OptiJ: Open-source optical projection tomography of large organ samples

The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts

Unraveling the macroevolutionary history of bryophytes, which arose soon after the origin of land plants but exhibit substantially lower species richness than the more recently derived angiosperms, has been challenged by the scarce fossil record. Here we demonstrate that overall estimates of net species diversification are approximately half those reported in ferns and similar to 30% those described for angiosperms. Nevertheless, statistical rate analyses on time-calibrated large-scale phylogenies reveal that mosses and liverworts underwent bursts of diversification since the mid-Mesozoic. The diversification rates further increase in specific lineages towards the Cenozoic to reach, in the most recently derived lineages, values that are comparable to those reported in angiosperms. This suggests that low diversification rates do not fully account for current patterns of bryophyte species richness, and we hypothesize that, as in gymnosperms, the low extant bryophyte species richness also results from massive extinctions.Assembling the Tree of Life programme at NSF; NSF [EF-0531730-002, EF-0531680, EF-0531750]; Scottish Government's Rural and Environment Science and Analytical Services Division; BeiPD-cofund Marie Curie fellowshipinfo:eu-repo/semantics/publishedVersio

Timing and Tempo of Early and Successive Adaptive Radiations in Macaronesia

The flora of Macaronesia, which encompasses five Atlantic archipelagos (Azores, Canaries, Madeira, Cape Verde, and Salvage), is exceptionally rich and diverse

Choosing and Using a Plant DNA Barcode

The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance

A miniature world in decline: European Red List of Mosses, Liverworts and Hornworts

AimThis Red List is a summary of the conservation status of the European species of mosses, liverworts and hornworts, collectively known as bryophytes, evaluated according to IUCN’s Guidelines for Application of IUCN Red List Criteria at Regional Level. It provides the first comprehensive, region-wide assessment of bryophytes and it identifies those species that are threatened with extinction at a European level, so that appropriate policy measures and conservation actions, based on the best available evidence, can be taken to improve their status.ScopeAll bryophytes native to or naturalised in Europe (a total of 1,817 species), have been included in this Red List. In Europe, 1,796 species were assessed, with the remaining 21 species considered Not Applicable (NA). For the EU 28, 1,728 species were assessed, with a remaining 20 species considered NA and 69 species considered Not Evaluated (NE). The geographical scope is continentwide, extending from Iceland in the west to the Urals in the east, and from Franz Josef Land in the north to theCanary Islands in the south. The Caucasus region is not included. Red List assessments were made at two regional levels: for geographical Europe and for the 28 Member States of the European Union.ResultsOverall, 22.5% of European bryophyte species assessed in this study are considered threatened in Europe, with two species classified as Extinct and six assessed as Regionally Extinct (RE). A further 9.6% (173 species) are considered Near Threatened and 63.5% (1,140 species) are assessed as Least Concern. For 93 species (5.3%), there was insufficient information available to be able to evaluate their risk of extinction and thus they were classified as Data Deficient (DD). The main threats identified were natural system modifications (i.e., dam construction, increases in fire frequency/intensity, and water management/use), climate change (mainly increasing frequency of droughts and temperature extremes), agriculture (including pollution from agricultural effluents) and aquaculture.RecommendationsPolicy measures• Use the European Red List as the scientific basis to inform regional/national lists of rare and threatened species and to identify priorities for conservation action in addition to the requirements of the Habitats Directive, thereby highlighting the conservation status of bryophytes at the regional/local level.• Use the European Red List to support the integration of conservation policy with the Common Agricultural Policy (CAP) and other national and international policies. For example, CAP Strategic Plans should include biodiversity recovery commitments that could anticipate, among others, the creation of Important Bryophyte Areas. An increased involvement of national environmental agencies in the preparation of these strategic plans, and more broadly in ongoing discussions on the Future CAP Green Architecture, would likely also ensure the design of conservation measures better tailored to conserve bryophytes in agricultural landscapes.• Update the European Red List every decade to ensure that the data remains current and relevant.• Develop Key Biodiversity Areas for bryophytes in Europe with a view to ensuring adequate site-based protection for bryophytes.Research and monitoring• Use the European Red List as a basis for future targeted fieldwork on possibly extinct and understudied species.• Establish a monitoring programme for targeted species (for example, threatened species and/or arable bryophytes).• Use the European Red List to obtain funding for research into the biology and ecology of key targeted species.Action on the ground• Use the European Red List as evidence to support multi-scale conservation initiatives, including designation of protected areas, reform of agricultural practices and land management, habitat restoration and rewilding, and pollution reduction measures.• Use the European Red List as a tool to target species that would benefit the most from the widespread implementation of the solutions offered by the 1991 Nitrates Directive (Council Directive 91/676/EEC), including the application of correct amounts of nutrients for each crop, only in periods of crop growth under suitable climatic conditions and never during periods of heavy rainfall or on frozen ground, and the creation of buffer zones to protect waters from run-off from the application of fertilizers.Ex situ conservation• Undertake ex situ conservation of species of conservation concern in botanic gardens and spore and gene banks, with a view to reintroduction where appropriate.</p

Pheromone variability and evolution in the butterfly genus Bicyclus, and implication in its diversification

The evolution of olfactive communication in generating reproductive isolation among species remains poorly understood (Smadja & Butlin 2009). In Lepidoptera, studies have mainly focused on long-distance pheromones produced by moths. Moth sex pheromones have been shown to display inter-population variation (e.g. Tòth et al. 1992, McElfresh & Millar 2008 and ref. within, Groot et al. 2009) and to be involved in interspecific isolation (e.g. Löfstedt et al. 1991, Groot et al. 2006). In butterflies, the few existing studies on sex pheromones have mainly focused on the identification of the male specific compounds and the demonstration of their behavioural activity in courtship (e.g. Grula et al. 1980, Nieberding et al. 2008, Yildizhan et al. 2009), but have failed so far to highlight a role in reproductive isolation (Friberg et al. 2008). In the species-rich Bicyclus genus Kirby, 1871 (Nymphalidae, Satyrinae) the structures producing the pheromones, i.e. the androconia, are key characters to discriminate among species (Condamin 1973). In B. anynana (Butler, 1879), the male sex pheromone (MSP) has been shown to play a role in mate choice (Costanzo & Monteiro 2007, Nieberding et al. 2008), to be heritable, and particular ratios of the pheromone components are under strong sexual selection (Nieberding et al, unpubl. data). Therefore, we expect that pheromone evolution is responsible for reproductive isolation and diversification in this butterfly group. In this framework, our research project aims at understanding the evolution of MSP at the interspecific level across the Bicyclus genus and specifically at testing their potential role in the speciation process. Potential MSP of several species across the Bicyclus genus have been identified by gas chromatography and mass spectrometry. Observed differences in pheromone composition between species are compared in a phylogenetic framework to the molecular tree of the species (following Oliver et al. 2009). We expect the evolutionary rate of MSP to be unlinked to the molecular tree if MSP are under sexual selection across the genus (i.e. saltational evolution following Symonds & Elgar 2004, Shirangi et al. 2009). Moreover, if MSP generated reproductive isolation between species in a “reinforcement” process, we expect higher differences of MSP composition between sympatric species than between allopatric species and an increase of this pattern for younger species compared to older species (Lukhtanov et al. 2006)

Identification and Characterization of eight Nuclear Microsatellite Loci in the Glasswort Genus Salicornia (Amaranthaceae)

Eight nuclear microsatellite loci were identified using the method of microsatellite-enriched libraries in the glasswort genus Salicornia. These markers yield specific alleles for discriminating diploid and tetraploid lineages and thus provide a reliable and efficient tool for routine determination of ploidy level in the genus. Within both the diploid and tetraploid lineages, the microsatellites further display a clear biogeographic signal. A significant partitioning of genetic differentiation was found between the diploid populations (F-stSCOPUS: no.jinfo:eu-repo/semantics/publishe