Quentin Groom

Global exchange and accumulation of non-native plants

All around the globe, humans have greatly altered the abiotic and biotic environment with ever-increasing speed. One defining feature of the Anthropocene epoch is the erosion of biogeographical barriers by human-mediated dispersal of species into new regions, where they can naturalize and cause ecological, economic and social damage. So far, no comprehensive analysis of the global accumulation and exchange of alien plant species between continents has been performed, primarily because of a lack of data. Here we bridge this knowledge gap by using a unique global database on the occurrences of naturalized alien plant species in 481 mainland and 362 island regions. In total, 13,168 plant species, corresponding to 3.9% of the extant global vascular flora, or approximately the size of the native European flora, have become naturalized somewhere on the globe as a result of human activity. North America has accumulated the largest number of naturalized species, whereas the Pacific Islands show the fastest increase in species numbers with respect to their land area. Continents in the Northern Hemisphere have been the major donors of naturalized alien species to all other continents. Our results quantify for the first time the extent of plant naturalizations worldwide, and illustrate the urgent need for globally integrated efforts to control, manage and understand the spread of alien species.

Species richness declines and biotic homogenisation have slowed down for NW-European pollinators and plants

Concern about biodiversity loss has led to increased public investment in conservation. Whereas there is a widespread perception that such initiatives have been unsuccessful, there are few quantitative tests of this perception. Here, we evaluate whether rates of biodiversity change have altered in recent decades in three European countries (Great Britain, Netherlands and Belgium) for plants and flower visiting insects. We compared four 20-year periods, comparing periods of rapid land-use intensification and natural habitat loss (1930–1990) with a period of increased conservation investment (post-1990). We found that extensive species richness loss and biotic homogenisation occurred before 1990, whereas these negative trends became substantially less accentuated during recent decades, being partially reversed for certain taxa (e.g. bees in Great Britain and Netherlands). These results highlight the potential to maintain or even restore current species assemblages (which despite past extinctions are still of great conservation value), at least in regions where large-scale land-use intensification and natural habitat loss has ceased.

The froh gene family from Arabidopsis thaliana : Putative iron-chelate reductases

A group of b-type cytochromes play central roles in both the uptake of iron by yeast, exemplified by the products of the FRE1 and FRP1 genes, and in pathogen defence by animals, exemplified by gp91phox from humans. There has been speculation that related proteins have similar roles in plants. We have recently isolated a family of genes from Arabidopsis thaliana, designated froh, which encode deduced proteins which fall into the same class as FRE1, FRP1 and gp91phox. This paper reports that root surface iron-chelate reductase activity was 2.7-fold greater in A. thaliana plants grown in 5 µM, relative to plants grown in the presence of 25 µM, Fe(III) EDDHA. Reversed transcriptase (RT) polymerase chain reactions (PCR) using RNA isolated from these plants detected increased accumulation of frohC transcripts in low iron. Products were RT-dependent and their identity confirmed by subsequent hybridisation to 32P-frohC probe and by sequence determination. The frohC transcripts accumulated in response to low iron in both roots and leaves while actin transcripts (control) remained constant. Exposure of leaves to salicylic acid (a potentiator of pathogen defense responses) led to an accumulation of transcripts encoding a pathogenesis-related protein, pr-1, but not frohC or actin transcripts. These observations suggest that FrohC is more likely to be involved in iron-reduction, either for uptake from the soil or re-translocation within the plant, than in pathogen defence.

The non-photochemical reduction of plastoquinone in leaves.

Although it is generally assumed that the plastoquinone pool of thylakoid membranes in leaves of higher plants is rapidly oxidized upon darkening, this is often not the case. A multiflash kinetic fluorimeter was used to monitor the redox state of the plastoquinone pool in leaves. It was found that in many species of plants, particularly those using the NAD-malic enzyme C4 system of photosynthesis, the pool actually became more reduced following a light to dark transition. In some Amaranthus species, plastoquinone remained reduced in the dark for several hours. Far red light, which preferentially drives Photosystem I turnover, could effectively oxidize the plastoquinone pool. Plastoquinone was re-reduced in the dark within a few seconds when far red illumination was removed. The underlying mechanism of the dark reduction of the plastoquinone pool is still uncertain but may involve chlororespiratory activity.

Some poleward movement of British native vascular plants is occurring, but the fingerprint of climate change is not evident.

Recent upperward migration of plants and animals along altitudinal gradients and poleward movement of animal range boundaries have been confirmed by many studies. This phenomenon is considered to be part of the fingerprint of recent climate change on the biosphere. Here I examine whether poleward movement is occurring in the vascular plants of Great Britain. The ranges of plants were determined from detection/non-detection data in two periods, 1978 to 1994 and 1995 to 2011. From these, the centre of mass of the population was calculated and the magnitude and direction of range shifts were determined from movements of the centre of mass. A small, but significant, northward movement could be detected in plants with expanding ranges, but not among declining species. Species from warmer ranges were not more likely to be moving northward, nor was dispersal syndrome a predictor of migration success. It is concluded that simply looking at northward movement of species is not an effective way to identify the effect of climate change on plant migration and that other anthropogenic changes obscure the effect of climate.

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: http://cetaf.org/cetaf-stable-identifiers

Enriched biodiversity data as a resource and service

Abstract Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts.

Integrating invasive species policies across ornamental horticulture supply chains to prevent plant invasions

Research was supported by COST Action TD1209 “Alien Challenge”. The authors are grateful to John David and Franziska Humair for valuable discussions on this topic. PP and JP were supported by project no. 14-36079G Centre of Excellence PLADIAS (Czech Science Foundation) and RVO 67985939 (The Czech Academy of Sciences). FE, SD, MC and MvK were supported by the ERA-Net BiodivERsA through the Austrian Science Fund, German Research Foundation and French National Research Agency. AN was supported by the Working for Water (WfW) Programme and the DST-NRF Centre of Excellence for Invasion Biology. HS acknowledges support by the DFG (grant SE 1891/2-1).

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

BackgroundThe systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.ResultsWe have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities.ConclusionsThe FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.

Estimation of vascular plant occupancy and its change using kriging

Abstract The grid square occupancies of vascular plants are estimated for the periods 1978–1994 and 1995–2011 across Great Britain. This was achieved by selecting well-surveyed 4 km2 grid squares from the pool of all records and deriving detection/non-detection data from them. From these, it was possible to extrapolate occupancy probabilities to the whole area. Grid squares were selected by setting a minimum threshold for the recording effort for each grid square based upon the number of species recorded and the number of surveys conducted. The spatial distribution of plants was modelled for these selected sites using variography, and kriging was used to interpolate across the whole area. This was conducted for the two time periods and differences in the occupancy probability were compared. This approach has several advantages over other methods. Recording effort is assessed and can be compared between time periods and regions. Absolute occupancy change can be estimated, rather than just relative change. The differences in the spatial distribution pattern of each species are accounted for and the predicted occupancy probabilities and their variance can be mapped. The change in occupancy probabilities between time periods is discussed with reference to known environmental drivers of change and the spread of neophytes. An important result was that in England each 4 km2 gained on average an additional neophyte every three years.