A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae).

The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4-trnS, trnL and trnL-F) of 1030 accessions (616 of them newly sequenced here) representing c. 420 species of Asplenium (60% of estimated species diversity), 16 species of Hymenasplenium, three Diplaziopsidaceae, and four Rhachidosoraceae were used to produce the largest genus-level phylogeny yet for ferns. Our major results include: (i) Asplenium as broadly circumscribed is monophyletic based on our inclusion of representatives of 32 of 38 named segregate genera; (ii) 11 major clades in Asplenium are identified, and their relationships are mostly well-resolved and strongly supported; (iii) numerous species, unsampled in previous studies, suggest new relationships and numerous cryptic species and species complexes in Asplenium; and (iv) the accrued molecular evidence provides an essential foundation for further investigations of complex patterns of geographical diversification, speciation and reticulate evolution in this family.

Molecular phylogeny of the fern family Blechnaceae (Polypodiales) with a revised genus-level treatment.

Blechnaceae, a leptosporangiate fern family nested within eupolypods II, comprises 200-250 species, typically divided among seven to nine genera. Despite recent molecular studies of the family, it still lacks a modern taxonomic update based on broad sampling from the two centres of diversity-the Neotropics and Australasia/Oceania. To test generic circumscriptions, we have assembled the broadest dataset thus far, from three plastid regions (rbcL, rps4-trnS, trnL-trnF) and with taxonomic sampling focused on both major diversity centres. Our sampling includes 156 taxa and 178 newly generated sequences. We recognize three subfamilies, each corresponding to a highly supported clade across all analyses (maximum parsimony, Bayesian inference and maximum likelihood). The genera Salpichlaena, Stenochlaena and Telmatoblechnum are monophyletic, while Blechnum is polyphyletic, because Brainea, Doodia and Sadleria all nest within it. We outline and explain a plan to resolve the polyphyly of Blechnum by recognizing additional, monophyletic, segregate genera.

Towards a phylogenetic generic classification of Thelypteridaceae: Additional sampling suggests alterations of neotropical taxa and further study of paleotropical genera.

Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta, was found to include species considered to be part of Parathelypteris. In Old World thelypteroids, which correspond to nearly half the diversity in the family, an increase in sampling is still needed to resolve relationships and circumscription of genera, particularly in the christelloid clade (i.e., Amphineuron, Chingia, Christella, Pneumatopteris, Pronephrium, and Sphaerostephanos). Based on currently available knowledge, we propose the recognition of 16 genera in the family.

Global phylogeny and biogeography of grammitid ferns (Polypodiaceae).

We examined the global historical biogeography of grammitid ferns (Polypodiaceae) within a phylogenetic context. We inferred phylogenetic relationships of 190 species representing 31 of the 33 currently recognized genera of grammitid ferns by analyzing DNA sequence variation of five plastid DNA regions. We estimated the ages of cladogenetic events on an inferred phylogeny using secondary fossil calibration points. Historical biogeographical patterns were inferred via ancestral area reconstruction. Our results supported four large-scale phylogenetic and biogeographic patterns: (1) a monophyletic grammitid clade that arose among Neotropical polypod ancestors about 31.4 Ma; (2) a paraphyletic assemblage of clades distributed in the Neotropics and the Afro-Malagasy region; (3) a large clade distributed throughout the Asia-Malesia-Pacific region that originated about 23.4 Ma; and, (4) an Australian or New Zealand origin of the circumaustral genus Notogrammitis. Most genera were supported as monophyletic except for Grammitis, Oreogrammitis, Radiogrammitis, and Zygophlebia. Grammitid ferns are a well-supported monophyletic group with two biogeographically distinct lineages: a primarily Neotropical grade exhibiting several independent successful colonizations to the Afro-Malagasy region and a primarily Paleotropical clade exhibiting multiple independent dispersals to remote Pacific islands and temperate, austral regions.

Trace explosives sampling for security applications (TESSA) study: Evaluation of procedures and methodology for contact sampling efficiency.

The detection of trace amounts of explosive materials is critical to the security at mass transit centers (e.g., airports and railway stations). In a typical screening process, a trap is used to probe a surface of interest to collect and transfer particulate residue to a detector for analysis. The collection of residues from the surface being probed is widely viewed as the limiting step in this process. A multi-institutional study was performed to establish a methodology for the evaluation of sampling media collection efficiencies. Dry deposited residues of 1,3,5-trinitroperhydro-1,3,5-triazine (RDX), C-4 (an RDX-based explosive), and pentaerythritol tetranitrate (PETN) were harvested from acrylonitrile butadiene styrene (ABS) plastic, ballistic nylon (NYL), and uncoated aluminum surfaces using muslin, Texwipe cotton, and stainless-steel mesh traps. Transfer and collection efficiencies of the sample media were calculated based on liquid chromatography-mass spectrometry analysis. Dry transfer efficiencies (DTE%) to all tested surfaces were greater than 75%, with transfer to ABS plastic being the lowest. Collection efficiency (CE%) varied significantly across the traps and the surfaces, yet some conclusions can be drawn; nylon had the lowest CE% for all cases (∼10%), and the stainless steel mesh had the lowest CE% for the evaluated traps (∼20%). Though the testing parameters have been standardized among the participants to establish a framework for an independent comparison of contact sampling media and surfaces, substantial variations in the DTE% and the CE% were observed, suggesting that other variables can affect contact sampling.

Optimization of proteomics sample preparation for forensic analysis of skin samples.

We present an efficient protein extraction and in-solution enzymatic digestion protocol optimized for mass spectrometry-based proteomics studies of human skin samples. Human skin cells are a proteinaceous matrix that can enable forensic identification of individuals. We performed a systematic optimization of proteomic sample preparation for a protein-based human forensic identification application. Digestion parameters, including incubation duration, temperature, and the type and concentration of surfactant, were systematically varied to maximize digestion completeness. Through replicate digestions, parameter optimization was performed to maximize repeatability and increase the number of identified peptides and proteins. Final digestion conditions were selected based on the parameters that yielded the greatest percent of peptides with zero missed tryptic cleavages, which benefit the analysis of genetically variable peptides (GVPs). We evaluated the final digestion conditions for identification of GVPs by applying MS-based proteomics on a mixed-donor sample. The results were searched against a human proteome database appended with a database of GVPs constructed from known non-synonymous single nucleotide polymorphisms (SNPs) that occur at known population frequencies. The aim of this study was to demonstrate the potential of our proteomics sample preparation for future implementation of GVP analysis by forensic laboratories to facilitate human identification. SIGNIFICANCE: Genetically variable peptides (GVPs) can provide forensic evidence that is complementary to traditional DNA profiling and be potentially used for human identification. An efficient protein extraction and reproducible digestion method of skin proteins is a key contributor for downstream analysis of GVPs and further development of this technology in forensic application. In this study, we optimized the enzymatic digestion conditions, such as incubation time and temperature, for skin samples. Our study is among the first attempts towards optimization of proteomics sample preparation for protein-based skin identification in forensic applications such as touch samples. Our digestion method employs RapiGest (an acid-labile surfactant), trypsin enzymatic digestion, and an incubation time of 16 h at 37 °C.

Fractionation of DNA and protein from individual latent fingerprints for forensic analysis.

Human touch samples represent a significant portion of forensic DNA casework. Yet, the generally low abundance of genetic material combined with the predominantly extracellular nature of DNA in these samples makes DNA-based forensic analysis exceptionally challenging. Human proteins present in these same touch samples offer an abundant and environmentally-robust alternative. Proteogenomic methods, using protein sequence variants arising from nonsynonymous DNA mutations, have recently been applied to forensic analysis and may represent a viable option looking forward. However, DNA analysis remains the gold standard and any proteomics-based methods would need to consider how DNA could be co-extracted from samples without significant loss. Herein, we describe a simple workflow for the collection, enrichment and fractionation of DNA and protein in latent fingerprint samples. This approach ensures that DNA collected from a latent fingerprint can be analyzed by traditional DNA casework methods, while protein can be proteolytically digested and analyzed via standard liquid chromatography-tandem mass spectrometry-based proteomics methods from the same touch sample. Sample collection from non-porous surfaces (i.e., glass) is performed through the application of an anionic surfactant over the fingermark. The sample is then split into separate DNA and protein fractions following centrifugation to enrich the protein fraction by pelleting skin cells. The results indicate that this workflow permits analysis of DNA within the sample, yet highlights the challenge posed by the trace nature of DNA in touch samples and the potential for DNA to degrade over time. Protein deposited in touch samples does not appear to share this limitation, with robust protein quantities collected across multiple human donors. The quantity and quality of protein remains robust regardless of fingerprint age. The proteomic content of these samples is consistent across individual donors and fingerprint age, supporting the future application of genetically variable peptide (GVP) analysis of touch samples for forensic identification.

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica.

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.

An algorithm for random match probability calculation from peptide sequences.

For the past three decades, forensic genetic investigations have focused on elucidating DNA signatures. While DNA has a number of desirable properties (e.g., presence in most biological materials, an amenable chemistry for analysis and well-developed statistics), DNA also has limitations. DNA may be in low quantity in some tissues, such as hair, and in some tissues it may degrade more readily than its protein counterparts. Recent research efforts have shown the feasibility of performing protein-based human identification in cases in which recovery of DNA is challenged; however, the methods involved in assessing the rarity of a given protein profile have not been addressed adequately. In this paper an algorithm is proposed that describes the computation of a random match probability (RMP) resulting from a genetically variable peptide signature. The approach described herein explicitly models proteomic error and genetic linkage, makes no assumptions as to allelic drop-out, and maps the observed proteomic alleles to their expected protein products from DNA which, in turn, permits standard corrections for population structure and finite database sizes. To assess the feasibility of this approach, RMPs were estimated from peptide profiles of skin samples from 25 individuals of European ancestry. 126 common peptide alleles were used in this approach, yielding a mean RMP of approximately 10-2.

Artificial fingerprints for cross-comparison of forensic DNA and protein recovery methods.

Quantitative genomic and proteomic evaluation of human latent fingerprint depositions represents a challenge within the forensic field, due to the high variability in the amount of DNA and protein initially deposited. To better assess recovery techniques for touch depositions, we present a method to produce simple and customizable artificial fingerprints. These artificial fingerprint samples include the primary components of a typical latent fingerprint, specifically sebaceous fluid, eccrine perspiration, extracellular DNA, and proteinaceous epidermal skin material (i.e., shed skin cells). A commercially available emulsion of sebaceous and eccrine perspiration material provides a chemically-relevant suspension solution for fingerprint deposition, simplifying artificial fingerprint production. Extracted human genomic DNA is added to accurately mimic the extracellular DNA content of a typical latent print and comparable DNA yields are recovered from the artificial prints relative to human prints across surface types. Capitalizing on recent advancements in the use of protein sequence identification for human forensic analysis, these samples also contain a representative quantity of protein, originating from epidermal skin cells collected from the fingers and palms of volunteers. Proteomic sequencing by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis indicates a high level of protein overlap between artificial and latent prints. Data are available via ProteomeXchange with identifier PXD015445. By including known quantities of DNA and protein into each artificial print, this method enables total DNA and protein recovery to be quantitatively assessed across different sample collection and extraction methods to better evaluate extraction efficiency. Collectively, these artificial fingerprint samples are simple to make, highly versatile and customizable, and accurately represent the biochemical composition and biological signatures of human fingerprints.

Effects of acute and chronic interval sprint exercise performed on a manually propelled treadmill on upper limb vascular mechanics in healthy young men.

Interval sprint exercise performed on a manually propelled treadmill, where the hands grip the handle bars, engages lower and upper limb skeletal muscle, but little is known regarding the effects of this exercise modality on the upper limb vasculature. We tested the hypotheses that an acute bout of sprint exercise and 6 weeks of training induces brachial artery (BA) and forearm vascular remodeling, favoring a more compliant system. Before and following a single bout of exercise as well as 6 weeks of training three types of vascular properties/methodologies were examined in healthy men: (1) stiffness of the entire upper limb vascular system (pulse wave velocity (PWV); (2) local stiffness of the BA; and (3) properties of the entire forearm vascular bed (determined by a modified lumped parameter Windkessel model). Following sprint exercise, PWV declined (P < 0.01), indices of BA stiffness did not change (P ≥ 0.10), and forearm vascular bed compliance increased and inertance and viscoelasticity decreased (P ≤ 0.03). Following manually propelled treadmill training, PWV remained unchanged (P = 0.31), indices of BA stiffness increased (P ≤ 0.05) and forearm vascular bed viscoelasticity declined (P = 0.02), but resistance, compliance, and inertance remained unchanged (P ≥ 0.10) compared with pretraining values. Sprint exercise induced a more compliant forearm vascular bed, without altering indices of BA stiffness. These effects were transient, as following training the forearm vascular bed was not more compliant and indices of BA stiffness increased. On the basis of these data, we conclude that adaptations to acute and chronic sprint exercise on a manually propelled treadmill are not uniform along the arterial tree in upper limb.

New combinations in Neotropical Thelypteridaceae.

288 new combinations of Neotropical Thelypteridaceae taxa are proposed in order to recognize monophyletic genera, based on the results of the most recent molecular phylogeny of the family, as well as the morphological uniformity of characters for each genus. The new nomenclatural combinations correspond to 186 Amauropelta taxa, 77 species of Goniopteris, and 25 Steiropteris taxa. A key to all native Neotropical genera of the family is also presented.

Adiantumshastense, a new species of maidenhair fern from California.

A new species of Adiantum is described from California. This species is endemic to northern California and is currently known only from Shasta County. We describe its discovery after first being collected over a century ago and distinguish it from Adiantumjordanii and Adiantumcapillus-veneris. It is evergreen and is sometimes, but not always, associated with limestone. The range of Adiantumshastense Huiet & A.R.Sm., sp. nov., is similar to several other Shasta County endemics that occur in the mesic forests of the Eastern Klamath Range, close to Shasta Lake, on limestone and metasedimentary substrates.

Confirmation of a continental-scale disjunction for the fern Campyloneurum decurrens (Polypodiaceae) / Confirmación de una disyunción a escala continental del helecho Campyloneurum decurrens (Polypodiaceae)

We confirm the presence of Campyloneurum decurrens in the western side of South America based on herbarium collections. Specifically, we report three additional localities for its geographical range, two in Peru and one in Ecuador, and provide additional morphological information on this species. This report confirms a disjunction for this species between the Atlantic Forest in southeastern Brazil and the lowland forests in the Peruvian Amazon, and in the Ecuadorean Choco.

Se confirma la presencia de Campyloneurum decurrens en el occidente de América del Sur en base a colecciones de herbario. Se reporta tres localidades adicionales para su distribución geográfica, dos en Perú y una en Ecuador y se provee de información morfológica adicional. Este reporte confirma también el patrón de disyunción entre la región del Bosque Atlántico en el sureste del Brasil y la de los bosques bajos de la amazonia peruana y del Chocó ecuatoriano.

New pteridophyte species and combinations from the Marquesas Islands, French Polynesia.

Intensive botanical exploration of the Marquesas Islands (French Polynesia) for the Vascular Flora of the Marquesas Islands and Flore de la Polynésie française projects has resulted in numerous additional new collections from these islands. Study of these collections has brought to light 11 new species of pteridophytes (ferns and lycophytes) which are described herein: Blechnum pacificum Lorence & A. R. Sm., sp. nov., Cyclosorus castaneus A. R. Sm. & Lorence, sp. nov., Cyclosorus florencei A. R. Sm. & Lorence, sp. nov., Dryopteris macropholis Lorence & W. L. Wagner, sp. nov., Dryopteris sweetorum Lorence & W. L. Wagner, sp. nov., Polystichum kenwoodii Lorence & W. L. Wagner, sp. nov., Polystichum uahukaense Lorence & W. L. Wagner, sp. nov., Pteris hivaoaensis Lorence & K. R. Wood, sp. nov., Pteris marquesensis Lorence & K. R. Wood, sp. nov., Pteris tahuataensis Lorence & K. R. Wood, sp. nov., and Thelypteris marquesensis Lorence & K. R. Wood, sp. nov. One new combination is made: Cyclosorus marquesicus (Holttum) Lorence & A. R. Sm., comb. nov. (based on Plesioneuron marquesicum Holttum). An analysis of the conservation status of these new Marquesas Islands taxa reveals they are in need of inclusion in the IUCN Red List with conservation status ranging from vulnerable (one species), and endangered (four species), to critically endangered (five species).

Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants.

We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also includes the pantropical Grammitidaceae. The loxogrammoid lineage diverges first and is sister to a large clade comprising the three remaining species-rich lineages. One paleotropical clade includes the drynarioid and selligueoid ferns, whereas the second paleotropical clade includes the platycerioids, lepisoroids, microsoroids, and their relatives. The grammitids nest within the neotropical clade, although the sister taxon of this circum-tropic, epiphytic group remains ambiguous. Microsorum and Polypodium, as traditionally defined, were recovered as polyphyletic. The relatively short branch lengths of the deepest clades contrast with the long branch lengths leading to the terminal groups. This suggests that the polygrammoid ferns arose through an old, rapid radiation. Our analysis also reveals that the rate of substitution in the grammitids is remarkably higher relative to other polygrammoids. Disparities in substitution rate may be correlated with one or more features characterizing grammitids, including species richness, chlorophyllous spores, and an extended gametophytic phase.

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences.

The phylogenetic structure of ferns (= monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of "core leptosporangiates" that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.