influential "outlier" genes in each data set. When removed from each data set, the inferred supermatrix trees matched the topologies obtained from coalescent analyses. We also demonstrate that, while the outlier genes in the vertebrate data set have been shown in a previous study to be the result of errors in orthology detection, the outlier genes from a plant data set did not exhibit any obvious systematic error, and therefore, may be the result of some biological process yet to be determined. While topological comparisons among a small set of alternate topologies can be helpful in discovering outlier genes, they can be limited in several ways, such as assuming all genes share the same topology. Coalescent species tree methods relax this assumption but do not explicitly facilitate the examination of specific edges. Coalescent methods often also assume that conflict is the result of incomplete lineage sorting. Herein, we explored a framework that allows for quickly examining alternative edges and support for large phylogenomic data sets that does not assume a single topology for all genes. For both data sets, these analyses provided detailed results confirming the support for coalescent-based topologies. This framework suggests that we can improve our understanding of the underlying signal in phylogenomic data sets by asking more targeted edge-based questions.

Phyx: phylogenetic tools for unix

Summary

The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx: a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.

Availability and Implementation

phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx

Supplementary information

Supplementary data are available at Bioinformatics online.

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

PREMISE OF THE STUDY

Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.

METHODS

We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.

KEY RESULTS

QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.

CONCLUSIONS

Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

PREMISE OF THE STUDY

The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales.

METHODS

We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in such a large data set, we developed an approach for clustering gene families that allowed us to analyze >300 transcriptomes and genomes. We then inferred the species relationships using multiple methods and performed gene-tree conflict analyses.

KEY RESULTS

Our phylogenetic analyses resolved many clades with strong support, but also showed significant gene-tree discordance. This discordance is not only a common feature of phylogenomic studies, but also represents an opportunity to understand processes that have structured phylogenies. We also found taxon sampling influences species-tree inference, highlighting the importance of more focused studies with additional taxon sampling.

CONCLUSIONS

Transcriptomes are useful both for species-tree inference and for uncovering evolutionary complexity within lineages. Through analyses of gene-tree conflict and multiple methods of species-tree inference, we demonstrate that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales. We also discuss a method for overcoming computational challenges associated with homolog clustering in large data sets.

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

PREMISE OF THE STUDY

Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.

METHODS

We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.

KEY RESULTS

QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.

CONCLUSIONS

Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.

Disparity, diversity, and duplications in the Caryophyllales

The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic occupancy. While we find that many diversification shifts occur after WGDs, it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution.

Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. We assembled a data set of transcriptomes and genomes from 168 species in Caryophyllales, of which 43 transcriptomes were newly generated for this study, representing one of the most densely sampled genomic-scale data sets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped the phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy. We identified 26 ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy. Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macroevolutionary implications compared with autopolyploidy.

Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

PREMISE OF STUDY

The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved.

METHODS

To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare West African liana family Dioncophyllaceae. We used a variety of methods to infer the species tree, examine gene tree conflict, and infer paleopolyploidy events.

KEY RESULTS

Phylogenomic analyses supported the monophyly of the carnivorous Caryophyllales, with a crown age of 68-83 million years. In contrast to previous analyses, we recovered the remaining noncore Caryophyllales as nonmonophyletic, although the node supporting this relationship contained a significant amount of gene tree discordance. We present evidence that the clade contains at least seven independent paleopolyploidy events, previously unresolved nodes from the literature have high levels of gene tree conflict, and taxon sampling influences topology even in a phylogenomic data set, regardless of the use of coalescent or supermatrix methods.

CONCLUSIONS

Our data demonstrate the importance of carefully considering gene tree conflict and taxon sampling in phylogenomic analyses. Moreover, they provide a remarkable example of the propensity for paleopolyploidy in angiosperms, with at least seven such events in a clade of less than 2500 species.

An efficient field and laboratory workflow for plant phylotranscriptomic projects

PREMISE OF THE STUDY

We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation.

METHODS AND RESULTS

A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms. These included difficult mucilaginous tissues such as those of Cactaceae and Droseraceae.

CONCLUSIONS

Our workflow is not only cost effective (ca. $270 per sample, as of August 2016, from tissue to reads) and time efficient (less than 50 h for 10-12 samples including all laboratory work and sample curation), but also has proven robust for extraction of difficult samples such as tissues containing high levels of secondary compounds.

Increased daily movement associates with reduced mortality among COPD patients having systemic inflammation

BACKGROUND

Emerging research demonstrates an interrelationship between systemic inflammation, physical activity and premature all-cause mortality among chronic obstructive pulmonary disease (COPD) patients. Less common in this literature is the use of objective measures of physical activity and representative samples of COPD patients.

OBJECTIVE

To examine the association between objectively measured physical activity and all-cause mortality among a national sample of COPD patients, with stratification by inflammatory status.

METHODS

Data from the 2003 to 2006 NHANES were employed, with follow-up through 2011. Physical activity was objectively measured via accelerometry; COPD was assessed via physician-diagnosis; and inflammation was assessed via C-reactive protein (CRP) levels from a blood sample.

RESULTS

Analysis included 385 adults (20+ years) with COPD. The median follow-up period was 78 months (IQR = 64-90), with 82 COPD patients dying during this period. After adjustment, physical activity was not associated with all-cause mortality among the entire sample (HR = 0.80; 95% CI: 0.61-1.05) or those with no systemic inflammation (HR = 0.89; 95% CI: 0.63-1.24). However, for every 60 min increase in physical activity per day, COPD patients with elevated CRP had a 31% reduced risk of all-cause mortality (HR = 0.69; 95% CI: 0.51-0.93).

CONCLUSION

Physical activity may help to promote survival among COPD patients, particularly those with elevated inflammation.

Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae)

PREMISE OF THE STUDY

Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae.

METHODS

We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession.

KEY RESULTS

The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions.

CONCLUSIONS

Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.

Spalt expression and the development of melanic color patterns in pierid butterflies

Background

Little is currently known about wing pattern development in the butterfly family Pieridae, which consists mostly of black melanized elements on white or yellow/orange backgrounds. A single transcription factor, Spalt (Sal), has been previously associated with the development of some pattern elements in Pieris rapae, but it is unclear to what extent Sal is associated with patterns in other pierid species.

Results

We use immunohistochemistry targeting Sal proteins across several pierids and show that Sal is associated with dense patches of melanization across species but is not associated with vein-melanization or diffuse melanization on the wing. In addition, Sal is expressed along cross-veins and wing compartment midlines that do not develop melanization. Male and female P. rapae spots are sexually dimorphic in size and this dimorphism is also present in the domains of Sal expression. Finally, by disrupting cells positioned in the center of the anterior black spots of P. rapae, before and during the time of Sal expression, spot size was reduced.

Conclusions

Our results suggest, but do not conclusively show, that pierid spots may develop in a manner similar to that of nymphalid eyespots, that is, containing a group of signaling cells at the center of the pattern responsible for the differentiation of the complete spot, and that spots and eyespots share at least one signal-response gene in common, the transcription factor Sal. We propose that focal differentiation and focal signaling mechanisms evolved prior to the split of the nymphalid and pierid lineages.

Stress, social support and housing are related to health status among HIV-positive persons in the deep south of the United States

Self-report health status measures are consistently associated with medical outcomes and are cost-effective. Studies using such measures find that those who live in rural areas or have limited access to support experience poorer health status and poorer outcomes. A survey addressing these issues was administered to 401 HIV-positive persons throughout Alabama. Hierarchical regression models examined the relation of housing stability, stress, substance use and other variables to physical (PCS) and mental (MCS) health status. The sample was 34% female and 66% African-American. Most were receiving antiretroviral medications, and nearly 20% were in unstable housing. Age showed a significant negative relationship to health status. CD4 cell count (p < 0.01) was positively associated with PCS; perceived general stress (p < 0.02) and housing stability (p < 0.04) were negatively associated. The model accounted for 14% of the variance in PCS (p < 0.001). For MCS, general stress (p < 0.001) was negatively associated and substance use tended towards a negative association (p < 0.075). Social support (p < 0.02) was positively associated with MCS. The model accounted for nearly 31% of the MCS variance (p < 0.001). Health status among HIV-positive persons may be improved by assessing and addressing social issues such as social isolation, life stressors and housing.

Pulmonary sensory and reflex responses in the mouse

Mouse model research is proliferating because of its readiness for genetic manipulation. Little is known about pulmonary vagal afferents in mice, however. The purpose of this study was to determine whether their pulmonary afferents are similar to those in large animals. Single-unit activity was recorded in the cervical vagus nerve of anesthetized, open-chest, and mechanically ventilated mice. We evaluated airway sensory activity in 153 single units; 141 were mechanosensitive, with 134 inflation receptors and 7 deflation receptors. The remaining 12 receptors were chemosensitive and mechanically insensitive, showing low basal firing frequency and behaving like C-fiber or high-threshold Adelta-receptors. In separate studies, phrenic activity was recorded as an index of respiratory drive to assess pulmonary reflexes. Lung inflation produced a typical Hering-Breuer reflex, and intravenous injection of phenylbiguanide produced the typical chemoreflex resulting in apnea, bradycardia, and hypotension. These reflexes were blocked by bilateral vagotomy. We conclude that mice possess a similar set of airway sensors and pulmonary reflexes as typically found in larger animals.

Water and solute mass balance of five small, relatively undisturbed watersheds in the U.S

Geochemical mass balances were computed for water years 1992-1997 (October 1991 through September 1997) for the five watersheds of the U.S. Geological Survey Water, Energy, and Biogeochemical Budgets (WEBB) Program to determine the primary regional controls on yields of the major dissolved inorganic solutes. The sites, which vary markedly with respect to climate, geology, physiography, and ecology, are: Allequash Creek, Wisconsin (low-relief, humid continental forest); Andrews Creek, Colorado (cold alpine, taiga/tundra, and subalpine boreal forest); Río Icacos, Puerto Rico (lower montane, wet tropical forest); Panola Mountain, Georgia (humid subtropical piedmont forest); and Sleepers River, Vermont (humid northern hardwood forest). Streamwater output fluxes were determined by constructing empirical multivariate concentration models including discharge and seasonal components. Input fluxes were computed from weekly wet-only or bulk precipitation sampling. Despite uncertainties in input fluxes arising from poorly defined elevation gradients, lack of dry-deposition and occult-deposition measurements, and uncertain sea-salt contributions, the following was concluded: (1) for solutes derived primarily from rock weathering (Ca, Mg, Na, K, and H(4)SiO(4)), net fluxes (outputs in streamflow minus inputs in deposition) varied by two orders of magnitude, which is attributed to a large gradient in rock weathering rates controlled by climate and geologic parent material; (2) the net flux of atmospherically derived solutes (NH(4), NO(3), SO(4), and Cl) was similar among sites, with SO(4) being the most variable and NH(4) and NO(3) generally retained (except for NO(3) at Andrews); and (3) relations among monthly solute fluxes and differences among solute concentration model parameters yielded additional insights into comparative biogeochemical processes at the sites.

Bradykinin stimulates respiratory drive by activating pulmonary sympathetic afferents in the rabbit

We recently identified a vagally mediated excitatory lung reflex by injecting hypertonic saline into the lung parenchyma (Yu J, Zhang JF, and Fletcher EC. J Appl Physiol 85: 1485-1492, 1998). This reflex increased amplitude and burst rate of phrenic (inspiratory) nerve activity and suppressed external oblique abdominal (expiratory) muscle activity. In the present study, we tested the hypothesis that bradykinin may activate extravagal pathways to stimulate breathing by assessing its reflex effects on respiratory drive. Bradykinin (1 microg/kg in 0.1 ml) was injected into the lung parenchyma of anesthetized, open-chest and artificially ventilated rabbits. In most cases, bradykinin increased phrenic amplitude, phrenic burst rate, and expiratory muscle activity. However, a variety of breathing patterns resulted, ranging from hyperpnea and tachypnea to rapid shallow breathing and apnea. Bradykinin acts like hypertonic saline in producing hyperpnea and tachypnea, yet the two agents clearly differ. Bradykinin produced a higher ratio of phrenic amplitude to inspiratory time and had longer latency than hypertonic saline. Although attenuated, bradykinin-induced respiratory responses persisted after vagotomy. We conclude that bradykinin activates multiple afferent pathways in the lung; portions of its respiratory reflexes are extravagal and arise from sympathetic afferents.

Effects of body mass on nicotine-induced thermogenesis and catecholamine release in male smokers

The aims of this study were to examine the effects of nicotine on resting energy expenditure (REE) and plasma catecholamine release following ad libitum smoking in fasted, middle-aged males; and, to determine if the acute responses in REE and catecholamine release to smoking differ between normal weight (< or = 25 kg/m(2)) and overweight (> 25 kg/m(2)) smoker groups. REE was measured by indirect calorimetry in 32 fasted male smokers prior to, and 30 minutes after, consuming either two 0.16 mg nicotine (low yield) or two 1.74 mg nicotine (high yield) cigarettes. Plasma nicotine and norepinephrine levels were simultaneously measured. There was no thermic effect of nicotine or catecholamine response after smoking low yield cigarettes in both groups, nor after smoking high yield cigarettes in the overweight group. In contrast, REE increased 7.2%, which was accompanied by an increase in plasma norepinephrine release, after smoking high yield cigarettes in the normal weight group. Controlling plasma nicotine level ablated these increases. In conclusion, body mass interacts with the thermic effect of nicotine and neuroendocrine function in male smokers. Smoking-induced increase in the plasma nicotine level accounts for the observed responses, which are blunted in overweight smokers. This finding may have implications for potential weight gain following smoking cessation by normal weight individuals, related to lost smoking-induced thermogenesis.

Effects of once-daily angiotensin-converting enzyme inhibition and calcium channel blockade-based antihypertensive treatment regimens on left ventricular hypertrophy and diastolic filling in hypertension: the prospective randomized enalapril study evaluating regression of ventricular enlargement (preserve) trial

BACKGROUND

The Prospective Randomized Enalapril Study Evaluating Regression of Ventricular Enlargement (PRESERVE) study was designed to test whether enalapril achieves greater left ventricular (LV) mass reduction than does a nifedipine gastrointestinal treatment system by a prognostically meaningful degree on a population basis (10 g/m(2)).

METHODS AND RESULTS

An ethnically diverse population of 303 men and women with essential hypertension and increased LV mass at screening echocardiography were enrolled at clinical centers on 4 continents and studied by echocardiography at baseline and after 6- and 12-month randomized therapy. Clinical examination and blinded echocardiogram readings 48 weeks after study entry in an intention-to-treat analysis of 113 enalapril-treated and 122 nifedipine-treated patients revealed similar reductions in systolic/diastolic pressure (-22/12 versus -21/13 mm Hg) and LV mass index (-15 versus -17g/m(2), both P>0.20). No significant between-treatment difference was detected in population subsets defined by monotherapy treatment, sex, age, race, or severity of baseline hypertrophy. Similarly, there was no between-treatment difference in change in velocities of early diastolic or atrial phase transmitral blood flow. More enalapril-treated than nifedipine-treated patients required supplemental treatment with hydrochlorothiazide (59% versus 34%, P<0.001) but not atenolol (27% versus 22%, NS).

CONCLUSIONS

Once-daily antihypertensive treatment with enalapril or long-acting nifedipine, plus adjunctive hydrochlorothiazide and atenolol when needed to control blood pressure, both had moderately beneficial and statistically indistinguishable effects on regression of LV hypertrophy.

The effect of smoking on energy expenditure and plasma catecholamine and nicotine levels during light physical activity

A number of studies have found that cigarette smoking causes an acute increase in resting energy expenditure, but the effect on energy expenditure during light physical activity is less clear. Since both smoking and activity have been shown to increase plasma catecholamines, these could produce additive effects on energy expenditure when smoking during light physical activity. In this study, the impact of cigarette smoking on energy expenditure, cardiovascular function, plasma nicotine and plasma catecholamine levels was determined in adult male subjects at rest and while engaged in light physical activity. Smoking at rest resulted in a 3.6% increase in energy expenditure above the resting baseline; whereas the increase in energy expenditure caused by smoking during light physical activity (compared with the light physical activity baseline) was 6.3%. This increase during light physical activity was significantly greater than the increase observed at rest (p < 0.025). As expected, plasma nicotine increased with smoking during both rest and light physical activity. An increase in plasma nicotine was associated with smoking during light physical activity. When this increase was adjusted as a covariate, the difference in smoking-related energy expenditure between light physical activity and rest disappeared, suggesting nicotine accounts for the effect. Plasma epinephrine and norepinephrine levels increased with smoking and showed a significantly greater increase during light physical activity compared to rest. Cigarette smoking caused a significantly greater increase in heart rate during light physical activity than it did while at rest, but there was no significant effect of smoking on mean blood pressure. It was concluded that there is enhanced energy expenditure associated with cigarette smoking during light physical activity when compared with smoking at rest which could be due in part to smoking-induced increases in circulating plasma catecholamines and perhaps nicotine.

Inhibition of seedling survival under Rhododendron maximum (Ericaceae): could allelopathy be a cause?

In the southern Appalachian mountains a subcanopy species, Rhododendron maximum, inhibits the establishment and survival of canopy tree seedlings. One of the mechanisms by which seedlings could be inhibited is an allelopathic effect of decomposing litter or leachate from the canopy of R. maximum (R.m.) on seed germination, root elongation, or mycorrhizal colonization. The potential for allelopathy by R.m. was tested with two bioassay species (lettuce and cress), with seeds from four native tree species, and with three ectomycorrhizal fungi. Inhibitory influences of throughfall, fresh litter, and decomposed litter (organic layer) from forest with R.m. (+R.m. sites) were compared to similar extractions made from forest without R.m. (-R.m. sites). Throughfall and leachates of the organic layer from both +R.m. and -R.m. sites stimulated germination of the bioassay species above that of the distilled water control, to a similar extent. There was an inhibitory effect of leachates of litter from +R.m. sites on seed germination and root elongation rate of both bioassay species compared with that of litter from -R.m. sites. Native tree seed stratified in forest floor material from both forest types had a slightly higher seed germination rate compared with the control. A 2-yr study of seed germination and seedling mortality of two tree species, Quercus rubra and Prunus serotina, in field plots showed no significant influence of litter or organic layer from either forest type. Incorporating R.m. leaf material into the growth medium in vitro depressed growth of one ectomycorrhizal species but did not affect two other species. Leaf material from other deciduous tree species depressed ectomycorrhizal growth to a similar or greater extent as leaf material from R.m. In conclusion, R.m. litter can have an allelopathic effect on seed germination and root elongation of bioassay species as well as some ectomycorrhizal species. However, this allelopathic affect is not manifest in field sites and is not likely to be an important cause for the inhibition of seedling survival within thickets of R.m.