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Background and Aims: Herbaria are the most important source of information for plant taxonomic work. Resources and technologies available today, such as digitised collections and herbarium DNA sequencing, can help accelerate taxonomic decisions in challenging plant groups. Here we employ an integrative methodology relying exclusively on herbarium specimens to investigate species boundaries in the Neotropical Myrcia neoobscura complex (Myrtaceae)., Methods: We collected morphometric data from high-resolution images of herbarium sheets and analysed it using hierarchical clustering. We posteriorly tested the obtained morpho-groups with phylogenomics using the Angiosperms353 probe kit. We also gathered phenological and geographic information from specimen labels and built phenological histograms and ecological niche models to investigate ecological differences amongst taxa., Key Results: Current circumscriptions of Myrcia arenaria, Myrcia neoglabra and Myrcia neoregeliana are confirmed in this study. Conversely, the four pieces of evidence together support Calyptranthes langsdorffii var. grandiflora, Marlierea regeliana var. parviflora and Marlierea warmingiana as separate from Myrcia marliereana, Myrcia neoriedeliana and Myrcia neoobscura, respectively, contrary to arrangements proposed by previous authors. Integrated analyses also support separation between Myrcia excoriata and two similar, undescribed taxa., Conclusions: Our data reveal the need for major changes in the systematics of the group, with recognition of 12 species. The successful delivery of our study aims was possible due to obtaining robust, high-quality data from museum specimens. We emphasise the importance of maintaining botanical collections physically and digitally available for taxonomic work and advocate their use to accelerate holistic taxonomic solutions of tropical species complexes. This is urgent, given the paucity of funds for fieldwork and unprecedented rates of habitat loss in the tropics., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Background and Aims: Understanding diaspore morphology and how much a species invests on dispersal appendages is key for improving our knowledge of dispersal in fragmented habitats. We investigate diaspore morphological traits in high-Andean Compositae and their main abiotic and biotic drivers and test whether they play a role in species distribution patterns across the naturally fragmented high-Andean grasslands., Methods: We collected diaspore trait data for 125 Compositae species across 47 tropical high-Andean summits, focusing on achene length and pappus-to-achene length ratio, with the latter as a proxy of dispersal investment. We analysed the role of abiotic (temperature, elevation and latitude) and biotic factors (phylogenetic signal and differences between tribes) on diaspore traits and whether they are related to distribution patterns across the Andes, using phylogenomics, distribution modelling and community ecology analyses., Key Results: Seventy-five percent of the studied species show small achenes (length <3.3 mm) and 67% have high dispersal investment (pappus length at least two times the achene length). Dispersal investment increases with elevation, possibly to compensate for lower air density, and achene length increases towards the equator, where non-seasonal climate prevails. Diaspore traits show significant phylogenetic signal, and higher dispersal investment is observed in Gnaphalieae, Astereae and Senecioneae, which together represent 72% of our species. High-Andean-restricted species found across the tropical Andes have, on average, the pappus four times longer than the achene, a significantly higher dispersal investment than species present only in the northern Andes or only in the central Andes., Conclusions: Small achenes and high diaspore dispersal investment dominate among high-Andean Compositae, traits typical of mostly three tribes of African origin; but traits are also correlated with the environmental gradients within the high-Andean grasslands. Our results also suggest that diaspore dispersal investment is likely to shape species distribution patterns in naturally fragmented habitats., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Annals of Botany Company.)

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and 2333 genera (17$\%$). A "first pass" angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world's natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]., (© The Author(s) 2021. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.)

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes, while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, 5-15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order groups, including the entire angiosperm clade itself., (© The Author(s) 2018. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

Introduction: Blast injuries in modern warfare are common, and tympanic perforation is often found. Spontaneous closures of large perforations that encompass greater than 80% of the tympanic surface are rare. Early closure of the tympanic membrane avoids the immediate infectious risk, which potentially complicates the initial management of these war-wounded patients, and allows for safe and early recovery of military activity. This study compared the outcomes of spontaneous closures and early biomembrane myringoplasty in subjects with large blast injury-induced tympanic perforation following a massive explosion., Materials and Methods: This is a retrospective, observational, cohort study military troops with large barotraumatic tympanic membrane perforation. The study investigates early surgical tympanoplasty versus observation for spontaneous closure. The hearing loss, tympanic perforation closure rate, and closure time were noted., Results: Fourteen patients (19 ears) were referred from May 2008 to April 2017, and 6 patients (9 ears) underwent early myringoplasty. A total of 89% (n = 8) and 100% (n = 9) of the ears exhibited successful sealing of the perforation at one and 6 mo, respectively. In contrast, 60% (n = 6) of the 10 ears (8 patients) without initial myringoplasty did not heal spontaneously at 6 mo, and these ears underwent a delayed tympanoplasty procedure. Notably, patients with early myringoplasty suffered lower conductive hearing loss and fewer functional signs remotely., Conclusion: Early myringoplasty using a biomembrane for blast injury-induced large tympanic perforation is a fast and minimally invasive method to achieve earlier tympanic closure and a higher closure rate for safe recovery of activity. It can be performed under general anesthesia concurrently with surgery for additional body-wide trauma. The deployment of ENT surgeons on the battlefield in the French Army has enabled early management of these patients.

Unlabelled: The objective was to describe a case series of penetrating neck injuries (PNIs) and compare their management in combat versus civilian trauma., Methods: From 2012 to 2014, all soldiers and civilians referred to Percy Military Training Hospital for PNI were analyzed. The mechanism of injury, type and site of the lesion, and initial emergency management were noted., Results: Among the 55 patients, 26 were wounded in action, and 29 were civilians. PNIs were commonly stab wounds resulting from an assault. Anatomical zone II, as well as the central neck compartment, was the most affected area. The most affected organ was the larynx. 74% of patients underwent computed tomography angiography (CTA), surgical exploration was performed for 42% of patients, and 33% of patients required intensive care unit monitoring. The differences between the two groups in terms of management were not statistically significant., Conclusions: The current management is based on clinical examination and CTA and is similar between soldiers and civilians. Surgical exploration is less commonly used than CTA, which is a fast and accurate method to evaluate PNI for stable patients. The classification by compartment seems more relevant than the classification by anatomical zone, particularly in absence of medical imaging., (Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.)

Background and Aims: The phylogenetic relationships between species of Coffea and Psilanthus remain poorly understood, owing to low levels of sequence variation recovered in previous studies, coupled with relatively limited species sampling. In this study, the relationships between Coffea and Psilanthus species are assessed based on substantially increased molecular sequence data and greatly improved species sampling., Methods: Phylogenetic relationships are assessed using parsimony, with sequence data from four plastid regions [trnL-F intron, trnL-F intergenic spacer (IGS), rpl16 intron and accD-psa1 IGS], and the internal transcribed spacer (ITS) region of nuclear rDNA (ITS 1/5.8S/ITS 2). Supported lineages in Coffea are discussed within the context of geographical correspondence, biogeography, morphology and systematics., Key Results: Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported. Other lineages with either geographical or ecological correspondence are recognized for the first time. Coffea subgenus Baracoffea is shown to be monophyletic, but Coffea subgenus Coffea is paraphyletic. Sequence data do not substantiate the monophyly of either Coffea or Psilanthus. Low levels of sequence divergence do not allow detailed resolution of relationships within Coffea, most notably for species of Coffea subgenus Coffea occurring in Madagascar. The origin of C. arabica by recent hybridization between C. canephora and C. eugenioides is supported. Phylogenetic separation resulting from the presence of the Dahomey Gap is inferred based on sequence data from Coffea.