PupDB: a database of pupylated proteins

Background

Figures of phylogenetic trees are widely used to illustrate the result of evolutionary analyses. However, one cannot easily extract a machine-readable representation from such images. Therefore, new software emerges that helps to preserve phylogenies digitally for future research.

Results

TreeSnatcher Plus is a GUI-driven JAVA application that semi-automatically generates a Newick format for multifurcating, arbitrarily shaped, phylogenetic trees contained in pixel images. It offers a range of image pre-processing methods and detects the topology of a depicted tree with adequate user assistance. The user supervises the recognition process, makes corrections to the image and to the topology and repeats steps if necessary. At the end TreeSnatcher Plus produces a Newick tree code optionally including branch lengths for rectangular and freeform trees.

Conclusions

Although illustrations of phylogenies exist in a vast number of styles, TreeSnatcher Plus imposes no limitations on the images it can process with adequate user assistance. Given that a fully automated digitization of all figures of phylogenetic trees is desirable but currently unrealistic, TreeSnatcher Plus is the only program that reliably facilitates at least a semi-automatic conversion from such figures into a machine-readable format.     

Multiple sclerosis and pregnancy: what does the patient think? a questionnaire study

Background

The first objective of a DNA microarray experiment is typically to generate a list of genes or probes that are found to be differentially expressed or represented (in the case of comparative genomic hybridizations and/or copy number variation) between two conditions or strains. Rank Products analysis comprises a robust algorithm for deriving such lists from microarray experiments that comprise small numbers of replicates, for example, less than the number required for the commonly used t-test. Currently, users wishing to apply Rank Products analysis to their own microarray data sets have been restricted to the use of command line-based software which can limit its usage within the biological community.

Findings

Here we have developed a web interface to existing Rank Products analysis tools allowing users to quickly process their data in an intuitive and step-wise manner to obtain the respective Rank Product or Rank Sum, probability of false prediction and p-values in a downloadable file.

Conclusions

The online interactive Rank Products analysis tool RankProdIt, for analysis of any data set containing measurements for multiple replicated conditions, is available at: http://strep-microarray.sbs.surrey.ac.uk/RankProducts     

Isotopic and anatomical signals for interpreting fire-related responses in Pinus halepensis

Key message

Our study aims to define isotopic and anatomical responses to fires of P. halepensis . Main results: decrease in tree growth and relative conductivity and increase in water use efficiency.

Abstract

We investigated the ecophysiological responses of a Pinus halepensis Mill. stand surviving two wildfires in southern France. Basal area, isotope composition and anatomical traits were analysed before and after fires, using tree rings to assess the ecological responses of trees to heat-related damage. The years were determined based on the presence of fire scars. Stable isotopes (δ¹³C and δ¹⁸O) were measured in tree rings before and after the “fire years”. Anatomical observations allowed qualitative analysis of the scar region and quantification of tracheid size in tree rings before and after the fire years. Relative and percentage conductivity of earlywood and latewood far from the woundwood were estimated. Results showed a decrease in tree growth after the fire events accompanied by an increase in ¹³C-derived water use efficiency (WUE_i) and a decrease in relative conductivity. The positive relationship between δ¹³C and δ¹⁸O suggested that both isotopic variations are mostly driven by changes in stomatal conductance following fire events. P. halepensis proved to be a strong isohydric species, able to survive frequent fires with temporary ecophysiological modifications and anatomical adaptations. Our findings afford new insights into post-fire survival strategies of this species in an environment where fires are predicted to increase in frequency during the twenty-first century.     

Replication of a hepatitis C virus replicon clone in mouse cells

Background

The duration of treatment for HCV infection is partly indicated by the genotype of the virus. For studies of disease transmission, vaccine design, and surveillance for novel variants, subtype-level classification is also needed. This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions.

Results

Different regions of the HCV genome yield inconsistent phylogenies, which can lead to erroneous conclusions about classification of a given infection. In particular, the highly conserved 5' untranslated region (UTR) yields phylogenetic trees with topologies that differ from the HCV polyprotein and complete genome phylogenies. Phylogenetic trees from the NS5B gene reliably cluster related subtypes, and yield topologies consistent with those of the whole genome and polyprotein.

Conclusion

These results extend those from previous studies and indicate that, unlike the NS5B gene, the 5' UTR contains insufficient variation to resolve HCV classifications to the level of viral subtype, and fails to distinguish genotypes reliably. Use of the 5' UTR for clinical tests to characterize HCV infection should be replaced by a subtype-informative test.     

Surprising results on phylogenetic tree building methods based on molecular sequences

Background

We analyze phylogenetic tree building methods from molecular sequences (PTMS). These are methods which base their construction solely on sequences, coding DNA or amino acids.

Results

Our first result is a statistically significant evaluation of 176 PTMSs done by comparing trees derived from 193138 orthologous groups of proteins using a new measure of quality between trees. This new measure, called the Intra measure, is very consistent between different groups of species and strong in the sense that it separates the methods with high confidence. The second result is the comparison of the trees against trees derived from accepted taxonomies, the Taxon measure. We consider the NCBI taxonomic classification and their derived topologies as the most accepted biological consensus on phylogenies, which are also available in electronic form. The correlation between the two measures is remarkably high, which supports both measures simultaneously.

Conclusions

The big surprise of the evaluation is that the maximum likelihood methods do not score well, minimal evolution distance methods over MSA-induced alignments score consistently better. This comparison also allows us to rank different components of the tree building methods, like MSAs, substitution matrices, ML tree builders, distance methods, etc. It is also clear that there is a difference between Metazoa and the rest, which points out to evolution leaving different molecular traces. We also think that these measures of quality of trees will motivate the design of new PTMSs as it is now easier to evaluate them with certainty.     

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing

Background

Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types.

Methods

Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction.

Results

The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource.

Conclusions

THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

     

Articles selected by Faculty of 1000: plant comparative mitochondrial genomics; open source proteomics database; identifying disease-associated enzymes; predicting microRNA targets; genome annotation using polymorphisms

Background

Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny.

Results

The phylogenetic tree constructed from sequencing information of twenty four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the formulation of a new lineage M30, distinguished by the presence of 12007 transition, and comprises of the recently defined M18 and a potential new sub-lineage possessing substitution at 16223 and 16300. M30 further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage M* with HVSI sequence 16223,16325. No new substitutions were found in M25 and the M3 mt DNA genome could only be tentatively rooted by 16126 mutation. M4 and M*(16251, 16267) lineages could not be resolved distinctly.

Conclusions

This study describes seven new basal mutations and fourteen lineages that substantially contribute to the present understanding of superhaplogroup M. The phylogenetic tree supported by median-joining network helps in distinctly identifying the genetic relation between different M lineages that could not be achieved solely by control region sequence information. Although high control region diversity has been reported in the different M lineages distributed in India, complete sequencing of M* and defined lineages suggests that these mt DNA genomes emerged from a limited number of branches arising from the M trunk.     

Populous: a tool for building OWL ontologies from templates

Background

Computing accurate nucleic acid melting temperatures has become a crucial step for the efficiency and the optimisation of numerous molecular biology techniques such as in situ hybridization, PCR, antigene targeting, and microarrays. MELTING is a free open source software which computes the enthalpy, entropy and melting temperature of nucleic acids. MELTING 4.2 was able to handle several types of hybridization such as DNA/DNA, RNA/RNA, DNA/RNA and provided corrections to melting temperatures due to the presence of sodium. The program can use either an approximative approach or a more accurate Nearest-Neighbor approach.

Results

Two new versions of the MELTING software have been released. MELTING 4.3 is a direct update of version 4.2, integrating newly available thermodynamic parameters for inosine, a modified adenine base with an universal base capacity, and incorporates a correction for magnesium. MELTING 5 is a complete reimplementation which allows much greater flexibility and extensibility. It incorporates all the thermodynamic parameters and corrections provided in MELTING 4.x and introduces a large set of thermodynamic formulae and parameters, to facilitate the calculation of melting temperatures for perfectly matching sequences, mismatches, bulge loops, CNG repeats, dangling ends, inosines, locked nucleic acids, 2-hydroxyadenines and azobenzenes. It also includes temperature corrections for monovalent ions (sodium, potassium, Tris), magnesium ions and commonly used denaturing agents such as formamide and DMSO.

Conclusions

MELTING is a useful and very flexible tool for predicting melting temperatures using approximative formulae or Nearest-Neighbor approaches, where one can select different sets of Nearest-Neighbor parameters, corrections and formulae. Both versions are freely available at http://sourceforge.net/projects/melting/and at http://www.ebi.ac.uk/compneur-srv/melting/under the terms of the GPL license.     

Characterization of small genomic regions of the hepatitis B virus should be performed with more caution

Background

Hepatitis B virus is a hepatotropic DNA virus that reproduces via an RNA intermediate. It can lead to an increased risk of serious liver diseases such as hepatocellular carcinoma and is a serious threat to public health. Currently, the HBV are designated based on greater than 8% nucleotide variation along the whole genome. The recombination of HBV is very common, a large majority of which are recombinants between 2 genotypes. The current work aims to characterize a suspected recombinant involving 3 genotypes.

Methods

Fifty-seven HBV full-genome sequences were obtained from 57 patients co-infected with HBV and HIV-1 by amplification coupled with sequencing. JpHMM and RDP4 were used to perform recombination analysis respectively. The recombination results of a suspected 3-genotypic recombinant were further confirmed by both maximum likelihood phylogenetic tree and Mrbayes tree.

Results

JpHMM recombination analysis clearly indicated one 3-genotypic HBV recombinant composing of B/C/D. The genotype assignments are supported by significant posterior probabilities. The subsequent phylogenetic analysis of sub-regions derived from inferred breakpoints led to a disagreement on the assignment of D segment. Investigating the conflict, further exploration by RDP4 and phylogenies revealed that the jpHMM-derived 3-genotypic recombinant is actually a B/C genotypic recombinant with C fragment spanning 1899 to 2295 (jpHMM) or 1821 to 2199 (RDP4).

Conclusions

The whole analysis indicated that (i) determination of small genomic regions should be performed with more caution, (ii) combinations of various recombination detection approaches conduce to obtain impartial results, and (iii) a unified system of nomenclature of HBV genotypes is necessary.

     

Foliar chemistry and tree ring δ13C of Pinus densiflora in relation to tree growth along a soil pH gradient

Background and aims

Soil acidification is known to be one of the constraints of tree growth; however, it is unclear how it affects tree growth at photosynthesis level (i.e., through affecting stomatal conductance vs. carboxylation rate) during the growth of trees. This paper studied the effects of soil acidification on Pinus densiflora foliar chemistry and tree ring C isotope ratio (¹³C/¹²C, expressed as δ¹³C) and their relationship with tree growth.

Methods

Tree growth (diameter, annual growth ring area, and root biomass), soil chemistry (pH, mineral N, and exchangeable Ca and Al), foliage chemistry (N, Ca/Al, and δ¹³C), and tree ring δ¹³C in P. densiflora stands along a soil pH gradient (from 4.38 to 4.83, n?=?9) in southern Korea were investigated.

Results

Overall, trees with relatively poor growth under more acidic soil conditions (low pH and Ca/Al) had lower values of foliar N concentration and δ¹³C and tree ring δ¹³C, suggesting that restricted N uptake under more acidic soil conditions caused N limitation for photosynthesis, leading to poor tree growth. In addition, relationships between mean annual area increment and carbon isotope discrimination of tree rings at five-yr intervals from 1968 to 2007 revealed that the impact of soil acidification on tree growth became severer during the last 15 yrs as negative correlations between them became significant after 1993.

Conclusions

Reduced N uptake under acidic soil conditions resulted in lower radial growth of P. densiflora via non-stomatal limitation of photosynthesis.     

Inferring angiosperm phylogeny from EST data with widespread gene duplication

Background

Most studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nuclear genomes, this has limited the exploitation of nuclear sequences for phylogenetic studies, such as those available in large EST libraries. One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants.

Results

A gene tree parsimony analysis based on EST data was undertaken for six angiosperm model species and Pinus, an outgroup. Although a large fraction of the tentative consensus sequences obtained from the TIGR database of ESTs was assembled into homologous clusters too small to be phylogenetically informative, some 557 clusters contained promising levels of information. Based on maximum likelihood estimates of the gene trees obtained from these clusters, gene tree parsimony correctly inferred the accepted species tree with strong statistical support. A slight variant of this species tree was obtained when maximum parsimony was used to infer the individual gene trees instead.

Conclusion

Despite the complexity of the EST data and the relatively small fraction eventually used in inferring a species tree, the gene tree parsimony method performed well in the face of very high apparent rates of duplication.

     

ReCoil - an algorithm for compression of extremely large datasets of DNA data

Background

The MatrixMatchMaker algorithm was recently introduced to detect the similarity between phylogenetic trees and thus the coevolution between proteins. MMM finds the largest common submatrices between pairs of phylogenetic distance matrices, and has numerous advantages over existing methods of coevolution detection. However, these advantages came at the cost of a very long execution time.

Results

In this paper, we show that the problem of finding the maximum submatrix reduces to a multiple maximum clique subproblem on a graph of protein pairs. This allowed us to develop a new algorithm and program implementation, MMMvII, which achieved more than 600× speedup with comparable accuracy to the original MMM.

Conclusions

MMMvII will thus allow for more more extensive and intricate analyses of coevolution.

Availability

An implementation of the MMMvII algorithm is available at: http://www.uhnresearch.ca/labs/tillier/MMMWEBvII/MMMWEBvII.php     

A composite genome approach to identify phylogenetically informative data from next-generation sequencing

Background

Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, multiple genome alignment, and annotation.

Results

For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered eight phylogenies that resolved the basal relationships among mammals using datasets with different levels of missing data. The three alternate resolutions of the basal relationships are consistent with the major hypotheses for the relationships among mammals, all of which have been supported previously by different molecular datasets.

Conclusions

SISRS has the potential to transform phylogenetic research. This method eliminates the need for expensive marker development in many studies by using whole genome shotgun sequence data directly. SISRS is open source and freely available at https://github.com/rachelss/SISRS/releases.

     

The natural abundance of 15N in litter and soil profiles under six temperate tree species: N cycling depends on tree species traits and site fertility

Aims

We investigated the influence of tree species on the natural ¹⁵N abundance in forest stands under elevated ambient N deposition.

Methods

We analysed δ¹⁵N in litter, the forest floor and three mineral soil horizons along with ecosystem N status variables at six sites planted three decades ago with five European broadleaved tree species and Norway spruce.

Results

Litter δ¹⁵N and ¹⁵N enrichment factor (δ¹⁵N_litter–δ¹⁵N_soil) were positively correlated with N status based on soil and litter N pools, nitrification, subsoil nitrate concentration and forest growth. Tree species differences were also significant for these N variables and for the litter δ¹⁵N and enrichment factor. Litter from ash and sycamore maple with high N status and low fungal mycelia activity was enriched in ¹⁵N (+0.9 delta units) relative to other tree species (European beech, pedunculate oak, lime and Norway spruce) even though the latter species leached more nitrate.

Conclusions

The δ¹⁵N pattern reflected tree species related traits affecting the N cycling as well as site fertility and former land use, and possibly differences in N leaching. The tree species δ¹⁵N patterns reflected fractionation caused by uptake of N through mycorrhiza rather than due to nitrate leaching or other N transformation processes.     

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot

Background

Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny.

Methodology/Principal Findings

Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history.

Conclusions/Significance

As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.     

Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements

Background

Phylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic change represented by a tree and are commonly compared with other measures of mutation to investigate the substitutional processes or the goodness of fit of a tree to the raw data. Up until now no universal tool has been available for calculating patristic distances and correlating them with other genetic distance measures.

Results

PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs.

Conclusion

The software overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses. It is available at http://biojanus.anu.edu.au/programs/ and requires the Java runtime environment.     

HAPSIMU: a genetic simulation platform for population-based association studies

Background

The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices.

Results

To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis.

Conclusion

Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.     

Disparity in 90Sr and 137Cs uptake in Alpine plants: phylogenetic effect and Ca and K availability

Background and aims

Uptake of ⁹⁰Sr and ¹³⁷Cs in plants varies widely between soil types and between plant species. It is now recognized that the radionuclide uptake in plants is more influenced by site-specific and plant-specific parameters rather than the bulk radionuclide concentration in soil. We hypothesized that the stress which Alpine plants experience because of the short growing season may enhance the phylogenetic effect on the ¹³⁷Cs and ⁹⁰Sr transfer factors as well as the dependency of the uptake by plant to the concentrations of exchangeable Ca and K of soils.

Methods

We carried out a field study on the ⁹⁰Sr and ¹³⁷Cs uptake by 11 species of Alpine plants growing on 6 undisturbed and geochemically different soils in the Alpine valley of Piora, Switzerland.

Results

Results show that a strong correlation exists between the log TF and the log of exchangeable Ca or K of the soils.

Conclusions

Cs uptake by Phleum rhaeticum (Poales) and Alchemilla xanthochlora (Rosales) is more sensitive to the amount of exchangeable K in the soil than the corresponding uptake by other orders. Moreover, the ⁹⁰Sr results indicate a phylogenetic effect between Non-Eudicot and Eudicots: the order Poales (Phleum rhaeticum) concentrating much less ⁹⁰Sr than Eudicots do.     

Effect of a glucose impulse on the CcpA regulon in Staphylococcus aureus

Background

A low genetic diversity in Francisella tularensis has been documented. Current DNA based genotyping methods for typing F. tularensis offer a limited and varying degree of subspecies, clade and strain level discrimination power. Whole genome sequencing is the most accurate and reliable method to identify, type and determine phylogenetic relationships among strains of a species. However, lower cost typing schemes are necessary in order to enable typing of hundreds or even thousands of isolates.

Results

We have generated a high-resolution phylogenetic tree from 40 Francisella isolates, including 13 F. tularensis subspecies holarctica (type B) strains, 26 F. tularensis subsp. tularensis (type A) strains and a single F. novicida strain. The tree was generated from global multi-strain single nucleotide polymorphism (SNP) data collected using a set of six Affymetrix GeneChip^® resequencing arrays with the non-repetitive portion of LVS (type B) as the reference sequence complemented with unique sequences of SCHU S4 (type A). Global SNP based phylogenetic clustering was able to resolve all non-related strains. The phylogenetic tree was used to guide the selection of informative SNPs specific to major nodes in the tree for development of a genotyping assay for identification of F. tularensis subspecies and clades. We designed and validated an assay that uses these SNPs to accurately genotype 39 additional F. tularensis strains as type A (A1, A2, A1a or A1b) or type B (B1 or B2).

Conclusion

Whole-genome SNP based clustering was shown to accurately identify SNPs for differentiation of F. tularensis subspecies and clades, emphasizing the potential power and utility of this methodology for selecting SNPs for typing of F. tularensis to the strain level. Additionally, whole genome sequence based SNP information gained from a representative population of strains may be used to perform evolutionary or phylogenetic comparisons of strains, or selection of unique strains for whole-genome sequencing projects.     

Evaluation of angiosperm and fern contributions to soil organic matter using two methods of pyrolysis-gas chromatography-mass spectrometry

Background

Ferns are an important plant group, and older phylogenies of non-polypod ferns contain relatively high concentrations of aliphatic leaf waxes, lignins, and tannins that could contribute to soil organic matter (SOM) biochemistry and stability.

Methods

Pyrolysis gas-chromatography mass-spectrometry (py-GC/MS) analyzes biochemical fragments which can be related to lignin, polysaccharide, lipid, nitrogen (N)-bearing, non-lignin aromatics, and phenol source compounds. Thermochemolysis using tetramethylammonium hydroxide (TMAH) combined with py-GC/MS improves detection of lignin, cutin, and suberin-derived compounds. To examine the advantages and disadvantages of both methods for characterizing plant and soil biochemistry, we characterized non-polypod and polypod fern and angiosperm live tissues, roots and soils from the Kohala Mountains, Hawaii.

Results

Py-GC/MS provided a broad biochemical overview of compound groups including lignin, polysaccharide, lipid, N-bearing, non-lignin aromatics and phenol groups while TMAH-py-GC/MS detailed lignin units and fatty acids at the expense of the other categories. TMAH-py-GC/MS provided more detailed data on lignin, cutin, suberin and tannin-derived compounds. Both methods detected differences in lignin units between species, although p-coumaric and ferulic acids, predominantly found in ferns, were only observed with TMAH-py-GC/MS.

Conclusions

Both py-GC/MS and TMAH-py-GC/MS are methods to detect compound-specific plant biomarkers, but are most useful when combined for their complimentary results.